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SELU / Science / Sci 111 / which of the following types of microscopes reveals the surface featur

which of the following types of microscopes reveals the surface featur

which of the following types of microscopes reveals the surface featur

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How do organisms acquire these nutrients?




1- define life) What are general characteristics all cells (both types) have?




How Do We “See” Cells?



Cell Structure and Function 1665 Robert Hooke - noted for coining the term “cells” - he viewed thin slices of cork  - he noticed the cork tissue was honeycomb like arrangement  that reminded him of empty chambers or “cells”. 1673 Antony van Leeuwenhoek - improved lens allowing for better magnification - see living organiIf you want to learn more check out mc = atc at the minimum of _________ .
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sms for the first time 1831 Robert Brown (English - botanist)  – described the nucleus of the cell, naming it Cell Theory - 3 parts and the contributors 1838 Matthias Schleiden (German - botanist)  - noticed all plants are made of cells  1839 Theodor Schwann (German - zoologist)  - noticed all animals are made of cells  1. All living things are composed of one or more cells. 2. Cells are the basic unit of life. (unicellular or multicellular organisms) 1850’s Rudolf Virchow (German - pathologist)  - interested in where cells come from and where disease comes from 3. All cells arise from pre-existing cells Louis Pasteur finally disproved spontaneous generation and replaced it with  biogenesis.  spontaneous generation – life comes for nonliving things biogenesis (bio = life; genesis = first) = life comes from life1 With the invention of the microscope, science has been able to explore microscopic  organisms for the first time. How Do We “See” Cells? Microscopy of Today resolution = the smallest distance separating two objects that allows them to  be seen as two distinct things rather than as a single entity human eye - approx. 0.1 of a mm. or 100 microns, approx. the diameter of  the human egg.  light microscope - made the study of cells possible - uses glass lenses and visible light to form a magnified image of an object - advantage of light microscopy over electron microscope = living cells  can be examined, they do not have to be killed/"fixed" electron microscope - expanded our knowledge of cellular structures - invented in Germany in 1931 and developed in the 1940's - e’ microscope uses powerful magnets in place of lenses to focus an e’ beam. The e’ are directed to a CRT screen or to photographic film. The  images are e’ micrographs - resolving power = about 100,000 times finer than that of the human eye o Limitation: biological material must be killed & dehydrated, then  coated with a heavy metal stain "e’ stains" to deflect e’ ▪ even large molecules such as DNA and proteins can actually  be seen with the electron microscope 2 Types of e’ microscopes: transmission e’ microscope (TEM) = e’s pass thru a sample to see internal  cellular features scanning e’ microscope (SEM) = reveals surface features on 3-D objects. - specimens are not sectioned and e’ do not pass through them; rather  the whole specimen is bombarded with e’.  - resolving power no better than 10 nm. (lower mag.than TEM)2 So What Is “A Cell”? cell = smallest unit with all the properties of life (refer to Ch. 1- define life) What are general characteristics all cells (both types) have? cell membrane = constructed mainly of a phospholipid bilayer; controls what  goes in and out of the cell genetic material = DNA that can be reproduced and passed on - can be found in the nucleus of eukaryotic cells - can be found in the nucleoid of prokaryotic cells chemical reactions = with the aid of enzymes, cells must be able to break down  food to provide E to perform necessary cellular processes (metabolism = net of all  chemical reactions) cytoplasm In prokaryotes, cytoplasm is considered all the material inside the  cell membrane In eukaryotes, it is the cell contents found between the membrane and  the nucleus ribosomes – site of protein synthesis Cell size:  Why are cells small?  - the answer is found in the cell surface-area-to-volume ratio  SA/V As a cell increases in volume, its’ cell surface area also increases, but not at the same rate or to the same extent. Cells require a large enough surface area to meet their need: - for nutrients to come in - for removal of waste products - signals between cells Surface area (cell membrane)-to-volume (cytoplasm) considerations  require that cells remains small.  The size of living things and their components. 3 Introducing Prokaryotic Cells Bacterial Cells Bacterial cells are between 1-10 microns (micrometers) in size and  are just visible with the light microscope. 1977 Carl Woese – observations lead to dividing cells into 3 domains (Bacteria,  Archaea, and Eukarya TWO major types of cells: (prokaryotic vs. eukaryotic) 1. Prokaryotes (1st life, 3.5 billion years) - pro = “before”, karyon = kernel “the nucleus” - no true nucleus, circular DNA  - relatively small and less complicated (simple) compared to eukaryotic - contains no membrane bound organelles (except ribosomes) Domain Bacteria ▪ decomposers of the world (recycle nutrients) ▪ known to cause serious human diseases Domain Archaebacteria (blue-green algae/cyanobacteria) ▪ DNA/RNA related more to eukary. cells than bacteria ▪ live in extreme environments ▪ perhaps the first cell to evolve Bacteria Structures - not every bacteria cell has all the following structures - each species differs from the other depending on how they obtain their  nutrients = autotrophic, heterotrophic, decomposer Cell Envelope: - includes plasma membrane, cell wall, and glycocalyx plasma (cell) membrane = encloses the cell, separates it from the  environment, regulates the molecular traffic that enters/exits the cell o a phospholipid bilayer with associated proteins cell wall = outside the cell membrane - provides support, shape, and protection4 capsule = encloses the cell wall of some bacteria o not easily washed off o composed mostly of polysaccharides (sugars) o the capsule of some bacteria may protect it from attack by white  blood cells in the animals they infect o it also helps keep the cell from drying out slime layer = gelatin-like sheath o easily washed off, removed o allows bacteria to stick to slick surfaces ex: bacteria that cause dental cavities have a slime layer that  allows it to adhere to tooth enamel In the Cytoplasm: cytoplasm = gel-like substance within the cell composed of two parts:  cytosol = consists mostly of water that contains ions, small  molecules and soluble macromolecules like enzymes insoluble suspended particles = ribosomes nucleoid = dense area in the cytoplasm that contains the hereditary  material (DNA) o the single bacterial chromosome, loop of DNA plasmids = tiny, circular extrachromosomal DNA o protective trait like antibiotic resistance o toxin and enzyme production of some bacteria o used for attack on other cells causing diseases ribosomes = function to manufacture proteins thylakoid = flat, membranous disk containing light-sensitive pigments o only found in photosynthetic bacteria (cyanobacteria) ▪ produces their own food Appendages: flagella = slender, long extension used for locomotion o flagellum - made of the protein flagellin o it spins on its axis like a propeller, driving the cell along5 sex pili = elongated, hollow appendage used for DNA transfer  o help bacteria to adhere to one another during mating, as well as to  animal cells for protection and food Archaea Structure: - cell wall composition differs - DNA/RNA more closely related to eukaryotic cells suggesting they are  the first to evolve - live in extreme environmental conditions: high salt, various pH and  temperature Although prokaryotes are structurally less complicated than eukaryotes, they  are functionally complex: - enzymes catalyze thousands of chemical reactions  - in addition to making thousands of enzymes, they are capable of shutting  down synthesis of these enzymes when not needed (when placed in a  particularly rich nutrient environment) Introducing Eukaryotic Cells Eukaryotic Cells 2. Domain Eukaryotes (2.7 billion years ago) – “true” nucleus Ex: Protista, Animal, Plant, Fungi - true nucleus (membrane bound organelles containing genetic  information) - relatively larger (10-100 microns) and more complex compared to  prokaryotic cells - contains membrane bound organelles  organelle (“little organs”) = performs a specific function for the cell  (the entire range of organelles listed seldom occur in a single cell) Evolution of Prokaryotic Cells into Eukaryotic Cells 2 thoughts: 1. plasma membrane was pulled into the cell to develop various  organelle’s like ER and Golgi apparatus6 2. Endosymbiotic Hypothesis  o observed in a lab setting with amoeba infected with bacteria which  become dependent on each other o ▪ mitochondria and chloroplast were prokaryotic cells that  where engulfed (endocytosis = inside, cell) by larger  prokaryotic cells (symbiotic = living together, share food  and O2) double member: 1 from vesicle, 1 from own  membrane both contain their own DNA which splits both have their own ribosomes for protein production both have RNA similar to eubacterial ribosomes  Cellular Membrane Structure and Function = my notes differ from the textbook, use book for references History of Membrane Models Organization of Cell Membrane - lipid-soluble molecules moved through the membrane  o water-soluble molecules not as easily - chemical tests found the membrane to be a phospholipids - 1925 Gorter and Grendel – bilayer o hydrophobic tails inward o hydrophilic heads outward - 1940’s Danielli and Davson suggested that proteins allowed  nonlipid substances to pass through it o the bilayer was filled with proteins (sandwich model) - 1950’s Robertson with a TEM said that all membranes had the  same composition - the unit membrane model o proteins with hydrophilic heads/hydrophobic tail - 1972 Singer and Nicolson introduced the fluid-mosaic model o membrane is a fluid phospholipd bilayer o protein molecules are partially or wholly embedded o proteins were distributed in a mosaic pattern7 Membrane Structure - surrounds the cell or any internal organelle - selectively permeable which means it allows some things to enter it and  blocks other things  - permeable - things can cross is easily without a barrier - impermeable - things can not cross - selectively permeable - only certain molecules can cross ⮚ Three things compose the membrane: lipids, proteins and carbohydrates 1. Lipids = keep hydrophilic particles out - phospholipid bilayer - makes up most biological membranes - arrange themselves spontaneously into a bilayer - polar heads (hydrophilic) will interact with the water on the  exterior and in the cytoplasm  - nonpolar tails (hydrophobic) interact with each other in the  internal part of the membrane - a stable structure which is also fluid  fluid mosaic model - glycolipids – protective function - a variety of sugars joined to form a straight or branching  carbohydrate chain - cholesterol - helps stabilize the membrane - it reduces membrane fluidity at moderate temperatures and  prevents membrane solidification in cold temperatures - sudden changes in environment can damage the membrane (liquid  part) causing death- houseplants - all membranes are similar, but their lipid composition will differ greatly  depending on the cell or organelle 2. Proteins = allow things to pass through the membrane, specialized function,  enzymes, respond to stimuli8 integral membrane proteins - embedded within the membrane transport proteins: regulate movement of a particular molecule or ion  through the membrane. channel proteins - allow a particular molecule or ion to pass through  the cell membrane freely (passive transport) = CF - a faulty chloride channel causing mucus build up  carrier proteins - binding sites for specific molecules, will change  shape (w/E) and move the molecule across the membrane  (active transport) receptor proteins: trigger cellular responses when specific molecules such  as hormones and nutrients bind to them. = pygmies/cell membrane growth receptors are faulty and cannot  interact with growth hormone recognition proteins: glycoproteins act as cell name tags on the outside  surface of membrane (communication) = organ transplants are difficult to achieve because the host’s body  does not recognize it, so it’s attacked by blood cells enzymatic protein: catalyzes a specific region inside the cell = interferes with proteins that make ATP, causes Na ions and water to  leave the intestinal cells causing death by severe diarrhea (cholera – bacterial infection) peripheral membrane proteins - not embedded in the bilayer, but attached to  exposed parts (adhesion proteins) - vary in their role and function for the cell - some allow particles to pass through the membrane by  creating channels 3. Carbohydrates - has a “sugar coating”  - important for protection and other functions - cell recognition of like cells (tissues) and unlike cells  (immunity), “fingerprint” of the cell - cell surface markers - like cell name tags9 - attached to lipids = glycolipids - attached to proteins = glycoproteins - they differ from: - species to species - individual to individual of the same species - cell to cell of the same individual - result can be rejection of transplant organs - result can be rejections to blood types Organelles found in Eukaryotic Cells: Nucleus = a membrane bound organelle known as the control center of the cell nuclear envelope = consists of a double membrane and nuclear pores that allows  small molecules (water, ions, ATP) to pass freely, whereas it regulates RNA  and protein passage. Therefore, the pores help control the flow of information  to and from DNA nucleoplasm = water and dissolved substances found surrounding the chromatin  within the nucleus - much like cytoplasm, but more protein rich nucleolus = site of ribosomal synthesis (rRNA) - also the site of protein synthesis - other types of RNA produced = messenger RNA – go between DNA and amino acids = transfer RNA – assemble amino acids for protein synthesis Contents of Nucleus: DNA = genetic information encoded as DNA (nucleic acid) - cellular processes are governed by the info. encoded in DNA o growth and repair o nutrient and energy gathering and use o reproduction ex. DNA contains the info for the sequencing of amino acids into proteins chromatin (color, stretch) = DNA and associated proteins - during interphase, it is stretched out and governing the cell’s actions - during cell division, the chromatin thickens forming strands called 10 chromosomes (color, body) = threadlike structures that are pieces of DNA  and associated proteins Cytoplasm = jelly-like material found inside the plasma membrane, but outside  the nucleus - composed mostly of water, ions, salts, and organic molecules Ribosomes = organelles that consist of protein and RNA - the sites of protein synthesis - the instructions delivered to the ribosome by RNA from  DNA is what dictates the protein it makes  2 types of ribosomes a. free ribosomes - suspended within the cytoplasm  - proteins made here will function as enzymes b. bound ribosomes - attached to the endoplasmic reticulum (ER) - proteins made here may end up as membrane proteins - coordinate amino acids into polypeptide chains (protein synthesis) Endomembrane System - much of the volume of a eukaryotic cell is taken up by its extensive  membrane systems which compartmentalizes the cell (work  stations within the cell) - all of the cell's membranes appear similar under the electron  microscope and all have similar composition (phospholipids) Endoplasmic Reticulum (within; something molded) = network of membranes  that branch from the nuclear envelope and continue throughout the  cytoplasm 2 types of ER Rough Endoplasmic Reticulum (ER) - contains bound ribosomes - site of protein synthesis - as the proteins are synthesized by the ribosomes on the outside of the rough  ER, they are transported into the channels inside  - proteins then move through the rough ER to accumulate in pockets at the  ends - pockets bud off and form vesicles that migrate to the Golgi apparatus11 vesicles – any sac-like structure made from membrane - grocery bags in the cell Smooth Endoplasmic Reticulum - no ribosomes - site for lipid synthesis - phospholipids, steroids, and fatty acid - vesicles break off and go the Golgi apparatus Golgi Apparatus = discovered in 1898 by Camillo Golgi - stacks of membranous sacks derived from ER that store, modify,  package, and distribute certain proteins  - Golgi separates proteins/lipids received from the ER according to their  final destinations (digestive enzymes are destined for lysosomes, hormones will be secreted from the cell) - it modifies some molecules  - it packages these materials into vesicles that are transported to other parts  of the cell or to the plasma membrane for export Lysosomes (loose; body) = vesicles that break off from the Golgi apparatus  that contain digestive enzymes - aid in intracellular digestion (the break down of proteins, fats,  and carbohydrates into their subunits {going from polymers  to monomers to be reassembled for use}) - acidic environment (they work best in acidic environment) where they  can digest macromolecules (and evading bacteria) safely within in the  cell without causing damage to the cell itself - lysosomes fuse with food vacuoles (large membrane bound sacs within  the cell) to allow their digestive enzymes to break down the food into  simpler forms to nourish the cell - lysosomes also recycle old organelles; part of apoptosis = programmed  cell death Ex: auto digestion of tadpoles’ tail in becoming a frog. The  tadpoles use the nutrients from the tail. Humans loose the webs  b/w their fingers as a fetus with aid of lysosomes. Missing or inactive lysosomes cause serious childhood diseases. Peroxisomes = membrane bound vesicles enclose enzymes12 - not part of the endomembrane system since they do not communicate  with it - contains hydrogen peroxide (H2O2), a toxic molecule, used to break down  lipids with the help of enzymes Mitochondria = involved in E production (ATP) - power generators of the cell (cellular respiration) C6H12O2 + O2 ???? CO2 + H2O  glucose + oxygen ???? carbon dioxide + water - largest and densest of all organelles - have their own ribosomes and DNA - has a double membrane system (inner and outer membrane) - cristae = inner membranes are folded to increase surface area - ATP production occurs here - matrix = inner space of mitochondria that contains enzymes that  breakdown food molecules (carbohydrates, fats, and other fuel  with the help of O2 to generate ATP known as aerobic respiration) The breakdown of food molecules begins in the cytosol, which does not have the  necessary enzymes to break down food using O2. This type of metabolism  (without O2 is anaerobic) does not convert very much food to ATP E. FERMENTATION Aerobic metabolism (with O2) occurs in the mitochondria producing 18-19 times  more ATP, than anaerobic metabolism. Therefore, cells that are very active  (muscle cells) contain a lot more mitochondria than cells that are not as active  (bone, cartilage cells) - 40+ different mitochondrial diseases in humans are the result of the  incomplete metabolism with toxic build up Specialized Plant Organelles chloroplast = organelle for photosynthesis13 contains the pigment chlorophyll to capture the sunlight which is converted  into sugar - opposite of cellular respiration CO2 + H2O ???? C6H12O2 + O2   carbon dioxide + water ???? glucose + oxygen  - have own ribosomes and DNA for replication Inside the chloroplast: stroma = gel-like substance within the chloroplast = site of photosynthesis - light independent reaction thylakoids = membrane disk-like sacs  = site of photosynthesis - light dependent reaction granum = stacks of thylakoids chromoplasts = no chorlophylls carotenoids = source of red-to-yellow colors of flowers, fruit,  vegetables, and changing seasons amyloplasts = pigment-free - store starch grains - found in stems, roots, and seeds central vacuoles = holds water for the cell  - takes up 50-90% of cell - provides support of plants - esp. non-woody ones *animals have reduced vacuoles for storage/waste removal *protista have food vacuoles that link to lysosomes for cellular digestion Cell Surfaces Specializations cell wall = semi-rigid structure outside cell membrane - made of cellulose - provides support (hydrostatic skeleton)  - limits volume of cell primary wall – allows for growth, adheres other cell together composed of pectin and other polysaccharides along with cellulose14 secondary wall – structure support, less flexible, re-enforces cell shape plasmodesma – junction between cells allowing them to communicate with  each other (connects between cytoplasm of cells) Matrixes Between Animal Cells: 1. junctions that occur between some types of cells 2. the extracellular matrix that is observed outside cells Even Cells Have a Skeleton cytoskeleton (cell; dried body) – 3-D network of 3 different protein filaments that is responsible for: - movement - the shape of the cell - internal organization 3 types of filaments that compose the cytoskeleton: 1. microtubules (small, little; pipe): - small hollow cylinders - composed of a globular protein tubulin 2. microfilaments: - play a structural role  pseudopods (false feet) = amoeba movement - web-like structures throughout the cell - globular actin monomers twisted into a helix - interact with myosin for movement 3. intermediate filaments: - made of a variety of proteins depending on the cell type - important in reinforcing and maintaining the cell shape,  - maintains spatial organization of cells Other cytoskeleton structures used for movement: cilia and flagella (see cytoskeleton structure) - cilia (eyelash hair) = short hair-like projections that move - Paramecium or lining of human upper respiratory  tract15 - flagella (whip) = usually found single or in pairs, snake-like  undulating movement - provides movement of human sperm cell centrioles (center; body): - basal bodies for the cilia and flagella - function during cell division - have 9 + 0 organization = 9 set of triplet microtubules with none in the middle Junctions Between Animal Cells  animal cells forms special junctions that help them adhere to other cells as  well as communicate with each other Three types of junctions exist that enable cells to make direct physical contact  and link with one another: 1) tight junctions - specialized proteins that link adjacent epithelial cells  lining a hollow structure  ex: intestines - Prevent leaks or seal by creating a zipperlike fastening.  Tight junctions prevent the movement of dissolved materials from  the intestines through the space between epithelial cells. Tight  junctions help ensure the directional movement of materials in the  body. Also, see in the kidneys by keeping the urine inside the organ. 2) adhering junction - hold adjacent cells firmly together, acting  like "spot welds" or "rivets" at individual points - each junction is attached to keratin fibers in the cytoskeleton - junction tightly link adjacent cells, but permit material to move  around them in the intercellular space - junction hold tissues together in organs that regularly get  stretched, i.e. the heart, stomach, and urinary bladder 3) gap junctions - made up of specialized protein channels, facilitate  communication between cells (communication proteins) - dissolved molecules and electric signals may pass from one cell to  another - in nerve cells, cardiac and smooth muscle cells, gap junctions allow the  passage of electrical signals from one cell to cell - cancer cells never develop gap junctions, which contributes to their  abnormal uncontrolled growth16 Introduction to Biology: an overview biology: science of living organisms and life processes, including the study  of structure, function, growth, origin, evolution and distribution of  organisms biology is an umbrella more specific areas of study: cytology - cells histology - tissue zoology - animals botany - plants limnology – brackish water ecology – the relationship between an organism and its environment pathology - diseases evolutionary biology – changing of an organism over time herpetology - reptiles ornithology - birds ichthyology - fish mammology - mammals vertebrate zoology – animals with backbones invertebrate zoology – animals without backbones taxonomy – classification anatomy - structure of bones morphology – shape/form osteology – bones biochemistry – chemistry of life genetics – heredity microbiology – bacteria entomology – insects animal husbandry – mating/breeding Overview of Life’s Unity (How to Define Life) - life is extremely diverse, yet there are some unifying characters all  living organisms share characteristics (unity) of life - all living things have:1 organization (unity) of life on earth: a hierarchy (molecules ???? cells  ????organs …) - most important is the DNA molecule - each level is based on the level below it and provides the  basis for the one above it (simple to complex) emergent properties – inactions between the parts making up the whole subatomic particles - particles that make up an atom (protons, neutrons,  and electrons) atom - smallest particle of an element that has the properties of that element  (H, Al, Fe, O) molecule - 2 or more joined atoms (H2 + O = water) organic molecules = composed mainly of C organelle - structure within a cell that performs a specific function, cannot  survive on its own cell - smallest unit of life unicellular - composed of one living cell - must contain DNA, be able to perform chemical reactions (gather  food for E, expel waste…), surrounded by a membrane for protection tissue - group of cells that perform a function together  (brain tissue, lung tissue) organ - structure composed of tissues that function together (brain, lung) organ system - two or more organs working together (nervous system) organism - all organ systems functioning together to make up a single living  individual multicellular organism – living individual composed of >1 cell  species - group of genetically similar organisms (lion) population - members of the same species living together (lion pride)2 community - populations of different species living together  (lion pride, zebra herd) ecosystem or biome - community plus its non-living environment (water, soil, temp…) - terrestrial (land) ecosystem = tropical rain forest, grasslands  - aquatic (water) ecosystem = lakes, ponds, coral reef  biosphere - earth and its’ living (biotic) & non-living (abiotic) components - in ecosystems, the same nutrients keep cycling through populations,  but E flows because it is eventually converted to heat  - human populations tend to modify existing ecosystems for its own purpose - biodiversity is being threatened by these changes biodiversity = # and size of populations in a community - estimated as high as 80 million species with only about 2  million identified and named - 24 – 100 species lost daily to human activity extinction – the death of a species or larger classification category extinct in the wild – only found in captivity, no longer in nature metabolism (implying change) - acquire and use materials (nutrients) to obtain E, this E carries  out chemical reactions such as growing/reproducing - nutrients from the air, water, soil energy (E) = the ability to do work How do organisms acquire these nutrients? producers (autotrophy - “self-feeder”) – photosynthesis consumers (heterotrophy - “other feeder”) decomposers – breakdown material to be recycled3 homeostasis (homo = the same; stasis = standing) - maintenance of relatively constant internal body conditions  (pH, temp (37oC), water)  - all organisms have a range of tolerance, cells perform chemical  reactions in order to maintain internal conditions within these  ranges ability to grow and develop ability to reproduce - all living things pass on their DNA, the  genetic information within all organisms ▪ asexual ???? DNA from one parent, identical offspring bacteria, plants, sponges, …. ▪ sexual ???? exchange of DNA, two parents, genetic mix ability to respond to stimuli – with the aid of receptors - light, sound, the presence of prey capacity to evolve - the genetic info. of one organism  stays the same over its lifetime; however, variations between  parents and offspring allow for the genetic material of a species  to change over time An Evolutionary View of Diversity = heritable change in a line of descent over time What causes change: mutations = changes in DNA three basic concepts of evolution: 1. genetic variation exists within a population: - differences in the actual genetic code occur in  individuals of the same population 2. inheritance of those differences occurs when parents  pass them to their offspring   3. natural selection occurs 4 - allows for the survival and increased reproduction of  the individuals with the most favorable genetic  variations over time  physiological processes (improved digestion) behavior (new way to gather food) shapes (better at hiding from predators) sizes (long legs for running) - evolve to enable an individual to be better suited to  its environment ???? this is an adaptation - if the environment changes, the adaptation may no longer be  beneficial over a long period of time; this may change the  genetic make-up of a population as new adaptations arise difference between acclimation and adaptation:  acclimation = a temporary adjustment to an environmental condition  = when you reduce the temp. in a fish tank; the fish responds by  changing their breathing rates - they are adjusting to a new  environment adaptation = an inherited genetic trait passed on from parent to  offspring - the result of evolution over a tremendous amount of time is  a vast variety of species each with its own set of requirements  for living:  = interrelationships between predators, prey, parasites  = temperature, nutrient & water requirements biodiversity - the diversity of species and the complex  interrelationships that surround each of them artificial selection – one form of a trait is favored over another in an  artificial environment under contrived, manipulated conditions.  (dogs, cats, cows, corn)5 If So Much Unity, Why So Many Species: Living Things Classified taxonomy (tasso - arrange, classify; nomas – usage, law) - the discipline of identifying and classifying organisms according  to certain rules - each species is given a binomial (bis = two; nomen = name)  Bison bison (Genus species) or Bison bison Carolus Linnaeus = Father of Taxonomy 1735 - developed the binomial system of naming organisms Categorizing the Diversity of Life - a hierarchy usually categorized by:  cell number ???? unicellular vs. multicellular cell type ???? prokaryotic vs. eukaryotic how E is acquired ???? producer vs. consumer Cell types: 1) Prokaryotic “no nucleus”: Domain: Bacteria “true-bacteria” – decomposers of the world = distributed in various environments Archaea - live in extreme environments = hot springs, high salinity, low pH, etc. - unicellular organisms which are structurally similar,  metabolically complex - can be autotrophic or heterotrophic or decomposers 2) Eukaryotic “true nucleus”:  Domain: Eukarya - mostly multicellular organisms - some unicellular organisms Kingdoms Protista – auto/heterotrophic or decomposers;  uni/multicellular (euglena, amoeba, kelp) - protists are currently being split up 6 Fungi - multicellular; heterotrophic or decomposers (molds, mushrooms) Plantia - multicellular; autotrophic  (photosynthesis ???? oaks, roses, grasses Animalia - multicellular; ingest their food  herbivores = plant eater (zebra, deer)  carnivores = meat eaters (lions, wolves) parasites = host eater (tapeworm) decomposers = eat dead things (vultures) insectivores = insect eaters (bats, spiders) omnivores = plant and meat eater (humans) - broken down further into: Phylum, Class, Order, Family,  Genus species (or Genus species) The Nature of Biological Inquiry: The Process of Science biology – the scientific study of life science: an organized body of knowledge that attempts to explain natural  phenomenon with a collection of facts and theories, a process of  discovery, it is self-correcting and solves problems, searches for  patterns with observable data, information processing. inductive reasoning – using isolated facts and creative thinking to come  up with a possible explanation for your observations; creating a  hypothesis deductive reasoning – once the hypothesis is stated, it is a general  statement that infers a specific conclusion; information based on  previous work Scientific Method - method of asking questions and testing those  questions  observation: using your senses7 - gather supporting information (Internet, journals) = previous data hypothesis: generate an explanation for your observation,  must be testable experiment: a test for data collection and results to support or  reject your hypothesis variables - within an experiment, one variable/ factor must change independent var. – what is changed dependent var. – response to change control – a standard used for comparison against one or more  experimental groups (the baseline) replication - repeats the experiment to obtain consistent results - gives “power” to the experiment, able to average results conclusions: explanation of your results in order to inform other  people (graphs, publication) theory: general explanation of a natural phenomenon, after much  testing; concepts that join together well-supported and related  hypotheses - fundamental principles of biology such as: cell theory - all living things are composed of cells  biogenesis (bio = life; genesis = first) – life comes from life  evolution – all living things have a common ancestor and are  adapted to a particular way of life gene – organisms contain coded information that dictates  their form, function, and behavior all science is based on a small number of assumptions thoroughly tested  and found to be valid:8 1. all events can be traced to natural causes that can be understood  (i.e. supernatural powers are not part of science) 2. laws derived from nature are uniform in space and time and do not  change: light, gravity, interactions between atoms, etc. 3. objectivity: science requires all people remain objective during  scientific pursuits Read through experiments at the end of the chapter (1.6) to understand the  scientist process including terms.9 Ground Rules of Metabolism - Energy and Enzymes Energy and Time’s Arrow energy (E) = the ability or capacity to do work  Thermodynamics = the study of E transfer (2 laws) First Law of Thermodynamics: sometimes referred to as the  Law of Conservation of Energy - assuming E is not being introduced, the total amount of E is constant E cannot be created or destroyed;  instead it is transformed from one form into another. eating food (chemical E being transformed into another chemical E  – ATP which is converted into potential E) 2 major types of E:  potential E = stored E  kinetic E = E of movement There are different forms of E: - mechanical E = used to move around - light E = see what you are doing - heat (thermal) E = maintain temperature - chemical-bond E = E stored in bonds that hold atoms together ???? potential E of molecules E can be changed into different forms of E - electrical E transformed into light E in a light bulb A power plant does not make E, it just transforms it into something usable for  modern society. Second Law of Thermodynamics: When energy is transformed one form into another, some useful energy  is always lost as heat; therefore, energy cannot be recycled. E is converted from more useful forms into less useful forms.1 - entropy: the tendency towards loss of organization (high E) to an  increase in disorganization (low E). E is needed to maintain  organization Food Web - respiration/heat (low E, loss) The E in our bodies is used to maintain our daily functions, that stored E is  potential E for another organism (bacteria, shark, buzzard). E flows through a  system starting with the sun. E from the sun is captured by plants (2% captured,  98% lost), then transferred throughout the system. During this process E is going  from one organism to another, when something is consumed only 10% of its E is  transferred/ used and 90% is lost as heat E from respiration. That’s why it is better to be a vegetarian. They are more efficient consumers using  much more of the original E in the system (its source is the sun). 10% 10% 10% 2% plant 1o2o3o 90%90% 90% 90% - E is flowing in one direction, from concentrated to less concentrated  forms Time’s Arrow and the World of Life Metabolic Reactions and Energy Transformations metabolism – sum of all the reactions that occur in a cell reactants – substances that participate in a reaction intermediates – substances formed before a reaction ends products – substances that form as a result of a reaction A + B ???? C + D (reactants) (products) free E = the amount of E availability - if there is free E, reactions can occur spontaneously 2 exergonic reactions (release E = breaking a bond)  - breakdown of organized, complex reactants (high E) into disorganized  and simple products with a release of E (low E) – cellular respiration endergonic reactions (require/use E = making bond)  - combining disorganized and simple reactants (low E) with the input of  E to produce organized, complex products (high E) – photosynthesis chemical equilibrium – reaction goes in both directions at the same rate coupled reactions (rx) - E released by exergonic rx is used for the endergonic reactions - they work together - not all the heat is used, a % is lost as heat - mitochondria will breakdown glucose during cellular respiration to  release E in the form of ATP, that E used to power other reactions - but only 39% glucose E is transformed to ATP, the rest is  lost as heat Metabolism – Organized, Enzyme-Mediated Reactions metabolic pathways = enzyme-mediated sequences of reactions in cells biosynthesis “life, making” (anabolic) = requires E (photosynthesis) degradative (catabolic) = releases E (cellular respiration) - reactions that go back and forth will move towards a state of chemical  equilibrium oxidation-reduction (redox) – e’s pass from one molecule to another oxidation = loss of e reduction = gain of e- - both reactions occur together – one mole. is losing e- while another  molecules is accepting those e- H+and e tend to travel together photosynthesis: 6 CO2 + 6 H2O + E ???? C6H12O6 + 6 O2 - E is used to combine CO2 and H2O to produce glucose - H2O = oxidized (lose e-) - CO2 = reduced (gain e-) - glucose is a high E molecule, so E is needed to produce it3 - that E comes from the capture of solar E by the chloroplast then converts  that E into ATP (chemical E) for use - ATP with H+can reduce glucose - NADP+(nicotinamide adenine dinucleotide phosphate) donates H  atoms (H+and e-) to a substrate - that substrate accepts the e and is reduced - the reaction that reduces NADP+ NADP+ + 2e- + H+ ???? NADPH cellular respiration: C6H12O6 + 6 O2 ???? 6 CO2 + 6 H2O + E - glucose is broken down to release E - NAD removes H atoms (H++ e-), the substrate has lost e and is oxidized NAD++ 2e- + H+ ???? NADH - end result is that glucose has been oxidized to CO2 and H2O and ATP has  been released electron transport system (E.T.C): - photo. and cellular respiration use this metabolic pathway to move e from one carrier to another - high E enters the ETC and lower E leaves it - as e- are passed down the ETC, E is released which is used to produce  ATP ATP Production: - ATP production is coupled with the E.T.C. - Peter Mitchell ( Nobel prize) for chemiosmosis theory of ATP  production (chemical “push”) - mitochondria and chloroplast both have the E.T.C. - H+ions collect on one side of the membrane because they are pumped  there by certain carriers - electrochemical gradient across the membrane is used to provide E for  ATP production - ATP synthase complexes span the membrane - contains a channel that allows H+ to flow down their  electrochemical gradient - H+flow through the channel allowing ADP + P ???? ATP - as solar E is collected by plants and converted to ATP, the  thylakoid membrane acts as a dam to maintain an E gradient,  formation of ATP occurs with the flow of ions ATP (adenosine triphosphate) = E of the cell4 - the body will produce lots of ATP, but storage is minimal because ATP is  constantly being broken down to ADP (adenosine diphosphate) ATP ???? ADP + P (goes back and forth as E is used and made) Use of ATP as a carrier of E: 1. it provides E for many types of reactions 2. when ATP ???? ADP, the amount of E is just enough to run everything  with little E loss overall 3. ATP breakdown is coupled with endergonic reactions for min. E loss Functions of ATP: chemical work: synthesize macromolecules that make up the cell transport work: pumps substances across the membrane mechanical work: cause muscles to contracts, cilia and flagella to  beat, chromosomes to move, etc. Structure of ATP: - a nucleotide with the organic base adenine - a sugar ribose - 3 phosphate groups - ATP is “high E” because of the easy removal of the phosphate group Electron Carrying Coenzymes – NAD+and FAD How Enzymes Make Substances React metabolic pathways: - there are thousands of reactions occurring in cells - these reactions must be compartmentalized to delegate different types of  reactions - these reactions are organized sequences of chemical reactions linked  together - many are exergonic reactions (E release)  = sugar broken down in the mitochondria - others are endergonic reactions (E input)  = lipids made in smooth ER A ???? B ???? C ???? D ???? E ???? F ???? G E1 E2 E3 E4 E5 E65 - letters A-F are reactants  - letters B-G are products - En are different enzymes needed for each reaction Cells regulate chemical reactions with the production of biological catalysts called  enzymes. What they do: - they bring together particular molecules in order for them to  interact - speed up only reactions that normally would occur, but at a slower rate - they are not altered by the reaction  - they can be recycled - they lower the activation energy of the reaction - they are proteins (shape is important) The reactants in an enzymatic reaction are called the substrates for the enzyme. A is the substrate for E1 with B as the product, then B as the substrate for E2 with C as the product ……. activation E - the amount of input E required to start a reaction - molecules tend to not react with one another unless they are activated in  some way - in a lab, heat can cause activation because molecules will collide more  often with one another - the E added to cause reactions is the activation E - without the correct enzyme, the E level needed for activation is high - more effort is needed for the reaction to occur - with the correct enzyme, the E level is much less enzyme-substrate complexes - each enzyme has a unique shape that makes each enzyme specific to that  substrate  - the region of the enzyme where the substrate binds is called active site - each enzyme catalyzes the reaction of a single molecule or a group of  closely related molecules substrate + enzyme enzyme-substrate complex6  + - products + enzyme - the active site will change shape to accommodate the substrate more  complexly which is instrumental in the reaction (known as the induced-fit model) - once the reaction takes place, the active site returns to its original state so  it can be re-used/recycled For ex, amylase is an enzyme in your saliva that breaks down starches.  Such enzymes, catalyze the breakdown of starch (polymer) into its  carbohydrate/glucose building blocks (monomers) through a hydrolysis reaction.  hydrolysis (hydro = water; lysis = breakdown) - decomposition of large molecules into smaller units by combining them  with water - other reactions can occur besides hydrolysis (Chapter 2) – e’ transfers,  condensation, rearrangements, cleavage In the case of starch digestion, the peptide bonds are broken with the insertion of  the components of water (H+and -OH) at the broken ends of the chain. Enzymes tend to be named for their substrates: - enzymes that digest lipids (lipase) - enzymes that digest urea (urease) - the name of enzymes tend to end with “ase”  Without enzymes, most biochemical reactions would not take place fast  enough to sustain life as we know it.  Reactions are controlled: - reactions are controlled within the cell, they are not occurring without  any constraints Factors Affecting Enzymes: 1) enzyme inhibition7 - active enzyme is not allowed to combine with its’ substrate - normally is reversible - enzyme or substrate is not permanently damaged - some can be irreversible depending on what is happening like effects of  poisons ????lead and cyanide can not be changed ways for negative feedback – stops production itself - competitive inhibition = another substrate is so closely shaped like the  enzyme’s substrate that it can compete with it, blocking the correct  enzyme to substrate match - noncompetitive inhibition = a molecule binds to an enzyme, but not at  the active site resulting in a shape change of the enzyme itself allosteric site (other; structure) = the location of the noncompetitive  inhibition site - feedback inhibition = the cell can also regulate activity by producing  inactive enzymes that can become active when needed or by the high  concentrations of the product that can inhibit enzyme activity positive feedback – starts production itself 2 substrate concentration - as substrate concentration increases, so does the reaction rate - more substrate = more collisions with enzymes - less substrate = less collisions with enzymes 3 enzyme concentration - as enzyme concentration increases, so does the reaction rate - increase enzyme concentration = increase reactions - decrease enzyme concentration = decrease reactions 4 temperature  - as temperature increases, so does the movement of molecules  resulting in faster reactions - increase temp = increase reactions - however, if the temperature rises beyond a point, the enzyme shape  is alternation which no longer allows reactions to occur (denature) 5 pH  - the measure of H ions in a solution8 - enzymes operate at a specific pH.  - any value different from the optimal pH of the enzyme will cause  the reaction to decrease.  denaturation  - when extreme conditions (pH or temp.) cause the enzyme to  loose its 3-D shape and become non-functional - in most cases, denaturation is not reversible.  6 salt - tonicity of an environment can effect the fluid (osmosis) which can affect  enzymes, they work in a specific range 7 enzyme cofactors  - inorganic or organic ion/molecule that bind to enzymes and serve as a  carrier for chemical groups or electrons - inorganic ions are metals such as copper, zinc, or iron - organic, non-proteins are coenzymes - assist enzymes in their function - coenzymes participate directly in the reaction by weakening the bonds of the substrate allowing the substrate to react with the enzyme vitamins = a component of coenzymes (antioxidant) - intake can effect this; vitamins synthesize coenzymes; with a  deficiency of any vitamin, the reactions can be effected resulting in  disease; antioxidants - antioxidants neutralize free radicals = attack the structure of DNA and  other biological molecules, increase as we age Movement into and out of the Cell concentration gradient = a difference in the number per unit volume of  molecules/ions of a substance between two adjoining regions 1. Passive Transport - requires NO energy for movement - works with the concentration gradient - flow goes from high to low concentration9 A. Simple Diffusion (5.5 textbook) - the process of random movement toward a state of  equilibrium = equal state - it’s the movement of particles from a high concentration gradient to a  low concentration gradient resulting in equilibrium - molecules pass through the membrane itself Facilitated Diffusion (Transport) - movement of substances from a high level of concentration to a low  level of concentration with the aid of channel or carrier proteins - channel protein allows molecules to pass through the membrane  - carrier protein is hydrophobic and connects to the particle changing  its’ shape to allow it to pass through the membrane bilayer Osmosis - the diffusion of water across a selectively permeable membrane - the movement of water molecules from an area of high  concentration of free water molecules to an area of low  concentration of free water molecules - biological membranes are selectively permeable osmotic pressure – pressure that develops in a system due to osmosis - the greater the pressure, the more likely the water will move in that  direction (bulk flow = the mass movement of one or more  substances in response to pressure, gravity, or another external  force) drinking water ???? large intestine ???? kidney ???? capillaries  - any substance added to pure water displaces some of the water  molecules; dissolved substances may form weak bonds with some  water molecules making them unavailable to move across the  membrane solute: a substance dissolved in a solution (sugar) solvent: a substance that can dissolve other substances (water) solution: a solute and its solvent combined (sugar dissolved in water) Three Types of Environments with respect to a Cell:10 tonicity (strength) – the degree to which a solution’s concentration of  solute versus water causes water to move into or out of cells a. isotonic (same as) = a state of equilibrium; equal concentrations  of water outside and inside the cell (water moves equally)  b. hypotonic = a lower concentration of solutes, than water (water  moves out of hypotonic environment) - hypo means “less than” - water flows into the cell and can burst the cell itself  - lysis means “to disrupt the cell” - hemolysis = the disrupted red blood cell c. hypertonic = a higher concentration of solutes, than water (water  moves toward hypertonic environment) environment - hyper means “more than” - water flows out of the cell and can shrink the cell  itself  - crenation means “notched, wrinkled” - refers to red blood cells - lettuce with salad dressing - refresh lettuce with ice water, water goes back  inside the lettuce cells - Animal cells prefer an isotonic solution. - Plant cells prefer a hypotonic solution (water flows into them). The  influx of water into the plant cell increases the turgor pressure (hydrostatic pressure) that is essential for support in nonwoody parts of  plants. - plants in a hypertonic solution (like salty water) have the cell member  pull away from the cell wall because vacuoles are losing water (cell  shrinks) - plasmolysis – shrinking of the cytoplasm due to osmosis Factors that effect movement across the concentration gradient (page 80):11 - includes diffusion and osmosis which work together to create a state of  equilibrium 1) steepness of the gradient – higher the steepness between two adjoining  regions, the greater the rate of movement 2) heat – temperature increase will increase movement; temperature decrease  will decrease movement 3) particle size – the smaller the particle/ion, the faster it moves 4) electric gradient – electric charges between two adjoining regions 5) pressure gradient – flow due to pressure exerted per unit volume between  two adjoining regions 2. Active Transport: ION PUMPS - requires E (ATP)  - works against the concentration gradient - flow goes from high to low concentration - this is the movement of particles from areas of low concentration  to areas of high concentration Primary Active Transport (Na-K Pump) - 3 Na+out, 2 K in - the release of ATP into ADP - active transporters see - Ca pumps is another example of a pump Secondary Active Transport - doesn’t use ATP, influenced by the primary pump - brings glucose into the cell along with Na+ - passive transporters Membrane-Assisted Transport (Vesicle Formation) Exocytosis (means outside, cell) - moving materials out of the cell, opposite of endocytosis - used for excretion of wastes - used for secretion of hormones Endocytosis (means inside, cell) - moving macromolecules into the cell by engulfing them12 - phagocytosis - “cell eating” creating food vacuoles with the use of  pseudopodia = extensions of the plasma membrane ex. Amoeba - pinocytosis - “cell dinking” creating water vacuoles -called bulk-phase in textbook - receptor mediated endocytosis - uses receptor proteins in coated pits  to obtain specific particles or molecules  - exocytosis and endocytosis will continuously replace and withdraw  patches of its plasmas membrane as the cells brings in or pushes out  material - the ER is responsible for replacement of this material Light Up the Night – And the Lab Many species have the ability to transfer varies energy into light E – bioluminescence (life, light) - the purpose may vary from defense (scaring off predators by suddenly  lighting up) to seeking mates (allowing potential mates to locate each  other) - ATP with O2 are transfers a P-group to luciferin, as molecules become  excited they release extra E in the form of fluorescent light luciferases????moves chemical bond E into light E Scientists have isolated the genes for bioluminescence and have placed them in  other species. medical purposed for bioluminescence: - detection of antibiotic – bacteria cells transferred to host ???? light means antibiotic does not work, bacteria alive ???? no light means antibiotic works, bacteria dead Christopher and Pamela Contag along with David Benaron - used bioluminescence in mice to track infection (how?) - could be used in gene-therapy - can be used to track metabolism as molecules are made and broken13 Where It Starts -- Photosynthesis How do we get our E? FOOD How does food get E? - from sunlight during photosynthesis - E is extracted from food by cellular respiration photosynthesis = solar E is converted to chemical E which is converted into carbohydrate molecules (glucose/sugar) How does photosynthesis and cellular respiration form a cycle? - products of one process is used to start the next one CO2 + H2O ???? C6H12O6 + O2 C6H12O6 + O2 ???? CO2 + H2O - products of photosynthesis (glucose and O2) are the starting  material for cellular respiration - cellular respiration is opposite of photosynthesis since it uses C  from glucose (C6H12O6) to provide E for other activities  How do plants use sugar? - plants use sugar to make other organic molecules (proteins, lipids)  by linking C-atoms together - plants store E in the form of sugar (newly made) - sugar can be transported to other parts of the plant that do not  photosynthesis (roots) - plants are autotrophs (make their organic molecules from  inorganic molecules) Does all the sugar that gets produced by photo. get used immediately? No, produce more sugar than can be used for - next day activity - rapid growth in the spring - turned into starch for short and long term storage - converted into oils and stored in seeds1 - photosynthesis allows us to live ???? E, food, oxygen - organisms rely directly and indirectly on sunlight (autotrophs) - heterotrophs (obtained C by consuming pre-existing organic cells  ???? released CO2, but could not use C from CO2) to autotrophs  (endosymbiotic hypothesis) ???? an advantage for organisms to use  O2 to harvest E, using inorganic substances like water and CO2 to  make organic molecules like sugar - another advantage is mixing O2with other oxygen molecules to  make O3 (ozone) which blocks harmful ultraviolet radiation from  the plant.  Why do plants often serve as food for animals? - rich organic molecules that store E - 250,000+ species with 150 plants grown for mass consumption - 3 major ones feed the world (rice, corn, wheat) Sunlight as an Energy Source What is in solar E that can be absorbed by autotrophs? solar E = described in terms of its’ E content and its’ wavelengths - travels as photons = tiny packages of solar E electromagnetic spectrum = complete range of solar E including  visible light (what we can see) - all forms of solar E differ in wavelengths and in the amount of E  they release - visible light (380-750 nm) = intermediate amounts of E and  include all the colors of light (purple, blue, green, yellow,  orange, red) - photosynthesis only utilizes this portion of the electromagnetic  spectrum - human eyes see visible light because they have light receptors that absorb those kinds of photons2 Are colors actually what they appear to be? - sunlight shines on an object - object surface is bombarded with photons - photons are either reflected, absorbed, or transmitted (pass through) - color of an object is a result of the visible light photons it reflects = leaves absorb mostly photons of red and blue to reflect green = pumpkins absorb mostly blue and green light to reflect orange = apples absorb mostly blue and green to reflect red How do plants absorb solar E? - photosynthetic pigments absorb photons - pigments = molecule that absorbs light to reflect color Two main pigments: chlorophyll = green pigment in plant that is responsible for absorbing  the solar E used in photosynthesis  chlorophyll a – absorbs violet and red light to reflect  green and yellow (why leaves are green) chlorophyll b – reflects green and blue, accessory  pigment assists chlorophyll a carotenoids = absorbs mostly blue and green lights to reflect reds,  yellow and orange (produces fall colors in leaves and the color  of fruits and vegetables)  - carotenoids - assist in photosynthesis by capturing E from light of  different wavelengths than those absorbed by chlorophyll Other pigments in flowers, fruit, and vegetables: xanthophylls – reflect yellow, brown, blue and purple light anthocyanins – reflect red, and purple light (cheerys and flowers) phycobilins – reflect red or blue-green light (algae and  cyanobacteria) Harvesting the Rainbow Wilhem Theodor Engelmann (botanist, 1882)  - experimented with photosynthesis3 - identified wavelengths that were most productive in  photosynthesis - Cladophora gathered by violet and red light, more O2 production - absorption spectrum indentifies absorption level of pigments at  various wavelengths - all photosynthetic pigments combined absorb most wavelengths in  the spectrum of visible light Overview of Photosynthesis What specialized structures do plants have that allow for sunlight to  be captured? chloroplasts = “green-molded” - organelle used for photosynthesis - tiny green organelle found only in eukaryotic cells that contain  chlorophyll = pigment in plants that absorb light How are plants specialized to photosynthesize? - leaves are complexly structured to photosynthesize - occurs inside the chloroplasts - thylakoid “sac-like” = flat membrane bound sacs found inside  chloroplasts - chlorophyll is found here - grana = individual thylakoid stacks - stroma “bed, mattress” = gel-like fluid in chloroplasts that  hold everything in suspension Photosynthesis: - involves 2 major reactions - each major reaction has several processes - F. F. Blackman (1905) discovered the two reactions because of the  enzyme requirements for photosynthesis to produce carbohydrates 1) light dependent reaction: light E is converted into chemical E - takes place in the thylakoid membrane in the presence of sunlight CO2 + H2O ???? C6H12O6 + O2 (water splits ????oxygen released) H+along with excited e’ converted to chemical E (ATP/ NADPH)4 Processes: - photosystem II and photosystem I (in that order) - electron transport chain (E. T. C.) 2) light independent reaction: chemical E is converted into glucose - ATP/NADPH move into the stroma, sunlight not neccessary - CO2 + H2O ???? C6H12O6 + O2 (carbon dioxide ????glucose) Processes: - CO2-fixation - CO2 reduction - regeneration of RuBP Light-Dependent Reactions and 7.5 Energy Flow in Photosynthesis Light Dependent Reaction (Light Reaction): - happens in the presence of sunlight, that’s why it is light dependent - happens in the thylakoid membrane - initiated when light is absorbed by the photosystems - C. B van Niel (1930) discovered that H2O ???? O2 - it was incorrectly thought that CO2 ???? O2 photosystem ( reaction centers ) = cluster of photosynthetic pigments that  contain chlorophyll a and b as well as carotenoids - light-gathering antenna complex absorbs solar E and funnels it to a  reaction-center chlorophyll a molecule, which then energizes e to an  electron-acceptor molecule Two Types of Photosystems: - two photosystems work in partnership A) Photosystem II (PS II) - occurs 1st - chlorophyll absorbs wavelengths of 680 nm to initiate reaction  (see reaction center description below) - noncyclic electron pathway (photophosphorylation)5 - H2O ???? ½ O2 + 2 H++ 2e- O2 = released into the atmosphere (product) photolysis = light; breaking e-= travel to PS I to get boosted to a higher E H+= temporarily stay within the thylakoid space along with  the e creating a high electrochemical gradient  - later used to produce ATP in the ATP synthase complex (chemiosmosis) - E used in the stroma - ADP + P ????ATP (chemical E) while e travel down the E.T.C. - H+ will also be used to convert NADP++ H ???? NADPH (chemical  E) with PS I ???? this chemical E is used in the stroma to produce  organic molecules (sugars, proteins, lipids) B) Photosystem I (PS I) - absorbs wavelengths of 700 nm - cyclic electron pathway (PS I to PS I) (photophosphorylation) - ADP + P ????ATP only - ATP produced used to the run this reaction Reaction Centers (photosystems): 1. light strikes a chloroplast organelle 2. chlorophyll a absorbs the light 3. solar E increases the E level of e boosting them to a higher E level (high temp. activate enzymes) 4. excited e leave chlorophyll a and jump to a nearby membrane bound protein 5. each excited e passes though a series of proteins and pigments - Electron Transport Chain (E.T.C.) 6. the E.T.C. contains a proton pump and is the means by which e are transferred between PS II and I 7. as e-are pumped through the transport chain extra ATP is  generated E.T.C. = a series of proteins and pigments through which e are pumped  which generates ATP ATP production by difference methods: photophosphorylation = ATP production with the use of solar E6 chemiosmosis = ATP production tied to the electrochemical gradient - ATP synthase complex where H+pass through a channel causing  ADP + P+ ???? ATP How do bacteria photosynthesize? - no chloroplasts, but have photosystems in their membrane - have the same pathways with the photosystems Light-Independent Reactions: The Sugar Factory Light Independent Reaction (Dark Reaction): - convert chemical E (ATP and NADPH with C) into glucose What is the point of photosynthesis? - extract C from CO2 in order to produce sugar = requires lots of E - E from the light-dependent reaction (NADPH and ATP) move into  the stroma - that E allows the light-independent reaction to occur - solar E is not directly required for this process to occur, but E from  the light-dependent reaction (ATP & NADPH) is required to reduce CO2 - CO2 diffuses through the leaf - Calvin (Benson) cycle - Melvin Calvin (Nobel prize 1961) determined that a series of reactions occur in the stroma of  the chloroplast reducing CO2 - Benson was also part of that research Steps in the LIGHT INDEPENDENT REACTION: A) CO2-fixation - CO2 attached to an organic compound (5-C mole. + CO2 = RuBP) (RuBP = ribulose biphosphate) - RuBR carboxylase = enzyme used to speed up this reaction = heavy abundance of the enzyme = it reactions much slower  than other enzymes; more needed to keep this reaction going  (accounts for 20-50% of proteins in chloroplast)7 B) CO2 reduction - 6-C mole. results from CO2-fixation which immediately breaks  down to form 2 PGA (3-phosphoglycerate) 3-C molecules result of this reaction: PGA ???? PGAL ATP ???? ADP + P NADPH ???? NADP+ = reduction of CO2 to CH2O (above E needed for this) C) Regeneration of RuBP - for every 3 turns of the Calvin cycle = 5-molecules of PGAL are  used to re-form 3-molecules of RuBP so the cycle can continue result of this reaction: 5 PGAL ???? 3 RUBP (continues)  2 PGAL (net gain) ???? C6H12O6 (product) 3 ATP ???? 3 ADP + P - going from 6 PGAL (CO2 reduction) to 5 PGAL (regeneration of  RuBP) results in a gain of 1 PGAL = 2 PGAL are needed to make 1 mole. of C6H12O6 - it will regenerate its starting material, but the end product is glucose - also called the C3 cycle because Calvin first indentified the  PGA (C3) molecule PGAL (glyceraldhyde-3-phosphate) = product of the Calvin cycle that is  converted to make various organic molecules PGAL = makes glucose ???? this is why PGAL is important ????it is the bases for ALL other organic molecules ????the start of the food web ????E transfer from the sun into a usable form of E glucose = blood sugar in humans (carbohydrates) - algae and plants have a diverse biochemical pathways:  - fructose and the phosphate removed makes sucrose - glucose phosphate makes starch and cellulose - hydrocarbon skeleton from PGAL makes fatty acids and 8 glycerol = plant oils (lipids) - N added to hydrocarbon skeleton from PGAL makes amino acids (proteins) Different Plants, Different Carbon-Fixing Pathways C3 plants = Calvin cycle fixes CO2 directly (normal photosynthesis process as described above) - 1st molecules following CO2 fixation is PGA (3-C molecule) ex: rice, wheat, and oats (major food crops) - when the stomata is closed (cells allowing gas exchange with the  plant and the environment), there is an O2 build up in the leaf with  rubisco attaching to O instead of the C causing photorespiration which results in a decrease in sugar production - C3 plants do not do will in hotter climates because of this C4 plants = fix CO2 by forming a C4 molecule prior to the involvement of  the Calvin cycle => too little CO2, too much O2 in the environment ex: corn, sugarcane, grasses – hot, dry climates - leaf structure is different, they have to make extra steps ???? bundle-sheath cells - photosynthesis rate is 2-3 times more than C3 plants - compensate for closed stomata during hot, dry days by  fixation C twice CAM plants = fix CO2 by forming C4 molecule at night when stomates  can open without loss of water  ex: succulent desert plants ????water-storing tissue ????thick surface layers to prevent water lose during the  day - C4 cycle converts CO2 into malate and other organic acids - malate releases CO2 which allows Calvin-Benson Cycle to  start Autotrophs and Biosphere Autotrophs are the based for the food web as well as O2 availability.9 As the world first developed, autotrophs used other atoms to produce  organic molecules. As O2 was released, the build-up resulted in an  evolutionary push for species to utilize O2 for carbohydrate produce. This  pushed out other species causing mass extinction and other s to survive  without O2 to live in extreme environments – thermal vents, geysers,  anaerobic soils The ocean is full of marine pastures ???? vast areas of photosynthesizing organisms their function ???? based of food web, O2 output, CO2 absorption without them, the based for the food web gone ???? fish starve than what? without them, CO2 build up ???? increase global warming, terrestrial plants? without them, O2 decreases ???? other organisms/ourselves can not respire  O2?10 Life’s Chemical Basis Introduction: Every process that goes on within plants, animals, fungi, and microbes is a  chemical reaction, collectively these reactions describe metabolism. These  reactions are biochemical (bio – life, so it’s the chemistry of life). Why is chemistry important in the study of biology? metabolism, biological molecules, energy, radioactive tracers, and medicine – all deal with chemical reactions chemistry = the study of matter and the changes that it undergoes matter = the “stuff” that makes up all material things in the universe - anything that has mass and, therefore, takes up space  = solid, liquid, or gas Matter is made up of elements (pure substance) - elements are made up of the same type of atom (i.e. oxygen gas) which can neither be broken down nor converted to other substances by  ordinary chemical means  - each particular type of atom forms a different element - 92 naturally occurring elements as seen in the PERIDOIC TABLE along  with man-made elements – developed by Dmitry Mendeleev - each element is designated a one or two-letter abbreviation of its Arabic,  English, or Latin name; this abbreviation is its SYMBOL C – carbon Fe – iron Na – sodium - 25 elements are essential to life o bulk elements = required in large amounts (C, H, O, N) o minerals = essential other than the bulk elements (P, Na, Mg, K, Ca) o trace elements = are required in small amounts Eight important elements make up 99.5% of the mass of living organisms:  O-65%, C-18.5%, H-9.5%, N-3.3%, Ca-1.5%, P-1%, K-0.4%, S-0.3% Other biologically important elements are: Na, Cl, Mg, and Fe1 Start with Atoms Atoms - makes up matter; everything is composed of  atoms. Atoms are the basic structural units of matter and are composed of  still smaller particles: protons, neutrons and electrons (e’) Structure of Atoms (proposed by John Dalton in the 1800’s): 1) nucleus – a central core composed of the 2 heavy subatomic  particles – protons (positive) and neutrons (neutral) 2) energy shells “e’ cloud” – surrounds the nucleus of the atom and  contains the electrons (negative); they are 1/2000 the mass of a  proton or neutron; they are located a various distances from the  nucleus within the E shells - the negative charge of the (electron) e’ exactly equals or balances the  positive charge of a proton - atoms vary in size, weight, and how they interact with others The chemical and physical properties of an atom are determined by the # of  protons and neutrons in the nucleus, and by the # and arrangement of electrons (e’) in its’ energy (E) shells. Atomic Number - number of protons in a nucleus Ex: Hydrogen (H) #1, Carbon (C) #6, Chlorine (Cl) #17 - this equals the number of e’ in the E shells mass number 12C – symbol of element atomic number 6 Atoms and their components all have mass. Protons and neutrons are equal  in mass while e’ are lighter. Atomic Mass – equal to the weight (mass) of the total # of protons and  neutrons in the nucleus of an atom o e’ weigh so little, their weight is not considered Atomic Weight – a measure of the Earth’s gravitational pull on mass Mass vs. Weight - weight is the measure of gravity on mass2 - different on different planets Measuring mass measures the amount of matter present,  the greater the mass the greater the amount of matter.  Putting Radioisotopes To Use Isotopes - atoms of the same element that have different numbers of neutrons in the atomic nucleus, but the same numbers of protons o different mass number, same atomic number - most C atoms are carbon-12 (6 protons and 6 neutrons) - some C atoms are carbon-13 (6 protons and 7 neutrons) - some C atoms are carbon-14 (6 protons and 8 neutrons) Some isotopes are radioisotopes and are useful as “labels” or  “markers” in studying biological processes because they are unstable and  decay over time; as they decay, the type of energy (alpha, beta, or gamma  radiation) they give off allows for dating of the atom. - Henri Becquerel (1896) discovered the use of uranium will produce a  bright image on a photograph - Marie Curie worked with Becquerel in the study of radioactivity and she  named it - Geiger counter are used to detect radiation Low Levels of Radiation - Melvin Calvin used isotopes as tracers to detect the various processes of  photosynthesis since radioactive isotopes are similar to the stable isotope - used to take images of organs/tissues = patients drink a tracer and doctors  can detect its movement helping to diagnose diseases High Levels of Radiation - harmful effects caused by radiation can led to cancer - Marie Curie and many coworkers developed cancer - radiation can stay in the environment causing years of harm to all  organisms - research has led to the use of high radiation in treating cancer What happens When Atom Bonds With Atoms chemical reactions - chemical changes that occur because of the behavior of e’3 - # of electrons in each atom of an element determines how that atom will  react with other elements Electrons constantly orbit the atomic nucleus. They are always in motion, in 3-D space; thus, it is impossible to tell exactly where an e’ will be, but 90% of the time  it is within its orbital. - the first orbital (valence shell – innermost shell)can have up to two e’ - atoms can have >1 orbital, each orbital has its own  characteristic shape and orientation.  - orbitals make up the E levels around the atomic nucleus called e’ shells - e’ shells are labeled K, L, M, N, O, P, and Q - e’ shell closest to the nucleus have the least E and the furthest has the  most E Atoms interact with one another by gaining, losing or sharing e’ from their  outer shells. The outermost shell is important in determining how the atom  combines with other atoms. If the outer shell is full of e’, the atom is not  chemically reactive, it is stable and will not react with other atoms. If the  outer shell is not full of the max # of e’, the atom is chemically reactive.  All atoms “seek” to be stable by having 8 e’ (or zero e’) in their outer  orbital. They can attain this by either sharing/gaining/losing one or more e’ from their outer orbital (octet rule). Bohr’s models - Danish physicist created a model to represent e’ rotations of an atom He H (highly flammable) When atoms share or exchange e’, they are bonded together creating a stable  associations of atoms called molecules = 2 or more atoms linked by  chemical bonds4 chemical bond - attractive force linking two or more atoms into a compound compound – molecules that consist of two or more different elements in  proportions that never do vary molecules (mass) = the smallest part of a compound that still has the properties of  that compound - strength lies in the stability of the atoms when their outer shells are full of e’ - E exist between those bonds which can be given off or absorbed - that E allows an organism to maintain a certain level of cellular organization O2 Cl2 Br I2 - Halogens (group 7) of the periodic table form  diatomic molecules – molecules composed of the same elements chemical reactions - making and breaking of chemical bonds Major Bonds in Biological Molecules TYPES of BONDS: 1) Covalent Bonds = “co” means a shared condition - the bond between two atoms when they share e’ -makes the atoms more stable, by filling outer shells Ex: H has one e’ in its outer shell. If two H are close together, the e’ in one  is attracted to the proton in the atomic nucleus of the other. When the two  are close enough, the e’ begin to share space, filling the outer shell of each  other’s orbital, thus the atoms are covalently bonded together into H2. This  molecule of H gas is very stable. O2 - double bonded - O atoms share two pairs (4 e’) N2 – triple bond – N atoms share three pairs (6 e’) C – four bonds –C atoms share 4 pairs (8 e’) Most biological molecules use covalent bonds. - living and once living are composed of C C has 2 e’ in its inner shell, four e’ in its outer shell, so it can react with up  to 4 other atoms. CH4 gas forms when C is in close contact with 4 H atoms, 5 filling every atom’s outer shell to become more stable by sharing 8 e’. Others: CO2, H2C (ethylene gas) In all of the examples provided, the e’ spend equal time orbiting each nucleus.  Therefore, the distribution of charges is symmetrical and the bond is called a  nonpolar covalent bond. Because of this equal sharing, the molecule is  electrically balanced and as a whole is neutral. Nonpolar substances have no attraction for polar substances. Hydrocarbons - molecules that primarily contain H and C. They produce the  “pure” covalent bonds (nonpolar). The e’s orbit each atom equally. ----------- Polar Covalent Bonds = a sharing of e’, but one atom holds onto their e’ more  tightly which is known as electronegativity ⮚ Example: N and O when they bond with less electronegative atoms (such  as C, H), they share e’s unequally resulting in a polar covalent bond and the e’s shared spend more time orbiting the more electronegative  atom. The bond is polar because this results in one side of the molecule  being more negative than the other side. Unequal sharing of e’ can produce polar molecules. Ex: H2O - O has high electronegativity, so the bonding e’ spend much more  time around the O atom, than around the weaker H atoms. Consequently,  the O end of the molecule is slightly negative, due to the e’ presence. While  the H end is slightly positive since H atoms are basically protons. Polar and Nonpolar Interactions:  Molecules with nonpolar bonds (e’ shared equally) do not interact with the  charges on polar bonds (unequally shared e’). nonpolar substances = fats/oils/hydrocarbon gases (butane) hydrophobic = “water-fearing” polar and ionic substances = water, salt, etc. hydrophilic substance = “water-loving” As a general rule of thumb, like dissolves like.  - no interaction between nonpolar and polar/ionic substance6 The water molecules form a H-bonded "cage" that surrounds the nonpolar  hydrocarbons and pushes them together. These water cages bring together  dispersed nonpolar molecules into larger groups.  - think about oil sheens on the surface of water - think about oil and vinegar - think about substances not dissolved by water ___________________________ 2) Ionic Bonds = attraction of charged atoms (ions) Atoms with outer shells that are not full can become stable by gaining e’ (filling their outermost shells) or by losing e’ (emptying their  outermost shell). Ionic bonds form because some atoms hold onto their e’ more tightly = electronegativity (like polar covalent bonds). Ionic bonds form by electrical  attractions between ions bearing opposite charges to make compounds. Ex: sodium (Na) has 1 e in its’ outer shell  chlorine (Cl) has 7 e in its’ outer shell If Na loses an e’, it becomes stable and if Cl gains one, it becomes stable. - becoming charged ions = atoms that have altered their balance between the #  of protons and e’ Since opposites attract, the atoms stay close together into a molecule of NaCl  forming crystals of salt. The electrical attraction between oppositely charged ions  = an ionic bond.  Ionic bonds are weak and easily broken - salt is dissolved in water 3) Hydrogen Bonds = arises form the attraction between the slight +charge  on a H atom and a slight -charge on a nearby O, N, or Fl atom H2O = the -O in one water molecule is attracted to the +H of another  molecule this results in an H bond O...H   - can also occur with H and an electronegative atom (N or O) H bonds form between molecules, covalent bonds form within molecules.  They are weak bonds, but can add up when a lot of them occur together. 7 Important in water molecules and in 3-D shapes of big molecules like DNA and  proteins. Types of Chemical Bonds How They Are Formed Covalent sharing of pairs of e’s, equal sharing produces nonpolar  covalent bonds; unequal sharing produces polar covalent  bonds very strong, holds atoms together to form molecules Ionic* attraction of opposite charges, + and – ions = atoms with a charge Hydrogen* sharing of H atom to link molecules to each other;  weak and in polar molecules  * weaker bonds, allow interactions between individual atoms or molecules van der Waal’s Attractions - brief, weak attraction between nonpolar  substances that occur because of the random variations in e’ distribution as  they orbit the atoms This creates opposite charges in adjacent molecules and results in a brief  weak attraction. These are important in holding together hydrocarbon chains  (H and C) that make up biological membranes and help to stabilize DNA  molecules and folded 3-D structures of proteins. Water’s Life-Giving Properties Water’s Life Giving Properties Why is water so important to life? - first cells evolved in water 3.5 billion years ago - water covers approximately 75% of the Earth’s surface - living organisms are composed of 70 to 90% water - all life depends on water and its unique properties - water contributes to the Earth’s habitability  o its ability to sustain life - life has a limited temperature range and water helps to regulate it8 Water has a high heat capacity and high specific heat, which allows it to resist  temperature changes and absorb heat and solar radiation.  temperature – a measure of molecular motion Ex: Living in a coastal zone provides mild winters and summers.  Also, hypothermia can result from prolonged exposure to even warm  water because the surrounding water can pull the heat from your body. Water has a high heat of vaporization, which allows for evaporative cooling.  The heat is absorbed from the environment in contact with the water; thus, cools the area. The more evaporation taking place, the more cooling. Ex: Sweating and cooling machines (mister with a fan) Water has a high heat of fusion, which allows water to freeze more slowly than  most other liquids. Most liquids become more dense when they form a solid, but not water. Ice is less  dense than water, which allows the ice to float because of the structure of the water  molecules and the hydrogen bonds between molecules.  What would happen if ice was denser than water?  Ponds and lakes would freeze from the bottom up in winter and kill  everything in them. Instead ice forms a protective layer at the top of bodies of  water, insulating them by reducing heat flow between the water and the colder air  above. Water is the solvent of life (universal solvent). Water is a very versatile  solvent able to dissolve a wide range of substances such as salts, sugars, and  proteins (solutes).  - solution – contains dissolved substances Water has the ability to dissociate ionic molecules and dissolve molecule held  together by polar covalent bonds.  Because of their electrical attraction and capability to dissolve in water, ions  and polar molecules are termed hydrophilic “water-loving”.  Nonpolar or uncharged molecules are termed hydrophobic “water-fearing” because they do not dissolve in water.  Ex: Oil in water, oil will form globules in water.9 Water is cohesive and adhesive: Cohesive – sticks to itself Adhesive – sticks to other things The making and breaking of H-bonds explain the cohesive strength of water.  The cohesive nature of water allows plants to suck water up their roots to their  leaves, the site of photosynthesis. The evaporation of water from the leaves acts  as a suction drawing more water up from the soil. The column of water moves  up as a result of the pull of the molecules at the top. surface tension - the surface tension of water is high, making it difficult to  puncture the surface of a water droplet. The water molecules in the surface layer  are H-bonded to other water molecules below. Surface tension permits a glass to  be over filled past the brim and for water-bugs to walk on water Acids and Bases Acids, Bases, and the pH Scale: Water can come apart into equal numbers of H+and OH ions in an ionization  process. Free H+ions in a cell alters the water environment in which reactions take  place. Acids donate H+ Bases accept H+ Acids - substances that give off H+ions (High H+ Concentration), creating  solutions with the concentration of H+ions exceeding the concentration of  OH ions Bases - substances that give off OH ions (Low H+ Concentration), creating  solutions with the concentration of OH ions exceeding the concentration of  H+ions pH scale Neutral = 7.0 pure water, tears Acids = 0-6 soda, stomach acid, beer, tomatoes Bases = 8-14 Great Salt Lakes, over cleaner, baking soda - each unit on the pH scale represents a ten-fold change in the  concentration of H+ions.10 Ex: The difference between water with a pH of 7.0 and cola with a  pH of 3.0 is that the cola contains 10,000 times more H+ions than  water. Salts and Water: - salts release ions other than H+and OH- - salt forms with the interaction of an acid and a base Living organisms survive in a narrow pH range. This is possible due to substances  called buffers. Buffers are substances, which can accept or donate H+ions to  maintain a constant pH. - CO2 acts as a buffer in our bodies - pH variations can cause sever health problems = respiratory acidosis – fall in blood pH resulting in coma = alkalosis – rise in blood pH which can be lethal Molecules of Life (Organic Molecules) – From Structure to Function 2 Types of Molecules: Inorganic molecules: includes carbon dioxide (CO2) and all molecules without  carbon (C). Ex: table salt Organic molecules: molecules with a C-skeleton that can be synthesized  and used by living organisms. Ex: DNA, Glucose C can form up to 4 covalent bonds, making complex shapes  - chains, rings, branches - versatility of C and the incorporation of functional groups allow for the  great diversity of organic molecules.  - C in organic molecules could have functional groups attached, which  are less stable than the C backbone and participate in chemical reactions.  - functional groups determine the characteristics and chemical reactivity of organic molecules Functional groups important in biological molecules: Group Properties Examples Hydrogen dehydration in almost all organic 11 -H+(release of H2O by combining molecules with another molecule) hydrolysis H++ OH- H2O (split molecules into parts  using H2O) Hydroxyl polar, dehydration and hydrolysis carbos, nucleic acids, OH alcohols, steroids Carboxyl acidic, releases H+and becomes -amino acids, fatty acids -COOH involved in peptide bonds Amino basic, may bond with H+and become + amino acids, nucleic acids -NH2 involved in peptide bonds  Phosphate acidic, E-carrier in ATP rxn nucleic acids,  -H2PO4 links nucleotides in nucleic acids phospholipids Methyl makes molecules hydrophobic lipids, many other  -CH3 molecules = other examples of functional groups in text Virtually all organic molecules from all forms of life: ⮚ use the same set of functional groups ⮚ use the “modular approach” to make large molecules - functional groups can make molecules hydrophilic or hydrophobic Isomers (equal; part, portion) = chemical compounds that have the same molecular formula but different molecular structures How Do Cells Build Organic Compounds? Macromolecules (big molecules) = contain hundreds or thousands of atoms and  have a very large molecular weight Ex: human hemoglobin contains more  than 6,000 atoms 12 Macromolecules are chains of small, individual units called monomers (one unit)  covalently bonded together to form a polymer (many units). The actual bonds  between the monomers can differ according to the particular polymer. No animal acquires macromolecules directly from food. Instead, it uses the  subcomponents of its’ food to make new macromolecules suited to its’ unique  needs (break down then reassembles). Organic molecules are synthesized by combining atom after atom to form small  subunits ????the monomers “one unit” - long chains of monomers ???? polymers “many units” In organisms, there are three types of polymers: polymer monomer  polysaccharide (carbohydrate) monosaccharide polypeptide (protein) amino acid nucleic acid nucleotide Lipids are not true polymers because they have no repeating units  (monomers), but they are large organic molecules (C based).  Metabolism = sum of all chemical reactions that occur within an organism 2 types: a) Anabolism = synthesis (to make), requires E  (dehydration/condensation) - polymers form when E is added to the system  = endergonic reactions b) Catabolism = break down, releases E (hydrolysis) - polymers break apart releasing E into the system  = exergonic reactions - the subunits of large organic molecules are linked together by  dehydration synthesis reactions which literally means “to form  by the removal of water” (anabolic = requires E) condensation reaction = forming of water - hydrolysis reactions break down polymers into monomers by  adding water, the universal solvent (catabolic = releases E) - hydro “water” and lysis “breaking”13 Other types of reactions: functional-group transfer = one molecule gives up a functional group  entirely, and a different molecule immediately accepts it electron transfer = one or more e’ stripped from one molecule are  donated to another molecule rearrangement = juggling of internal bonds converts one type of organic  compound into another cleavage = a molecule splits into two smaller ones (hydrolysis) - enzymes (protein) are needed for chemical reactions to occur Nearly all organic molecules fall into one of FOUR categories: 1. Carbohydrates 2. Lipids (not a macromolecule) 3. Proteins 4. Nucleic Acids The Most Abundant Ones – Carbohydrates Carbohydrates(CH2O)n - provide quick E to fuel cell/organism and structure General formula: CH2O carbon, hydrogen and oxygen (1:2:1 ratio) Three carbon sugars: triose Four carbon sugar: tetrose Five carbon sugar: pentose deoxyribose (DNA) ribose (RNA) Six carbon sugar: hexose Types Example Function monosaccharide: glucose E source for cells, sap  (one-sugar) fructose sugar in fruit galactose sugar in milk deoxyribose sugar in DNA ribose sugar in RNA Glucose, fructose & galactose are isomers (C6 H12 O6).  - all 6-carbon sugars (hexose)14 Types Example Function disaccharide: sucrose table sugar (two-sugars) (glucose + fructose) lactose milk sugar (glucose + galatose) maltose seed sugar (glucose + glucose) - 2 monosaccharides linked by dehydration process which results in the  removal of 1 H2O molecules (C12H22O11)  Types Example Function oligosaccharide: glycoprotein - sugar attached to protein (3-100 sugars) (cell surface marker like with blood) Types Example Function polysaccharide: starch E storage in plants (many-sugars) glycogen E storage in animals (liver/muscles) cellulose structural material in plants (cell wall) ▪ not easily digestible ▪ abundant on earth chitin structural material in the fungi and exoskeletons of arthropods and  crustaceans (shrimp, crabs, crawfish  shells) and cell walls of fungi ▪ not easily digestible ▪ abundant on earth - “many” sugars formed by the monosaccharides (monomers) binding  together - chemical formula more difficult to predict because of dehydration  (lose of H2O) Greasy, Oily – Must Be Lipids Lipids(C and H = hydrocarbons, O) - all are insoluble in water because of the many nonpolar covalent bonds and 15 the lack of polar groups - defined by solubility vs. structure (like other organic molecules) - close proximity of nonpolar molecules cause a weak attractive force…van der  Waals forces 4 main types: A) Fats and Oils: Triglycerides oil, fat E storage in animals, some plants “true fats” (long-term E storage) - composed of glycerol (a sugar alcohol) + 3 long chain fatty acids—nonpolar hydrocarbon tails. fats - solid at room temperature (20 degrees C) = butter, bacon grease, lard oils - liquid at room temperature = corn oil, vegetable oil, olive oil, peanut oil saturated = solid at room temp, C-atoms saturated w/ H atoms, nestled  close together and that makes them rigid unsaturated = liquid at room temp, room between atoms - C-atoms  are double bonded, so fewer H-atoms giving the lipid flexibility monounsaturated fat - one double bond Ex: olive oil….which  research suggests raises good cholesterol, while lowering bad  cholesterol. polyunsaturated fat – 2+ double bonds Ex: corn oil, canola oil Diets that limit saturated fats and favor unsaturated fats help to reduce the heart  attacks. Animals store fat rather than glycogen for long-term E storage because of the  numerous C-H bonds in their fatty acid chains = a rich source of E B) Steroids - signal molecules  - ringed C structures that do not resemble the triglycerides, but have lipid  properties. 16 cholesterol: - biologically active steroid that is synthesized in the liver - a component part of cell membrane (makes it stable) - starting molecule for the production of testosterone & estrogen - bile salts that help digest fats  - as a hormone, they function as chemical messengers - absorbed from milk, butter and animal fat (deposited in artery walls) Some lipids are vitamins  Fat soluble vitamins are formed by plants and bacteria. Man typically  obtains these vitamins from dietary sources.  Vitamin A - formed from B-carotene, found in green and yellow vegetables.  role –vision Vitamin D - regulates absorption of Ca from the intestines.  role--skeletal development Vitamin D2 - produced in the skin by the action of U.V. light on cholesterol. Vitamin E - not a single vitamin, but a group of related lipids that protect cells  from damaging effects of oxidation-reduction reactions role--anti-oxidant, anti-aging Commercially, used to slow spoilage of some food stuffs. C) Waxes (similar to fats): fatty acid + alcohol plants: waterproof covering on leaves and stems (cuticle) animals: skin and fur maintenance in waterproofing (prevents dirt and microbial infiltration) beehives D) Phospholipids (similar to oils): - Like triglycerides, phospholipids have fatty acids bound to glycerol by ester  linkages, however one of the fatty acid chains has been replaced with a P containing compound.  Phospholipids form cell/organelle membranes: one end is hydrophilic (polar – head = soluble in water)  = glycerol with the P-group17 one end is hydrophobic (non-polar – tail = insoluble in H2O) = fatty acid  - P functional group has a negative charge (polar), so this portion is hydrophilic, attracting water molecules.  - the two fatty acid tails are hydrophobic ("water fearing"), so they are  pushed together by the water.  - the phospholipids forms a bilayer because of the polar & nonpolar regions Proteins – Diversity in Structure and Function Protein (C, H, O, N, S) amino acid chains - held together by peptide bonds (covalent bond) peptide = chain of a few amino acid polypeptide = lots of amino acids in a chain (several chains) Protein Functions Examples structure collagen and elastin in the skin; keratin in hair, horns, and  claws or nails, silk from spiders and worms movement actin and myosin in muscle tissue transport hemoglobin to move O in blood  membrane transport proteins defense antibodies in the blood stream, venom in snakes hormones insulin and growth hormone catalysts enzymes to speed up reactions without becoming a part of it Proteins are formed by chains of amino acids:  amino acids are the monomers and the protein is the polymer  amino acids are composed:  amino group, carboxyl group, H-atom and a R Group surrounding a C 18 - the R groups differs among amino acids giving each its distinct property -- 20  different amino acids - amino acids link together by a dehydration synthesis reaction, which forms a  peptide bond between the carboxyl group of one amino acid and the amino  group of another  - one amino acids join through covalent bonding to form a peptide bond - two amino acids join together to form a dipeptide - three amino acids join together to form a tripeptide - many amino acids join together to form a polypeptide (polymer/protein) - Frederick Sanger 1953 = developed a method to determine the sequence of  amino acids in a polypeptide. A protein may contain more than one polypeptide chain. There is a great range in protein size. Some are only a few amino acids (50  or less), others are composed of thousands.  Each protein has its own characteristic amino acid composition, arranged in  a particular sequence. Different proteins have different shapes. The shape of the protein  determines its function. There are FOUR levels of organization in protein structure: Primary Structure The unique linear sequence of the amino acid chain in a  straight chain. Secondary Structure Alpha helix, a spiral (screw) formed by H-bonds  between every 4th peptide bond (ex. – keratin). Beta pleated sheet, polypeptide chain folds back on itself  and the parallel region are held together by H bonds (silk  fibers). Tertiary Structure The folding into a 3-D shape due to disulfide bridges and  hydrophobic interactions. Quaternary Structure The joining of two or more polypeptide chains held  together by H bonds. The 3-dimensional structure (shape) of a protein will determine its’ function. 19 Certain environmental changes may cause the protein to unravel and lose its  structure (3-D shape). If this happens, the protein cannot function and is  biologically inactive.  Why Is Protein Structure So Important? Protein sequencing is extremely important. One mistake will completely alter the  molecule, thus altering its’ function. - hemoglobin – four tightly packed polypeptides (globins) globins ???? folded chains create pockets (heme group) heme ???? large organic molecules with an Fe center - 2 types: alpha and beta- 2 of each are needed to make up hemoglobin - normal sequence in beta ???? glutamate at the sixth amino acid = negative charge, normal function - abnormal sequence in beta ???? valine at the sixth amino acid = no net charge, abnormal function = mutation in DNA - purpose of hemoglobin is to carry O to different parts of the body - an individual who inherits a mutant gene from each parent will have sickle-cell  anemia ???? O flow will be disrupted, results in oxygen starved tissue = the shape of the protein effects its’ function ???? change in shape, change in function (denature) Extreme pH, temperature, and salt concentrations can denature (change the  shape of a protein). When the protein loses its’ shape, it can no longer  function as it was meant to do – denature. This is usually irreversible. Sometimes denaturation is reversible …. Renaturation. - done at the cellular level - amino acid sequences is very important – read about protein related diseases Nucleotides, DNA, and the RNAs Nucleic Acids (C, H, O, N, P) - chains of nucleotides: 5C sugar (pentose) + phosphate + base - nucleotide = monomer20 Example Function deoxyribonucleic acid (DNA) genetic material “informational molecules” forming genetic code - this information pertains to replication and protein production - two strands of DNA are held together by H-bonds between the bases  - the shape is called the double-helix – like a twisted ladder - bases for DNA: adenine, guanine, cytosine, thymine  o complementary base pairs for DNA: A - T and G - C Example Function ribonucleic acid (RNA) genetic material of some viruses,  transfer DNA into proteins - bases for RNA: A, G, C, uracil (A - U, G - C) - RNA is copied from DNA o RNA takes the genetic code, deciphers it, and uses it  - main function is protein synthesis o since DNA can not leave the nucleus, information is transferred to RNA  which will let the nucleus to make the proteins - single strand - nucleotides are linked by H-bonds between the 5-C sugar and the P- group  Single nucleotides that are important such as cyclic AMP and ATP: Cyclic adenosine monophosphate (cyclic AMP) = a single nucleotide that is  produced when a hormone comes in contact with the cell membrane. Cyclic  AMP acts as a messenger between the cell membrane and other molecules  within the cytoplasm or the nucleus stimulating necessary reactions.  Adenosine triphosphate (ATP) = a single nucleotide with two extra  P- groups. This molecule carries E. ATP acquires E within the cell where it  is produced and releases it during necessary reactions.  Other E carrier within the cell (coenzymes): NAD (nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide)  both serve as temporary E carriers within the cell.21

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