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Cell and Molecular Biology Final Outlines

by: Abigail Kopp

Cell and Molecular Biology Final Outlines Cell and Molecular Biology

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Abigail Kopp
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These notes are very well done detailed notes of each of the chapters. Reading these over a few times carefully and looking at pictures provided in the book should give you the grade you are lookin...
Cell Biology
Hoyt,Eric Rutledge
Study Guide
Biology, cellular biology, Molecular
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This 116 page Study Guide was uploaded by Abigail Kopp on Monday April 18, 2016. The Study Guide belongs to Cell and Molecular Biology at Rensselaer Polytechnic Institute taught by Hoyt,Eric Rutledge in Spring 2016. Since its upload, it has received 19 views. For similar materials see Cell Biology in Biology at Rensselaer Polytechnic Institute.

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Date Created: 04/18/16
Chapter 1  Cells: The Fundamental Units of Life  175 years ago marked a revolution of thinking, all living things (organisms) are built from cells.  Cells are small, membrane-enclosed units filled with a concentrated aqueous solution of chemicals and that can create copies of themselves and then dividing into two.  Unity and Diversity of Cells  Cells are not all alike.  But they all have similar properties  Cells Vary Enormously in Appearance and Function  Size  A bacterial cell is a few micrometers, µm, in length  Frog egg (also single cell) is about 1 mm.  Shape  A Nerve Cell is 10,000 times longer than it is thick and receives signals from other nerve cells through a mass of shorter processes that sprout from its body like branches from a tree.  A Paramecium in a drop of pond water is shaped like a submarine and is covered with thousands of cilia (hair-like extensions whose sinuous beating sweeps the cell forward, and rotates it)  In the cell on the surface layer of the PLANT it is immobile because it is surrounded by a rigid box of cellulose with an outer waterproof coating of wax.  In ANIMAL cells, a neutrophil or a macrophage crawls through tissues, constantly changing into new shapes, as it searches for and engulfs debris, foreign microorganisms and dead or dying cells.  Chemical requirements  Some cells require oxygen to live, for others it will kill them.  Some cells consume more than air, sunlight, and water as their raw materials. Others need a complex mixture of other molecules produced by other cells.  Cell Functions  Some cells are specialized factories for the production of particular substances  Some produce particular substances such as hormones, starch, fat, latex or pigments.  Others are engines, example muscle cells burn fuel to do mechanical work.  Others are electricity generators, like the muscle cells in the electric eel.  In multicellular organisms, there is a division of labor among cells, allowing some cells to become specialized to complete a specific task.  Living Cells All Have a Similar Basic Chemistry  Life  Growth, reproduction, and an ability to respond to the environment.  All cells resemble one another on the inside  Cells are composed of the same sorts of molecules and participate in the same types of chemical reactions.  In organisms, the genes are kept in the DNA molecules. This information is written in a chemical code.  DNA polymer chains are made from the same set of four monomers, called nucleotides strung together in sequences to convey information  RNA reads the encoded information that DNA gives and translate it into proteins.  The flow of information from DNA to RNA is central dogma.  What do the proteins do?  Dictate the appearance and behavior of a cell.  Serve as structural supports, chemical catalysts, molecular motors.  Proteins  Built from amino acids, and all organisms use the same set of 20 amino acids to make their proteins  Fundamental of life  Cell  Viruses , cannot reproduce themselves. They reproduce by parasitizing the reproductive machinery of the cells they invade.  All Present-Day Cells Have Apparently Evolved from the Same Cell  Mutations  When a cell reproduces, the DNA replicates and then divides into two.  The copy of the genetic code in the DNA is passed to the daughter cells. (Why they resemble the parent cell)  But copying is not always a perfect match, the instructions are occasionally corrupted by mutations that change he DNA.  It can create an offspring that is changed for the worse, better, or changed in a neutral way.  The mutations over billions of cell generations are the basis of evolution.  Evolution  Process by which living species become gradually modified and adapted to their environment in sophisticated ways.  Explains why cells are so similar  Estimated that LUCA (Last Universal Common Ancestor) existed between 3.5 and 3.8 billion years ago.  Genes Provide the Instructions for Cell Form, Function, and Complex Behavior  Genomes  Entire sequence of nucleotides in an organism’s DNA  Provide a genetic program that instructs the cell how to behave  For plants and animal embryos, the genome directs growth and development with hundreds of different cell types.  All different cell types are made during embryonic development from a single fertilized egg cell and all contain identical DNA  Each cell is capable of carrying out of variety of biological tasks, depending on environment and history, it selectively uses the information encoded into is DNA to guide its activities.  Cells Under the Microscope  Light microscopes  Use visible light to illuminate specimens, and they allowed biologists to see for the first time the intricate structure that lives in all things  Electron microscopes (1930)  Use beams of electrons instead of beams of light as well as a source of illumination  Can see finer details of cells and some of the larger molecules  The Invention of the Light Microscope Led to the Discovery of Cells  Happened from the development of the glass lenses  The lenses were now powerful enough to make out details invisible to the naked eye  Robert Hooke examined a piece of cork and in 1665 saw chambers and later called them cells.  Leeuwenhoek reports his discovery of protozoa in 1674. Nine years later, he sees bacteria for the first time.  Hooke and Leeuwenhoek later then observed living cells.  Schleiden and Schwann documented results of plant and animal tissues with the light microscope. Which showed that cells were the building blocks of all living tissues in 1839  This work led to the realization that all living cells are formed by the growth and division of existing cells (Cell Theory)  In 1994, Chalfie introduced green fluorescent protein (GFP) as a marker to follow the behavior of proteins in living cells.  Light Microscopes Allow Examination of Cells and Some of Their Components  cut a very thin slice of plant or animal tissue and use a light microscope to see cells  the cells can either be closely packed or separated from one another by an extracellular matrix. (a dense material often made of protein fibers embedded in a polysaccharide gel.)  Since cells are often transparent, we do things to see them  dye to organelles in cells different colors.  Use a refractive index, which causes the light rays to be deflected as they pass from one medium to another.  Fluorescence microscopes use methods of illumination and electronic image processing to see fluorescently labeled cell components in finer details. (The best one can push resolution to the size of a ribosome which is rly fuckin small like 20 nanometers)  Tissue needs to be fixed (preserved in a chemical solution)  The Fine Structure of a Cell is Revealed by Electron Microscopy  Electron microscopes  Reveal details down to a few nanometers  Samples have to be..  fixed,  supported by embedding in a solid wax or resin,  cut or sectioned into thin slices,  and stained before it is viewed.  After this is done, you can clearly see the distinct organelles.  A 5 nanometer membrane is visible  Plasma Membrane, membrane that separates the interior of the cell from its external environment, is visible  A single large molecule can be seen.  For electron microscopy, similar procedures are required, but sections have to be much thinner and the cells have to be dead.  Transmission electron microscope  Looks at thin sections of tissue  Similar to light microscope, except it transmits a beam of electrons rather than a beam of light.  Scanning Electron microscope  Scatters electrons off the surface of the sample and looks at surface details of cells and other structures.  The Prokaryotic Cell  Bacteria have the simplest structure and come closest to showing us life stripped down to its essentials.  It has no organelles, not even a nucleus that holds DNA.  Organisms whose cells do not have a nucleus are called prokaryotes.  Another form of prokaryote are archaea  Prokaryotes are..  Typically spherical, rod-shaped, or spiral shaped  Small  Often have a protective coat or cell wall surrounding the plasma membrane  In the plasma membrane is just DNA and cytoplasm.  Reproduce very fast  Prokaryotes Are the Most Diverse and Numerous Cells on Earth  Most prokaryotes live as single-celled organisms, some join together to form chains, clusters, or other organized multicellular structures.  Prokaryotes have the most diverse and inventive class of cells.  They are in an enormous range of habitats, from hot puddles of volcanic mud to interiors of other living cells, and they outnumber the eukaryotic organisms.  Some are aerobic, using oxygen to oxidize food molecules  Some are anaerobic and are killed by the slightest exposure to oxygen.  Any type of carbon-containing material can be used as food by some type of prokaryote  Some can live entirely off inorganic substances also  Some perform photosynthesis  The World of Prokaryotes is Divided into Two Domains Bacteria and Archaea  Two groups of prokaryotes  Bacteria  Archaea  Bacteria are familiar from everyday life  Archaea are found in the in environments that are too hostile for most other cells.  The Eukaryotic Cell  Bigger and more elaborate than prokaryotes  Some live as single-celled organisms (ex. Yeasts and amoebae)  Others live in multicellular assemblies (plants, animals, fungi)  Eukaryotic Cells have a nucleus  The Nucleus is the Information Store of the Cell  Nucleus is usually the most prominent organelle in eukaryotic cell.  Enclosed with two concentric membranes that form the nuclear envelope and it contains DNA. (very long polymers that encode genetic information.  In a light microscope, the DNA molecules become visible as chromosomes.  Mitochondria Generates Usable Energy from Food to Power the Cell  Mitochondria are present in almost all eukaryotic cells and they are among the most noticeable organelles.  Enclosed within two separate membranes, with the inner membrane forming into folds that project into the interior of the organelle.  Generates chemical energy for the cell  Harness energy from oxidation of food to produce ATP (adenosine triphosphate)  Since the mitochondria consumes oxygen and releases carbon dioxide, it goes through cellular respiration. (breathing on cellular level(  Without this plant, fungi and animals would be unable to use oxygen to extract energy.  They evolved from aerobic bacteria  Contain their own DNA and reproduce by dividing into two.  They are thought to have been derived from bacteria that were engulfed by some ancestor eukaryotic cell.  Mutual relationships helped the cell survive and reproduce  Chloroplasts Capture Energy from Sunlight  Chloroplasts large, green organelles that are found in cells of plans and algae.  Have two surrounding membranes, and possess internal stacks of membranes containing chlorophyll.  Carry out photosynthesis- trapping the energy of sunlight in their chlorophyll molecules and using this energy to drive the manufacture of energy-rich sugar molecules. Then release oxygen as a molecular by-product. Plant cells can then extract the chemical energy when they need it by oxidizing these sugars in the mitochondria. Then creating ATP.  Chloroplasts also contain their own DNA, reproduce by dividing in two, and are thought to have evolve d from bacteria.  Internal Membranes Create Intracellular Compartments with Different Functions  Endoplasmic reticulum  Irregular maze of interconnected spaces enclosed by a membrane  Where materials that are leaving the cell are made.  Enlarged in cells where secretion of proteins is specialized.  Golgi Apparatus  Modifies and packages molecules made in the ER that are destined to be either secreted from the cell or transported to another cell compartment.  Lysosomes  Small, irregularly shaped organelles that digest food and release nutrients.  Break down unwanted molecules for either recycling within the cell or excretion from the cell.  Peroxisomes  Small membrane-enclosed vesicles that provide a safe environment for a variety of reactions in which hydrogen peroxide is used to inactivate toxic molecules.  Transport vesicles  Membranes form these to move materials between one membrane-enclosed organelle and another.  A continual exchange of materials takes place between the ER, Golgi Apparatus, Lysosomes, and the outside of the cell.The exchange is mediated by transport vesicles that pinch off from the membrane of one organelle and fuse with another.  Endocytosis is where portions of the plasma membrane tuck inward and pinch off to form vesicles that carry material captured from the external medium into the cell.  Animal cells can engulf very large particles, or even foreign cells by this process.  Exocytosis is when vesicles from inside the cell fuse with the plasma membrane and release their contents into the external medium.  Most hormones and signal molecules that allow cells to communicate with one another are secreted from cells do this  The Cytosol is a Concentrated Aqueous Gel of Large and Small Molecules  Part of the cytoplasm that is not contained within intracellular membranes is the cytosol.  Largest single compartment.  Contains a host of large and small molecules that are close together and behaves like a gel.  This is where many chemical reactions that are fundamental to the cell’s existence exist.  Breakdown of nutrients molecules take place here  Proteins are made by ribosomes  The Cytoskeleton is Responsible for Directed Cell Movements  Eukaryotic cells have cytosol that is mixed with long, fine filaments.  The filaments are seen to be anchored at one end to the plasma membrane or to radiate out from a central site next to the nucleus.  The protein filaments are called cytoskeleton. There are three major types  Actin filaments  Thinnest, abundant in all eukaryotic cells, are very abundant in muscle cells.  Microtubules  Thickest filament, small hollow tubes, in dividing cells they become reorganized into an array that helps pull the duplicated chromosomes in opposite directions and distribute them evenly into the daughter cells.  Intermediate filaments  Medium in thickness, serve to strengthen the cell.  Together these filaments with other attached proteins form a system of girders, ropes and motors that give the cellist mechanical strength, controls its shape, and drives and guides its movements.  Found in both animal (so it can be flowy) and plant (so it can be stiff) cells  Very important in cell division.  The Cytoplasm is Far from Static  The cell interior is in constant motion.  Has a bunch of protein ropes that are continually being strung together and taken apart.  Motor proteins use the energy stored in molecules of ATP to trundle along these tracks and cables and carry organelles and proteins throughout the cytoplasm.  The different size molecules move due to thermal motion and constantly collide with one another  Eukaryotic Cells May Have Originated as Predators  The ancestral eukaryotic cell was a predator that fed by capturing other cells.  The nucleus may have evolved to keep the DNA segregated from the physical and chemical combination.  Protozoans is a single celled eukaryote who is animal like with its mobility and predator like.  Example: Didinium is a large carnivorous protozoan with a diameter 10x as big as a human cell. It swims at high speed to catch up to prey then releases paralyzing darts from its snout and then attaches to the victim and devours it.  Not all are predators. Some can be photosynthetic or carnivorous, motile or sedentary.  LUCA  Last Universal Common Ancestor (more than 3 billion years ago)  Shows that bacteria got mitochondria’s, then chloroplasts and has led up to what we are today.   Cell Architecture  Model Organisms  Model organisms is a non-human species that is studied a lot to understand a particular biological phenomena.  Molecular Biologist Have Focused on E. coli  E. coli is the model organism for bacterium.  The small rod shaped grows happily and reproduces rapidly in a simple nutrient broth in a culture bottle  From these studies, we have received most of our knowledge of the fundamental mechanisms of life (ex. How cells replicate their DNA and how they decode these genetic instructions to make proteins)  Brewer’s Year is a simple Eukaryotic Cell  Yeast (saccharomyces cerevisiae) is the same microorganism that is used for brewing beer and baking bread.  S. Cerevisiae is a single-celled fungus that is at least as closely related to animals as it is to plants.  Has a rigid cell wall, relatively immobile, and possesses mitochondria but no chloroplasts.  When in the right settings it reproduces almost as quickly as the bacterium, yet it carries out all the eukaryotic functions. (including cell division cycle)  Arabidopsis Has been Chosen as a Model Plant  Arabidopsis thaliana is a small weed which can be grown indoors in large numbers  One plant can produce thousands of offspring within 8-10 weeks  Studying this plant will provide insights into the development and physiology of the crop plants that our lives depend on, as well as into the evolution of all the other plant species that dominate every ecosystem on earth.  Model Animals Include Flies, Fish, Worms and Mice  Majority of al living multicellular species are animals  Insects are the majority of the animals  So the small fruit fly, Drosophila melanogaster, provided proof that genes are carried on chromosomes. It has shown us how the genetic instructions encoded into DNA direct the development of a fertilized egg cell (zygote) into an adult organism.  Mutated fruit flies have provided the key to identifying and characterizing the genes that are needed to make a properly structured adult body, with guy, wings, legs, and eyes and etc. in their correct places.  These genes define how each cell will behave in its social interactions.  It is very close to human gene development  They also study the worm (Caenorhabditis elegans) a harmless relative of the eelworms that attack the roots of crops.  Smaller and simpler than fruit fly  Has 959 body cells  Learned the sequence of events when the cells divide, move and become specialized  70% of human genes have some counterpart in the worm.  Studies have led to a detailed molecular understanding of apoptosis (a programmed cell death where extra cells are disposed of in all animals) which is important for cancer research.  The zebrafish provides insights into the developmental processes in vertebrates  It is transparent for the first 2 weeks of its life so it provides an ideal system to observe how cells behave during development in a living animal.  Mammals are the most complex of animals, so we use a mouse.  Allows us to study mammalian molecular biological techniques,  it is now possible to breed mice with engineered mutations in any specific gene  we can test what a given gene is required for and how it functions.  Almost every human gene has a counterpart in the mouse, and has a similar DNA sequence and function.  Comparing Genome Sequences Reveals Life’s Common Heritage  Most human cells given perfect conditions will survive, proliferate, and even express specialized properties in a culture dish.  Experiments using culture dishes are called ‘in vitro’ (in glass)  Experiments on intact organisms are ‘in vivo’ (in the living)  Many types of cells grown in culture display the differentiated properties appropriate to their origin  Ex. Fibroblasts continue to secrete collagen.  Embryonic skeletal muscles fuse to form muscle fibers  Because ‘in vitro’ cells are contained in a controlled environment, they are accessible to study in ways that are not possible in ‘in vivo’  Humans are unique because they report and record their own genetic defects  In no other species are individuals so intensively examined, described, and investigated.  Comparing Genome Sequences Reveals Life’s Common Heritage  At the molecular level, evolutionary change has been super slow.  This is why molecular bio was built  When looking into an organism’s genome we look at overall size and how many genes it packs into that length of DNA.  Prokaryotes carry very little superfluous genetic baggage and squeeze a lot of information in their small genomes.  This is why the differences in gene numbers are not so great between E. coli and humans.  When genes from different organisms have similar nucleotide sequences they are said to be homologous (descended from a common ancestral gene).  We can now span this enormous evolutionary divide by taking stock of the common inheritance of all living things.   Genomes Contain More than Just Genes  The vast bulk of our DNA includes a mixture of sequences that help regulate gene activity, plus sequences that seem to be dispensable.  The large quantity of DNA contained in the genomes of eukaryotic multicellular organisms allows for enormous complexity and sophistication in the way genes are brought into action at different times and places.  DNA can program the growth, development, and reproduction of living cells and complex organisms is cool. Chapter 2: Chemical Components of Cells  Introduction  It was believed that animals contained a vital force –an ‘animus’- that was responsible for their distinctive properties in the 19 century.  It is based on carbon compounds which is known as organic chemistry.  Life also depends on chemical reactions that take place in aqueous solutions  Our cells are very complex chemistry  Our body is dominated and coordinated by collections of enormous polymeric molecules- chains of chemical subunits linked end to end. These properties enable cells and organisms to grow and reproduce and to have other characteristics of life.  Cells deploy a variety of mechanisms to make sure that all their chemical reactions occur at the proper place and time.  Chemical Bonds  Matter is made up of a combination of elements  Substances such as hydrogen or carbon that cannot be broken down by chemical means.  Smallest particle of an element that retains its distinctive chemical properties is an atom.  Substances other than pure elements depend on atoms that are linked together in molecules.  Cells Are Made of Relatively Few Types of Atoms  Atom  Has at its center a dense, positively charged nucleus, which is surrounded at some distance by a cloud of negatively charged electrons (held there by electrostatic attraction to nucleus)  Nucleus  Consists of protons and neutrons  The number of protons determines the atomic number.  Isotopes  An element can exist in several physically distinguishable but chemically identical forms  Each has a different number of neutrons but the same number of protons.  Most occur naturally, including some that are unstable and radioactive.  Atomic Weight (molecular weight)  Mass relative to that of a hydrogen atom.  Number of protons plus the number of neutrons that the atom or molecule contains.  Because electrons are so light they do not contribute much to the total mass.  Unit: Dalton’s  Avogadro’s Number  Allows us to relate everyday quantities of chemicals to numbers of individual atoms or molecules. 23  6x10  If a substance has a molecular weight of M, M grams of the 23 substance will contain 6x10 molecules  There are 90 naturally occurring elements. Living organisms are made of only a small selection of these elements  Carbon, Hydrogen, Nitrogen, and Oxygen  The Outermost Electrons Determine How Atoms Interact  In living tissues, only the electrons of an atom undergo rearrangements.  Electron shells: st  1 shell  2 electrons  2ndshell  8 electrons  3 shell  8 electrons th th  4 and 5 shell  18 electrons  Each shell has electrons that are less tightly bound  Electrons in an atom are most stable when all of the electrons occupy the closest shells.  Atoms whose outermost shell is entirely filled with electrons is especially stable and chemically unreactive.  Chemical bonds bind atoms together  Ionic bond- formed when electrons are donated by one atom to another  Covalent bond- formed when two atoms share a pair of electrons  The number electrons an atom must acquire or lose to attain a filled outer shell determines the number of bonds the atom can make.  Metals how incomplete outer shells with just one or a few electrons whereas the inert gases have full outer shells  Covalent Bonds Form by the Sharing of Electrons  A molecule is a cluster of atoms held together by covalent bonds. (Electrons are shared not transferred)  Bond length is the attractive and repulsive forces that are in balance when the nuclei are separated by a characteristic distance  There are Different Types of Covalent Bonds  Single Bonds  Sharing of two electrons, one donated by each participating atom  Allows rotation  Double Bonds  Sharing of four electrons, two from each participating atom  Shorter and stronger than single bonds  Prevents rotation, producing a more rigid and less flexible arrangement of atoms.  Polar Covalent Bonds  Electrons are shared unequally  There is a positive charge at one end of molecule and negative charge toward the other.  Covalent Bonds Vary In Strength  Bond strength  Measured by the amount of energy that must be supplied to break the bond (kJ/mol)  In living organisms covalent bonds are usually broken during specific chemical reactions that are controlled by specialized protein catalysts called enzymes.  Ionic Bonds Form by the Gain and Loss of Electrons  Ionic Bonds  Usually formed between atoms that can attain a completely filled outer shell most easily by donating or accepting another atom.  When an electron jumps from Na to Cl to make both atoms valence shell full, they become charged ions.  If you lose and electron, you are positive. If you are a positive ion, you are a cation  If you gain an electron, you are negative. Negative ion means anion.  Ions held together solely on ionic bonds are generally called salts rather than molecules.  Non covalent Bonds Help Bring Molecules Together in Cells  In an aqueous solution, ionic bonds are 10-100 times weaker than the covalent bonds that hold atoms together in molecules.  Biology depends on specific but transient interactions between one molecule and another.  These associations are made by non-covalent bonds.  They are individually weak, but their energies can sum to create an effective force between two molecules.  The ionic bond that hold together ions in a salt crystal are a form of non- covalent bonds called electrostatic attraction.  these are attractions that are strongest when the atoms involved are fully charged.  Weaker electrostatic attraction also occurs between molecules that contain polar covalent bonds  Polar covalent bonds are extremely important because they allow molecules to interact through electrical forces.  Any large molecule with a bunch of polar groups will have a pattern of partial positive and negative charges on its surface  When this type of molecule encounters a second molecule with the same set of charges, they will be attracted to each other by electrostatic attraction  Hydrogen Bonds are Important Non-covalent Bonds for many Biological Molecules  Water is 70% of a cells weight and most intracellular reactions occur in an aqueous environment  Hydrogen Bonds  When a positively charged region of one water molecule (H atoms) comes close to a negatively charged region (O atom) of a second water molecule, the attraction between them makes this weak bond  These bonds are weaker than covalent bonds and are easily broken.  Bonds last a short time  Water is a liquid at room temperature because of all the hydrogen bonds being continually broken and formed  They can occur in different parts of a molecule to help it form into a particular shape.  Molecules that contain polar bonds and that can form hydrogen bonds mix well with water  Molecules carrying positive or negative charges dissolve readily in water. These molecules are termed hydrophilic (water loving)  Ex. Sugars, DNA, RNA, and majority of proteins  Hydrophobic (water fearing) molecules are uncharged and form few or no hydrogen bonds and do not dissolve in water  Hydrocarbons are important hydrophobic cell constituents  The H atoms are covalently linked to C atoms by nonpolar bonds.  Because H atoms have almost no net positive charge, they can’t make effective hydrogen bonds to other molecules.  It makes membranes that are constructed mostly of lipid molecules that have long hydrocarbon tails.  Lipids do not dissolve in liquid so it can make membranes that keep the aqueous solution inside  Some Polar Molecules Form Acids and Bases in Water  When a highly polar covalent bond between a hydrogen and another atom dissolve in water. The hydrogen atom that gave up its electron entirely becomes a proton (H+)  When the polar molecule becomes surrounded by water molecules, the proton will be attracted to the partial negative charge on the oxygen atom. Creating a hydronium atom (H30+)  Substances that release protons when they dissolve in water, forming H30+, are acids.  The higher concentration of h30+ the more acidic the solution is.  Strong acids lose their protons easily.  Many acids important in the cell are weak.  Bases accepts a proton when dissolved in water.  Raisins concentration of hydroxyl (OH-) ions by removing a proton from a water molecule.  Weak acids are important in the cell because they contain an amino (NH2) group  The interior of a cell is kept close to a neutral pH by buffers.  Mixtures of weak acids and bases that can adjust proton concentrations by releasing protons or taking them up.  Small Molecules in Cells  A Cell Is Formed from Carbon Compounds  Besides water, almost all the molecules in a cell are based on carbon.  Carbon is great at forming large molecules  It can form four covalent bonds with other atoms  It can form chains and rings  Small and large carbon compounds made by cells are organic molecules.  All other molecules (including water) are said to be inorganic  Certain combinations of atoms such as methyl, hydroxyl, carboxyl, carbonyl, phosphoryl and amino groups occur repeatedly in organic molecules.  Each of these chemical groups have distinct chemical and physical properties that influence the behavior of the molecule in which the group occurs.  Cells Contain Four Major Families of Small Organic Molecules  Organic molecules that roam around the cytosol are used as monomer subunits that construct the cell’s giant polymeric macromolecules.  Ex. Proteins, nucleic acids, and large polysaccharides  Some other molecules serve as energy sources, which are broken down and transformed into other small molecules.  All organic molecules are synthesized (broken down into) the same set of simple compounds.  Four major families of small organic molecules are:  Sugars  Fatty acids  Amino acids  Nucleotides  When these small organic molecules connect into macromolecules they make  Polysaccharides, glycogen, and starch (plants)  Fats and membrane lipids  Proteins  Nucleic acids  Sugars are Both Energy Sources and Subunits of Polysaccharides  Monosaccharides (simplest sugars)  Compounds with the formula (CH O) where n is usually 3, 4, 5, or 6. 2 n  Linked by covalent bonds called glyosidic bonds to form larger carbohydrates  Two monosaccharaides linked together create disaccharide (sucrose) which is composed of a glucose and fructose unit.  Larger sugar polymers range from the oligosaccharides (tri, tetra saccharides) to giant polysaccharides  Sugars and the larger molecules made from them are also called carbohydrates because of that formula.  Glucose has the formula C H 6 12 6  The bonds can be placed in different spots and create different sugars.  Isomers- sets of molecules with the same chemical formula but different structures  Optical isomers- mirror- image pairs of molecules  Sugars are linked together when a bond is formed between an – OH group on one sugar and an – OH group on another by a condensation reaction. When this happens, a molecule of water is expelled.  Proteins and nucleic acids are linked by condensation reactions  When these bonds are broken, a molecule of water is consumed and hydrolysis occurs.  Glucose has a specific role as an energy source for cells. It breaks down into smaller molecules that release energy that the cell can harness to do useful work.  Simple polysaccharides composed of only glucose units are used as long term stores of glucose, held in reserve for energy production (glycogen in animals and starch in plants)  Sugars don’t function just in the production and storage of energy. They are also used to make mechanical supports  Cellulose that forms plant cell walls is a polysaccharide of glucose.  Chiten of insect exoskeletons and fungal cell walls is also a polysaccharide  Also when wet, they are typically slippery. (slime, mucus and gristle)  Smaller oligosaccharides can be covalently linked to proteins to form glycoproteins, or to lipids to form glycolipids.  These are found in the cell membranes.  The sugar side chains attached are thought to help protect the cell surface and often help cells stick to one another.  Fatty Acid Chains are Components of Cell Membranes  A fatty acid molecule has two chemically distinct regions  A long hydrocarbon chain  Hydrophobic and not very reactive  Carboxyl (-COOH) group  Behaves as an acid  In an aqueous solution it is ionized (- - COO ), extremely hydrophilic, and chemically reactive .  Almost all the fatty acid molecules in a cell are covalently linked to other molecules byu there carboxylic acid group.  If molecules possess both hydrophobic and hydrophilic regions they are called amphipathic.  The hydrocarbon tail of palmitic acid is saturated  There are no double bonds and contains the maximum amount of Hydrogens  Oleic acid has an unsaturated tail.  There are one or more double bonds along their length creating a kink in the hydrocarbon tail. This interferes with its ability to stack together  Fatty acid tails can be found in the cell membrane.  They serve as a concentrated food reserve in cells  They can be broken down to produce 6x as much usable energy as glucose.  Stored in the cytoplasm of many cells and form of fat droplets composed of triacylglycerol molecules  Compounds made of three fatty acid chains covalently joined to a glycerol molecule.  Animal fats that are found in meat, butter, cream, corn oil and olive oil.  When a cell needs energy, the fatty acid chains can be released from triacylglycerol’s and broken down into two-carbon units.  They are identical to those derived from the breakdown of glucose  Fatty acids and triacylglycerol’s are examples of lipids.  Lipids are loosely defined as molecules that are insoluble in water but soluble in fat and organic solvents such as benzene.  They typically contain long hydrocarbon chains (fatty acids) or multiple linked aromatic rings (steroids)  Most unique function of fatty acids is in the formation of the lipid bilayer. Which is the basis of all cell membranes  They are largely composed of phospholipids.  Phospholipids are constructed from fatty acids and glycerol.  The glycerol is joined in two fatty acid chains  (rather than three like the triacylglycerol’s)  The –OH group on the glycerol is linked to a hydrophilic phosphate group.  These are strongly amphipathic.  Readily form membranes in water. They form a monolayer with their hydrophobic tails facing the air and their hydrophilic heads in contact with the water. (this forms the lipid bilayer  Amino Acids are the Subunits of Proteins  Amino Acids small organic molecules that all possess a carboxylic acid group and an amino group linked together by a carbon. The amino acid has a side chain attracted to its carbon, this is what distinguishes one amino acid from another.  Amino acids are used to build proteins, polymers of amino acids.  The covalent bond between two adjacent amino acids is called a peptide bond.  The chain of amino acids is also known as a polypeptide.  Polypeptides have a structural polarity (not electrical)  Twenty types of amino acids are commonly found in proteins  These 20 types of amino acids are found in all proteins whether they are from animals, plants, or bacteria.  There are two types of optical isomers, D and L forms. Only L forms are found in proteins.  Five of the 20 amino acids have side chains that can form ions in solution and can carry a charge.  The others are uncharged.  Nucleotides are the Subunits of DNA and RNA  DNA and RNA are built from subunits called nucleotides  Nucleosides are made of a nitrogen-containing ring compound linked to a give carbon sugar.  Nucleotides are nucleosides that contain one or more phosphate groups attached to the sugar.  They come in two forms:  Those containing ribose : ribonucleotides  Those containing deoxyribose :deoxyribonucleotides  There is a strong family resemblance between the different nucleotides bases.  Cytosine, Thymine, Uracil are called pyrimidines because they come from a six-membered pyrimidine ring  Guanine and Adenine are purines they have a five membered ring fused to the six-member ring.  Nucleotides can act as short-term carriers of chemical energy  ATP participates in the transfer of energy in hundreds of metabolic reactions.  ATP is formed through reactions that are driven by the energy released by the breakdown of food.  It has three phosphates that are linked in series by two phosphoanhydride bonds. When these bonds are broken, a large amount of energy is released.  The final phosphate group is often split off by hydrolysis.  Transfer of this phosphate to other molecules releases energy that drives energy-requiring biosynthetic reactions.  Nucleotides also have a fundamental role in the storage and retrieval of biological information.  They are building blocks for the construction of nucleic acids.  Long polymers in which nucleotide subunits are linked by the formation of covalent phosphodiester bonds between the phosphate group attached to the sugar of one nucleotide  Nucleic acid chains are synthesized from energy-rich nucleoside triphosphates by a condensation reaction that releases inorganic pyrophosphate during phosphodiester bond formation.  There are two main types of nucleic acids  RNA  Contain the bases A, G, C and U.  Based on the sugar ribose  Occurs in cells as single-stranded poly nucleotide chain  DNA  Contain the bases A, G, C and T.  Based on the deoxyribose  Double-stranded  Held together by Hydrogen Bonds  The linear sequence of these molecules encodes genetic information.  They have different roles in the cell.  DNA acts as a long-term resporsitory for hereditary information  RNA is more of a carrier of molecular instructions.  Base pairing- the ability of the bases in different nucleic acid molecules to recognize and pair with each other by hydrogen bonding.  G and C  A and T/U  Macromolecules in Cells  Macromolecules are the most abundant of organic molecules in a living cell.  They are the building blocks from which a cell is constructed and are the things that confer the most distinctive properties on living things.  Macromolecules are constructed simply by covalently linking small organic monomers, or subunits, into longs chains, polymers.  Proteins act as enzymes that catalyze the chemical reactions that take place in cells.  Enzyme in plant called ribulose bisphosphate carboxylase, convers CO2 to sugars  Each Macromolecules Contains a Specific Sequence of Subunits  Polymer grows by the addition of a monomer onto one end of the polymer chain from a condensation reaction, where a molecule of water is lost with each subunit added.  Macromolecules are made from a set of monomers that are slightly different from one another  Ex. Proteins are constructed from 20 different amino acids  The polymer chain is not assembled at random from these subunits, they are added in a particular sequence, or order  Biological functions of proteins, nucleic acids, and many polysaccharides are dependent on the particular sequence of subunits in the linear chains.  By varying the sequence of subunits, the cell can make diverse polymeric molecules.  Noncovalent Bonds Specify the Precise Shape of a Macromolecule  Single covalent bonds that link together the subunits in a macromolecule allow rotation of the atoms they join; the polymer chain has great flexibility.  The macromolecule can adopt an almost infinite number of shapes or conformations.  But shapes of most biological macromolecules are highly constrained between different parts of the molecule because of weaker noncovalent bonds.  These weaker bonds ensure the polymer chain adopts one particular conformation, determined by the linear sequence of monomers.  Most protein molecules and many RNA molecules found in cells fold tightly into one highly preferred conformation.  These folded conformations, shaped by evolution, determine the chemistry and activity of these macromolecules and dictate their interactions with other molecules.  Hydrogen bonds are important in determining the unique properties of water and important in the folding of a polypeptide chain and in holding together the two strands of DNA.  A third type of noncovalent interaction is from van der Waals attractions, which are a form of electrical attraction caused by changing electric charges that occur when two atoms are close to each other. They are weaker than hydrogen bonds, but in large numbers they play an important role in attraction between macromolecules with complementary shapes.  Hydrophobic interaction- hold together phospholipid molecules in cell membranes and play a crucial part in the folding of protein molecules into a compact globular shape.  Noncovalent Bonds Allow a Macromolecule to Bind Other Selected Molecules.  Although noncovalent bonds are individually weak, they can add up to create a strong attraction between two molecules when they fit together very closely. This form of molecular interaction provides for great specificity in the binding of a macromolecule to other small and large molecules because of the multitude of contacts required to make a strong bind  Binding of noncovalent bonds make it possible for proteins to function as enzymes. It also can stabilize associations between any macromolecules, as long as their surgaces match closely.  They allow macromolecules to be used as building blocks for the formation of much larger structures. Subunits ----(convalent bonds)-> macromolecules---(noncovalent bonds)-> macromolecular assembly Chapter 3  Energy, Catalysis, and Biosynthesis  Living things create and maintain order in a universe that is tending always toward greater disorder.  Sometimes amino acids, sugars, nucleotides, and lipids are taken apart or modified to supply the many other small molecules that the cell requires.  Sometimes they are used to construct an enormously diverse range of lager molecules, including proteins nucleic acids, and other macromolecules.  To make a lot of chemical reactions, a living organism requires both a source of atoms in the form of food molecules and a source of energy.  The atoms and the energy come out of nonliving environment  Most chemical reactions that cells perform would normally occur only at temperatures that are much higher than those inside a cell  They get a boost from specialized proteins called enzymes, each of which accelerates, catalyzes, just one of the many possible kinds of reactions that a particular molecule might undergo  These enzyme-catalyzed reactions are usually part of a connected series, so that the product of one reaction becomes the starting material for the next. These metabolic pathways that result are in turn linked to one another, forming a complex web of interaction.  Catalyst allow the cell to precisely control its metabolism-the sum total of all the chemical reactions it needs to carry out to survive, grow, and reproduce. This control is the chemistry of life.  Two different streams of chemical reactions occur in cells  Catabolic pathways  Break down foods into smaller molecules, generating a useful form of energy for the cell and some of the small molecules the cell needs as building blocks  Anabolic pathways  Also known as biosynthetic. Use the energy harnessed by catabolism to drive the synthesis of the many molecules in the cell.  Together these sets of reactions make the metabolism of the cell  Biochemistry is the individual reactions that comprise cell metabolism  The Use of Energy by Cells  Nonliving things left to themselves decay.  Livings things are special because they use these nonliving things as energy and then are able to replace and recycle them.  Biological Order is Made Possible by the Release of Heat Energy From Cells  Second Law of Thermodynamics- in the universe or in any isolated system the degree of disorder can only increase, unless there is work or energy involved. Systems will change spontaneously toward those arrangements that have the greatest probability.  The measure of a system’s disorder is called the entropy of the system. So the greater the disorder, the greater the entropy.  Living cells, (by surviving, growing, and forming complex communities and even whole organisms) generate order and appear to defy the second law of thermodynamics. But this isn’t true.  Cells are not an isolated system. They take in energy from their environment (food, inorganic molecules, or photons from the sun) and use that energy to build order within the cell by forming new chemical bonds and building macromolecules.  Some energy is lost in the form of heat to its surroundings. Heat is energy in its most disordered form.  When heat is dispersed to the cell’s surroundings, the heat increases the intensity of the thermal motions of nearby molecules and increase the entropy of the environment.  The amount of heat realized by a cell must be enough that the increased order generated inside the cell is more than compensated for by the increased disorder generated in the environment.  Cells Can Convert Energy from One Form to Another  First Law of Thermodynamics- energy cannot be created nor destroyed, but can be converted from one form to another.  Cells use this to take energy from sunlight into the energy in the chemical bonds of sugars and other small organic molecules during photosynthesis.  When an animal cell breaks down foodstuffs, some of the energy in the chemical bonds (chemical-bond energy) will be converted into the thermal motion of molecules (heat energy). This conversion of chemical energy into heat energy causes the universe to become more disordered.  Photosynthetic Organisms Use Sunlight to Synthesize Organic Molecules  The original energy comes from the sun, which then gets taken in from plants. Animals live on energy stored in the chemical bonds of these organic molecules because they allow them the atoms they need to construct new living matter  Solar energy enters the world through photosynthesis, a process that converts the electromagnetic energy in sunlight into chemical-bond energy in cells.  Photosynthetic organisms use the sunlight’s energy to synthesize small chemical building blocks such as sugars, amino acids, nucleotides and fatty acids. Then those molecules are turned into macromolecules of polysaccharides, proteins, lipids, and nucleic acids.  Photosynthesis takes place in two stages. st  1 stage: energy from sunlight is captured and transiently stored as chemical-bond energy in specialized molecules called activated carriers. All of the oxygen in the air we breathe is generated by the spndtting of water molecules during this first step.  2 stage: the activated carriers are used to help drive a carbon fixation process, where sugars are made from carbon dioxide gas. Photosynthesis generates an essential source of stored chemical-bond energy and other organic materials, for the plant itself and any animal that eats it.  Cells Obtain Energy by the Oxidation of Organic Molecules  All animal and plant cells require chemical energy stored in chemical bonds of organic molecules, either the sugars for food or a mixture of large and small molecules that an animal has eaten.  To use this energy, organisms must extract it from the usable form  Energy is extracted from food molecules by a process of gradual oxidation, controlled burning.  Earth’s atmosphere is 21% oxygen  The most stable form of carbon is CO 2  The most stable form of hydrogen is H O 2  So cells are able to obtain energy from sugars and other molecules the carbon and hydrogen atoms combine with oxygen- thus becoming oxidized- to produce H O2and CO (a 2rocess known as respiration)  Photosynthesis and cellular respiration are complementary processes.  They don’t only go one way.  The oxygen released by photosynthesis is consumed by nearly all organisms for the oxidation breakdown of organic molecules.  The CO m2lecules are incorporated into organic molecules by photosynthesis  Carbon utilization forms a huge cycle that involves the biosphere (all living things on Earth) as a whole, crossing boundaries between individual organisms.  Oxidation and Reduction Involve Electron Transfers  Cells don’t oxidize molecules in one step.  Through enzyme catalysts, metabolism directs the molecules through a bunch of reactions where only a few use oxygen.  Oxidation means the addition of oxygen atoms to a molecule. Oxidation is said to occur in any reaction where electrons are transferred from one atom to another. (more negative)  Reduction involves the addition of electrons to an atom (more positive)  The number of electrons is conserved in a chemical reaction, reduction and oxidation happen at the same time.  These terms apply when there is only a partial shift of electrons between atoms linked by a covalent bond.  When a carbon atom becomes covalently bonded to an atom with a strong electronegativity, it gives up more than its equal share of electrons and forms a polar covalent bond.  The positive charge on the carbon nucleus now exceeds the negative charge of its electrons and becomes partial positive and oxidized.  In carbon-hydrogen bonds, the carbon bond is slightly negative and reduced.  When a cell picks up an electron it also picks up a H+ to neutralize it  These are said to be hydrogenation reactions and are still reductions because an electron is added. Number of C-H bonds increases  The opposite is dehydrogenation reactions that are oxidations. Number of C-H bonds decrease  Cells use enzymes to catalyze the oxidation of organic molecules in small steps, through a sequence of reaction that allows energy to be harvested in useful forms.  Free Energy and Catalysts  Enzymes promote catalyst, the acceleration of the specific chemical reactions needed to sustain life.  Chemical reactions proceed in the Direction that Causes a Loss of Free Energy  Free energy, energy that can be harnessed to do work or drive chemical reactions  Loss of orderliness, downhill reactions are energetically favorable.  Enzymes Reduce the Energy needed to Initiate Spontaneous Reactions  A molecule requires a boost over an energy barrier before it can undergo a chemical reaction that moves it to a lower energy state.  This boost is activation energy  Inside cells, the push over the energy barrier is aided by specialized proteins called enzymes.  Each enzyme binds tightly to one or two molecules, called substrate and holds them in a way that greatly reduces the activation energy needed to facilitate a specific chemical reaction between them.  A substrate that can lower the activation energy is a catalyst  Enzymes are the most effective catalyst  Enzymes are highly selective  The Free-Energy change for a Reaction Determines Whether it Can Occur  Useful energy in system is known as its free energy, or ΔG.  Energetically favorable  ΔG is negative  Enzymes can create biological order by coupling energetically unfavorable reactions with energetically favorable ones.  ΔG Changes as Reaction Proceeds Toward Equilibrium  Whether a reaction will proceed depends not only on the energy stored but also on the concentration of the molecules in each reaction mixture  Chemical reactions occur until they reach equilibrium, ΔG = 0  rate of forward reaction=rate of reverse reaction  The Standard Free-Energy Change, ΔG°, makes it Possible to Compare the Energies of Different Reactions  Standard free energy change  ΔG° RT ln[x]  ΔG = ΔG° + [y] , at 37°C RT = 0.616  The Equilibrium constant is Directly Proportional to ΔG°


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