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PSU / Biology / BI 10400 / which scientist developed the system for classifying organisms? woese

which scientist developed the system for classifying organisms? woese

which scientist developed the system for classifying organisms? woese

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School: Portland State University
Department: Biology
Course: Principles of Biology I - BI 211 - 002
Professor: Mandy cook
Term: Fall 2016
Tags: Biology, Bio, Molecular, PSU, and PSUBio
Cost: 50
Name: Final Notes
Description: This is a compilation of all my notes from this term, I hope you find them helpful. Dr. Cook recently posted this to D2L just in case you didn't catch it: Chapters with ZERO questions: CH26 Chapters with 1 question: CH33 Chapters with 2 questions: CH18 Chapters with 3 questions: CH1, CH2, CH3, CH8, CH19 Chapters with 4 questions: CH4, CH5, CH6, CH11, CH12, CH14, CH16, CH20 Chapters with 5 qu
Uploaded: 12/04/2016
47 Pages 171 Views 0 Unlocks
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COMPLETE STUDY GUIDE EXAM 1 Chapter 1 - Biology and the Tree of Life Biology -​ bio (life) ology (study of). In short, biology is the study of life! Everything living is encompassed in biology, from you and I to crystals, the sky, cells, animals and plants. In this chapter we are narrowing in on how organisms operate at a molecular level and their evolutionary history. 5 characteristics of an organism​: Organism -​ is a living thing made up of one or more cells cell(s) -​ to be considered a cell, it must have a membrane, phospholipid bilayer Replication - the goal of a cell’s life Evolution -​ what made a cell into an organism. Also change in population characteristics over a period of time. (See notes on Darwin) Genes -​ encoded information given to the organism to continue replication Information - genes as well as environmental circumstances that allow the organism to stay alive and continue prospering. This can be information at this time and moment (environmental) as well as past (genes). Energy -​ whatever outside circumstance that’s required to keep the organism alive, such as sunlight or food Robert Hooke - coined the term “cells” Lecture note: He observed a piece of bark under a crude microscope which he made himself at 30X and saw what he coined “cells” which he decided they resembled because it reminded him of monk’s living quarters (also called cells) Because of microscopes we know that cells are separated by a membrane barriers. Smallest organisms - bacteria (200 nanometers) Cell theory - Rudolph Virchow, a German Scientist in 1858 said that cells arise from other cells that already exist. - Cell theory and theory of evolution says: 1. The cell is the fundamental unit in all living things 2. (Darwin) All species are related by common ancestry and because of natural selection have changed over time Louis Pasteur - conducted an experiment to figure out if Virchow’s hypothesis were correct by conducting his experiment of using a straight-necked flask which had nutrient broth. He sterilized the broth (boiled it) and set it out. This caused the broth to grow more cells because bacteria and fungi which were attached to dust particles fell into the flask. He conducted the same study with a swan neck flask and found that nothing grew in the flask because the shapeof the flask caused the broth to continue to be sterile. Any dust would collect at the neck curve of the flask instead of in the tube! Lecture note: She talked about this in class. The book has the same info on page 3 if you would like to see an illustration. Both experiments were conducted in the exact same manner (broth nutrient amount, boil time, time sitting out) the only thing that changed was the flask. Because Virchow’s theory could not be proven wrong, we continue on with the cells-from-other-cells theory… however, see chemical evolution in “Vocab” Cell division​ - because the purpose of a cell is to live, it must replicate and it does so by most of the time by dividing and making an exact copy of themselves Charles Darwin & Alfred Russel Wallace - in 1858 discovered the 2nd greatest founding idea in biology which is that all identifiable types of organisms are connected by ancestry Darwin - wrote On the Origin of Species - Descent with modification - contrasted the idea at that time which was believed that as generations continued, species didn’t change. Spouted the talk of evolution. - Natural selection - 2 conditions make an individual fall into the category circumstance of natural selection: individuals within a population which inherit traits and pass them to their successors & environmental circumstances which those traits help the individual to survive long enough to continue their duty of life: replication. So if a person or animal inherits traits that help them to reproduce, this is natural selection. The adverse is true as well, natural selection would not work in a person or animal’s favor if they did not died before reproducing. Note: Evolutionary change vs. natural selection - evolutionary change happens in populations of people or animals or organisms and natural selection happens in the individual. Therefore natural selection will hopefully favor many individuals within a population and the population will continue its evolutionary change for the better, keeping the species alive and thriving for generations. - Darwin & Wallace introduced the terms fitness & adaptation trait by observing varieties of finches from the different Galapagos Islands. Finches continue changing even today. Because of evolutionary success we see population growth but also populations of species change into other species. - Species come from preexisting species - Species are all related back to a single common ancestor Chromosome theory of inheritance - ​ proposed by Walter Sutton and Theodor Boveri in 1902 says that within cells are genes which have genetic information encoded in them. The Central Dogma​ - DNA is a double stranded helix proposed by James Watson & Francis Crick. Made of 4 pieces which we use letters to symbolize the information: A, T, C, G. Thesequence of these letters in the DNA strand tells us something about that gene. The sequence is the encoded genetic information, and the letters help us to identify what that gene carries by its patterns. There are some rules you should know: - A will always pair with T - C will always pair with G - Strands of double helix are connected by these pieces Central Dogma​ - how information is transmitted. See page 6 of text for DNA/RNA illustration for how DNA is transmitted Sometimes mistakes occur when DNA is copied, this means that the sequence of symbols were messed up and lead to differences in crucial proteins needed for the cell and organism to live. Because proteins control the appearance of an organism, if there is a mishap in the transmission of DNA, the organism may appear or operate differently. - For individuals DNA mis transmissions would lead that increase or decrease fitness - For populations this leads to changes in heritage passed down through generations leading to evolution of a group Two needs for an organism: - ATP (adenosine triphosphate) : action of an organism getting energy using this molecule - Getting molecules that are used for synthesis of DNA, RNA, proteins, cell membranes and complex compounds Note: different organisms go about getting these 2 needs which creates diversity in organisms, such as otters vs. dragon flies etc. the list continues and we see it every day in different life forces. See Tree of Life on page 7 in text! Cook also has this in her slides, it’s a purple and orange chart. To loosely summarize, this tree shows species who are closely related with branches that are connected Tree of life ​- organized chart of all organisms. Sometimes called Universal Tree & Phylogenetic Tree. Continually changing because of the evolution of an organism LUCA ​- tree of life’s main node. Stands for “last universal common ancestor” 3 fundamental groups in Tree of Life: - Bacteria - Archaea - Eukarya Classify Life (Taxonomy) Carolus Linnaeus invented binomial nomenclature, this nomenclature is great because if you are anywhere in the world you can use this binomial nomenclature to identify animals. Global identification! - Genus - names are always capitalized and italicized- species - names are always italicized See Diagram on Taxa (divisions) - animal kingdom - To classify life forms, ask movement? Nucleus? Similarity of molecular sequences? However, this classification continues evolving. - As you go from kingdom to species, the # of animals decreases Vocab: Theory -​ explanation for something such as a phenomenon that has a vast amount of evidence, such as gravity. Lecture note: Gravity is a theory because we cannot prove it wrong. A theory is true until proven WRONG. A theory cannot be proven correct… otherwise it would be fact. Hypotheses​ - testable idea which loosely proves a phenomenon or observations Theory vs. Hypotheses - theory: used by scientist for a broad spectrum, hypotheses: used by scientists for a more specific idea. A theory is used by scientists to zone in on building hypothesis. Chemical Evolution -​ Since Pasteur’s experiment, biologists have found Earth’s early history showed evidence proving that life started from nonlife Species -​ distinct and identifiable organism types Population - ​group of people or species living in the same specified location and time Seciation - ​populations of species which change into other species. Fitness - a species or persons ability to reproduce Adaptation -​ note: the biology definition is different from the english definition. A trait that increases fitness DNA (deoxyribonucleic acid) - h​ eredity material molecule which is what a chromosome consists of RNA (ribonucleic acid) -​ has multiple functions but one of the main functions is for messenger RNA molecules to communicate what the book calls “building blocks”, the A, T, C, G symbols are required to make protein which are important for the cell to live Tree of Life Vocab: Phylogeny - organism relationships to one another. Translates to “tribe-source” Phylogeny tree -​ aka: Tree of Life & Universal Tree shows relationships between different species Eukaryotes -​ Means “true kernel”. Multicellular and have nucleuses Prokaryotes -​ “before kernel”. Bacterial and archaeal cells often times lack a nucleus and are unicellular (one celled) Taxonomy - ​naming system to classify organisms Taxon(taxa plural) -​ named group Domain​ - proposed by Woese which is a category of taxon including the vocab Bacteria, Archaea, and Eukarya. Life is separated into these three domains. phylum(phyla plural) - word used when referencing large lineages of one domain such as “Insecta” which as over a million different types of insectsReview of chapter 1: 3 most important ideas in biology: - Cell theory - everything that is living is made up of cells & cells are the structure of life - Theory of evolution - Common ancestry - Natural selection (over time) - Chromosome theory of inheritance - Genes are in chromosomes - DNA molecules hold vital genetic information and make up genes - Central dogma - movement of DNA to RNA to protein - Energy collection of an organism's changes depending on the organism, making organisms extremely diverse (sunflower vs. human being) Tree of Life: - LOTS of vocab! Review vocab section - All species trace their ancestry back to LUCA - Phylogeny (naming system) determined by examining genetics - 3 domains : Bacteria, Archaea, Eukarya Biology: - To do biology you must first have a hypothesis and experiment using a control. Experimenting many times to narrow down your results until you cannot prove your theory wrong. Chapter 2 Notes (up to what we covered in class): In order to understand Biology, we must know a LITTLE about chemistry, since chemistry is linked to the evolution of life. We will mainly study the water and carbon molecule. Dr. Cook says biology is a “gray science” whereas chemistry and physics take a huge role in giving us hard facts proven with computation. 4 atoms linked to 96.3% of all matter: 1. Hydrogen 2. Carbon 3. Nitrogen 4. Oxygen 92 elements are found naturally on Earth Basic structure of a molecule: - The nucleus​ (center) is made of : - Protons​ - (+) charge - Neutrons​ - neutral (get it?) charge - Electrons​ float around the nucleus forming an electron cloud - (-) charge Periodic Table consists of: - Elements, which have:- Atomic # - which is the # of protons in nucleus (no calculation needed - atoms are in order of proton count!) - Mass number - sum of protons and neutrons in the atom (calculation is needed here) Life is carbon based, because it has a valence of 4. This means that carbon molecules want to bond with other molecules because it would like to fill those 4 valence spots, making it extremely versatile. 2 types of molecules we will focus on in this class (per lecture): - Isotopes​ - chemistry of an atom doesn’t change but the weight changes. When a molecule is an isotope of that element, it means that it has a different # of neutrons. - Covalent​ - molecules that share electrons. Such as 2 Hydrogen atoms (H subscript 2) Hydrogen atoms both have one unpaired electron so they will attract together to fill the empty space by sharing each other’s electrons. - 2 types of covalent bonds: 1. Polar covalent​ - one or more nuclei “electron negative” spends more time at that nucleus, giving the molecule a negative charge 2. Nonpolar covalent - ​ when electrons spend an equal amount of time with both nuclei Compound​ - 2 or more molecules joined together Strength​ - the strength of a molecule will depend on the # of shared electron pairs. These are depicted by rings you see illustrated around the nucleus. Different types are: - Single - Double - Triple (strongest) Neutral atoms​ - same # of protons & electrons Ionic bonds​ - electrons transferred from one atom to another when the atom receiving electrons has space in their valence shells. 2 types: - Cation​ (net (+) charge) - Anion​ (net (-) charge) Electronegativity​ - when shared electrons of different elements form a bond and pull their nuclei at different strengths Slide 20 from chapter 2 information is very important! You will be tested on this material!! To sum this slide up: Electron Sharing Continuum Far Left: - Hydrogen example: As you go from 2 Hydrogen atoms sharing electrons, they are sharing equally, they are nonpolar covalent bonds​ which makes them atoms with no charge (pos/neg). They are neutral and there is an equal sharing of electrons - Another example shown is methane. Middle:- Water example: When a molecule becomes polar covalent,​ meaning they have a partial charge - Additional example of Ammonia Far Right: - Sodium chloride - this is an ionic bond which means atom have full charge. And at this point in the spectrum, there is a transfer of electrons that is happening vs. the far left where atoms had equal sharing of electrons. Chapter two continued, according to what was covered in slides: Table 2.3 is VERY IMPORTANT (slide 23 of chapter 2) We need to know the below information AND R-group 6 Functional Groups & their families: 1. Amino - Amines 2. Carboxyl - Carboxylic acids 3. Carbonyl - Aldehydes & Ketones 4. Hydroxyl - Alcohols 5. Phosphate - Organic phosphates 6. Sulfhydryl - Thiols Important info about moles (the measurement): 23 - 1 mole of a molecule = 6.022 × 10 molecules - Moles = mass ¨ molar mass How to find a mole of something: Molar mass example: H2O = 2 H’s = 2 x 1 = 2 1 O = 1 x 16 = 16  So… Molar mass of water is 18. What if we wanted to find TWO moles of H2O molecule? 18 x 2 = 36 Molarity - concentration of molecules per liter Solutions: - Comprised of solvents and solutes. Solvents being the dissolvers and solutes being the dissolved - Ie: water is the “universal solvent” Wacky Water: (more in lecture notes!!) Cohesion & adhesion characteristics - cohesion (attracted to water), adhesion (any compound that allows water to form hydrogen bonds) Review table 2.2!! P. 65 of notes or 35 of slides Ionizes (pH) Ionization - when ions spontaneously formpH scale - acids(below 7), neutral, bases (above 7) Chemical reactions: Vocab: - Reactants (molecules before reaction) & products (result of reaction) - Types: (these appear after the molecule to indicate their form in the reaction) - Gas (g) - Liquid (l) - Solid (s) - Aqueous solution (aq) - Reactions will always be balanced! - Temperature - can cause a chemical reaction - Concentration - Catalysts (factors that speed up chemical reaction) Spontaneous Chemical Reactions - Products will have lower energy - Ie: think about match example. After you strike a match that potential energy from the red tip is gone. - Products will usually have more entropy (disorder in a system) than reactant Energy - Heat and work Potential energy - stored Kinetic energy - motion activated Thermal - kinetic energy of molecules System - interacting components (molecules) Endothermic (“within heating”)/Endergonic (input of energy) - when a system turn liquid to gas after absorbing enough thermal energy Ie: baking bread Exothermic (“outside heating”)/Exergonic (release of energy) when systems go from vapor to liquid Ie: rust Review slide 53 on chemistry of water! Oxygen most electron negative bond, then nitrogen, carbon Non polar covalent - long, weak bonds Polar covalent bonds - shorter, stronger bonds Biology takes place in water - Ionic bonds dissociate making them weaker in biology - Non polar covalent bonds strong in biology because they stay together in waterOrganic structure Ways to display molecules: 1. molecular formula (shortest way to display just with Letters and subscripts) 2. Structural formula (more information than structural) 3. Ball-and-stick models (3D shows bond angles, color matters) 4. Space-filling models (most accurate, relative sizes, color matters) That’s the basic chemistry we are going to do in this course. Carbon is the basis for all living things Organic means carbon Carbon can form 4 different bonds or 2 double bonds “Functional groups” REVIEW TABLE 2.3 - NEED TO KNOW MAJOR FUNCTIONAL GROUPS AS THEY APPLY TO BIO - Amino NH2 group - Carboxyl - C double bond OOH - Hydroxyl - Make molecules dissolve in water - Phosphate - Important for ATP - Sulfhydryl - Interact with each other, making a stable structural bonds Need its name, recognize formulas 6 functional groups, ID how it should act in a biological system Molecular weight - quantity of molecules using a unit of mole. Mass equal to weight expressed in grams Molarity - concentration, often times we are talking about something that is in liquid form Water is essential, critical for life to exist. When exploring other planets, we look for water to indicate life. Water is wacky: Oxygen is most electronegative, and that puts it above hydrogen. It kind of looks like Micky Mouse’s head upsidedown. Highly polar. They very reaidly form a 3rd type of bond: hydrogen bond. Partial charge from polar covalent bond which is exceptionally weak but in bulk they are strong - Hydrogen bond ex: belly flopping Likes H-bonds Water molecules exclude non polar molecules - Oil & waterHydrophobic- means “water-fearing” molecules non polar molecules shrink when conacting with water Hydrophilic - means “water-loving” molecules polar molecules which want to mix with water and bond with it Water and oil do not make solutions because they don’t mix. Water - “universal solvent” Solution vocab: - Solvent & solute Ionic (and polar) compounds dissolve in water Hydrogen bonding - Cohesion - attracted to water - Adhesion - attracted to unlike compounds Ice lightest form (least dense) of water. Ice floats because of hydrogen bonds Ice insulates water below it so life can form slowly below it Any other liquid would freeze from the bottom up! High specific heat because it takes a lot of energy to heat up and a long time to cool down Regulates life on earth High heat of vaporization (liquid to gas water) Evaporation cools you off and consumes heat REVIEW table 2.2!! Water ionizes (pH) Ionization - dynamic equilibrium pH Scale (log base 10 scale): Acid - below 7 Basic - above 7 Examples of basic/acidic substances and where they fall on the scale: Basic - Lye, household bleach Middle ground/ on basic side - baking soda, seawater, human blood Neutral - water Slightly acidic - milk, urine, black coffee tomatoes, wine Acidic - lemon juice, stomach acid Buffer - acts as a reservoir for hydrogen atoms Carbonic acid - major player in blood Bicarbonate - your body uses this if your blood is too acidic Stanley Miller’s “Ocean Edge” experiment - explaining origins of the building blocks (see below...amino acids) Amino Acids - Building block molecules - Have 4 components: (central carbon bonded to:)1. H atom 2. Amino functional group (as mentioned in chapter 2 notes) 3. Carboxyl functional group 4. R-Group (ionized forms of original molecule) - Combo of amino and carboxy functional group show us how molecules behave - Functional group charges are important a) They help the amino acid stay intact in a solution and therefore be able to come into contact with other solutes creating more bonds (what valence shells on hydrogen atoms always want) b) Chemical reactivity is affected by either a (+) or (-) charge - R-group aka “side chain” - unique aspect of the amino acid - In other words, all amino acids have those core components and this is how you can tell them apart from one another! YOU WILL WANT TO MEMORIZE THESE FOR THE EXAM - Review figure 3.2 p. 80!! - Different types of r-groups/side chains:​ - (charged) Acidic​ (2) - C bearing / (charged) Basic (​ 3) - NH bearing - hydrophilic - (uncharged) Polar​ (5) - Oxygen bearing - hydrophilic - Nonpolar​ (10) - (the rest!) Hydrogen bearing - hydrophobic Other tips on remembering the groups: (YOU DO NOT NEED TO MEMORIZE ALL 20 INDIVIDUALLY) - Negative charge = narrows down to Acidic or Basic. If it has a (-) charge, it’s Acidic. Loses a proton (Vice versa for Positive charge…steps again) - Positive charge = narrows down to Acidic or Basic. We know now that Acidic has a (-) charge, so it has to be Basic. Gains a proton - Uncharged = O present? Then it’s going to be electronegative which is a polar covalent… giving us polar side chain - Not charged, no O? Last resort is nonpolar. Boom. Molecule vocab: Macromolecules - large molecules made up of tons of smaller molecules Monomer (“one part”)- smaller molecules within a macromolecule Polymer (“many parts”) - tons of monomers coming together to make a macromolecule Polymerization - process of monomers coming together as a polymer. Leads to creation of proteins Condensation reactions/ dehydration reactions - new bonds that in turn make the polymer loose a water molecule Hydrolysis - breaks the polymer apart and adds a water moleculeProtein functions: Catalysis​ - catalyze (speed up chemical reactions). When a protein is acting as a catalysis, it is called an enzyme! Most important protein function Defense​ - you have heard the term antibody before. This is a protein that attack and kill viruses when you are sick and/or have a disease Movement ​- when a cell needs to move, it uses motor and contractile proteins to move. This is true when we use our muscles, even. Signaling -​ Carrying and receiving messages between cells in our bodies are a protein’s responsibility. Structure -​ Literally what it means. What we see, like hair and skin, these proteins keep red blood cells flexible and in the correct disk-like shape Transport -​ getting molecules into and out of the cell. Regulation​ - how genes are expressed Spontaneous reactants have more order and potential energy - Favored in experiments (higher energy) Non-spontaneous reactions are the opposite More bonds you have you are adding potential energy Amino acid - always ionic (reacted with water) 5 things - Central carbon - R chain - Amino Use process of info to identifying amino acids: Acidic and basic - hydrophillic Polar side chain - (-) charge hydrophillic Non-polar side chain - no charge, no oxygen, hydrophobic New material: Isomers: - Structural isomer - Easiest to identify - Geometric isomer - Because of the double bond, the molecule is stuck in that specific position - Transbutine - mirrored, but upsidedown - cis - mirrored but molecules in different arrangement with relation to double bond in the center - Optical isomer - Mirrored images Polymer: protein with repeating unit - so an amino acid bound to an amino acid to an amino acid PEPTIDE BOND - how amino acids are linked to create proteins Condensation reaction/dehydration synthesis- Monomers that combine to make polymers - Then macromolecule polymers are created and make water Depolymerization (hydrolysis - hydro (water) lysis (break apart)) - Reverse previous process Proteins will not form spontaneously in a solution of amino acids and water because hydrolysis reactions are energetically favored. Dehydration sythesis: Peptide bond - has a lot of characteristics of a double bond. It gets stuck, linear because of the inflexibility of the bond. Requires energy Polypeptides bonds - Amino terminus (N-terminus) - Carboxyl terminus (C-terminus) - Synthesis (and numbering) proceeds N -> C 20 amino acids all have their own names and can be represented by a 3-letter acronymn Residue - amino acid chain (N-terminus to C-terminus, reading left to right) Peptide bonds - Backbone of protein, inflexible which stabilizes the growing polypeptide Protein structure - primary structure is a specific sequence of amino acids - So reading the residues left to right - If we change the primary structure of a protein it can have devastating impacts - Mutations are silenced in human bodies but is not always the case - Ie: sickled cell. Polypeptide should be: Pro-Glu-Glu but is Pro-Val-Glu Does not carry oxygen well Primary structure- amino acid sequence Secondary structure - motifs of amino acid sequence - (Alpha) helix - (Beta) pleated sheet Tertiary Structure - 99% of proteins final shape - Take 2ndary structure and fold it together hydrophobic on inside and hydrophilic outside - Domains of highly stable sections How proteins fold down is spontaneous reactions - and it’s not fast Chaperonins proteins - helps things go properly (folding) - They are taken in and refolded and if they do not refold for some reason they are DESTROYED Tertiary Protein structures: (final folded shape) - Hydrogen bond - Between polar side chains and peptide backbone or other R-groups - Hydrophobic - occurs within an aqueous solution with a hydrophilic polar side chain (this is intuitive, because aqueous solutions are water solutions and need to attract polar side chains which love water) - van der Waals- The further stabilized hydrophobic side chain electrical attraction phenomenon - Covalent - Disulfide (‘two sulfur“) bonds - Aka bridges - Strong links between polypeptides of the same type OR strong links between 2 completely separated polypeptides - Sulfhydrul groups - Ionic - Completely full and opposing charges so this would be between the acidic and basic groups Quaternary Structure - - When interactions and combinations happen between polypeptides Disulfide bonds/bridges Hair example: ​composed of amino acid residues - Disulfide bridges - Curly - bonds at different levels vs straight same levels Your hair is more fragile when wet! Hydrogen bonds break apart when hair is wet and that’s because instead of the H bonds connecting with the amino acids in your hair, it’s connecting with the water As it dries, they reform H-bonds with amino acids Folding is often regulated but is also spontaneous Disordered - inactive - takes less time to keep disordered, assembled and ready to go so our bodies keep proteins folded Ordered - active Unfolding of proteins Generated by a change in enviornment, such as: - Heat, salt concentration and pH imbalances Chapter 4 DNA Sugar-phosphate backbone Nitrogenous bases connecting to double strands Backbones antiparallel to each other 5’ carbon to 3’ carbon Complementary base pairing Guanine with cytosine ALWAYS PAIR 3 bonds, slightly positive polar covalent bond Adenine and thymine ALWAYS PAIR 2 bonds, slightly weaker than ^ Purine-purine not enough space Pyrimidine- pyrimidine too much Phosphodiester bond - covalentHydrogen bonds 1double strand 2Deoxyribose 3thymine nitrogenous base RNA Nitrogenous bases hanging off backbone Tends to be more reactive/less stable 1Single strand 2Ribose sugar (5 carbon string - extra oxygen) 3uracil nitrogenous base Specific sequences fold into a 3D structure mRNA splicing Acts as a unique enzyme - “ribozyme” Foldling “stem-loop” or hairpin turns ie: tRNA RNA replication - 1. Complementary bases pair 2. Copied strand polymerizes 3. Copy and template separate 4. Copy serves as a template 5. New copy polymerizes 6. New copy is identical to original template DNA replication Semi conservative 1. Strand seperation - hydrogen bonds seperate 2. Base pairing - complementary base pairing nucleotides read and build replacements since G-> C A->T 3. Polymerization - recreate strand with hydrogen bond “RNA World” Hypothesis - Rna can fn as an enzyme - Stores info - Random populations of rna make molecules w/enzymatic activity - First self-replication, ‘living’ system Nucleic acids and proteins Chapter 5 Carbohydrates - Monomer -> polymers - Carbon hydrogen and oxygen 1:2:1- non polar bonds polar covalent bonds - Mono & di saccharides (glucose, lactose) short term storage of energy - Carbonyl group (C=O) aldihid or keytone LOCATION MATTERS - Tri, pen, hex-ose - Hydroxyl groups (-OH) - Glucose - Linear form always the same - When it makes a ring, changes the way we process it - Alpha trans - Beta sis - Fructose - Galactose - Sugar isomers - same formula different spot sis/trans - - Different form dictates different function - Glycosidic linkage - Dehydration synthesis - Maltose & water - Alpha - 1,4 - Beta - 1,4 - Beta galactose and glucose - lactose intolerance - Polysaccharides - long term energy - Energy storage, structure, cell identity - Exoskeleton - Sugar, hydrogen, oxygen - Starch - corn, potato - long term energy storage for starch - Apha 1,6 linkages - Alpha glucose - Glycogen - long term energy storage for animals - Muscles and liver - More Alpha 1,6 linkages than starch - Cellulose - plant structural polymers - Plants - Alternate flipping allows for hydrogen bond - Beta 1, 4 glycosidic linkage - Animals cannot digest cellulose, FIBER - Fungi, bacteria and rumen and termites - Starch and cellulose - our enzymes cant digest it - Chitin - animal structural polymer insect & crustacean exoskeleton - Anti flea medicine interferes with the larvae to create an exoskeleton to become a flea - Peptidoglycan - bacteria to build cell walls - Amino acids involved - Penicillin - inhibit peptidoglycan synthesis take out good bacteria as well- Structural Carb polymers - strands organized into fibers or shees (hydrogen or peptide bonds) - Glycoproteins - protein/carbohydrate combination - cell identity - Example: A, B, O blood groups - O most common - AB - universal recipient - based on presence of glycoprotein - Transmembrane proteins - Oligosaccharide - few sugars - Completely unique per person - Reproduction - PHOTOSYNTHESIS - Plants - Carbon dioxide(polar covalent) and water in sun and make carbohydrates - Residual is oxygen - Energy gets locked into plant as a bond - Much more potential energy - Polar to non polar - Energy stored in glucose to make ATP - Stored in c-H and C-C bonds transferred to ATP - Free energy in ATP (energy currency of the cell) is used to drive endergonic reactions (not spontaneous) and perform cell work ATP makes chemical energy useful to the cell - Burning carbs to make ATP Chapter 6 Lipids (fats) Build cells Phospholipid (biolayer)- phosphate head, amphipathic (part hydrophilic and phobic) Membrane - sheets that define compartments and cells Passages thru membranes - control in/out traffic for compartments and cells LIpid - Loosely defined - Carbon containing - Insoluable in water - Non polar covalent bonds - Isoprene - Hydrocarbon chain - doesnt like water - 14-20 - 3 types: - Steroid - Carbon rings - OH group - hydrophilic- The rest is hydrophobic - Fats (true) - Glycerol linked to 3 fatty acid tails - Ester linkage - Triglyceride - Lack polar end - Phospholipids (amphipathic) - Hydrophilic head - Charged - polar head hydrophilic - Non polar tail - hydrophobicMidterm 3 Notes - Viruses contain DNA & protein ○ Not in lecture: Viruses can also solely contain RNA, but in this case are not considered alive. - Confusing example about Hershey-Chase experiment, I consider referencing Kahn Academy vs. he slides if you want to know how we figured out that DNA is a genetic material. - DNA replication is an exergonic reaction​ that is unzipped and become single helixes, nucleotides are brought in for replication. There are 2 rounds of replicating (per DOUBLE helix- 2 strands) so after replication we get 4 strands of DNA - Nucleotides are assembled by polymerization and are ALWAYS assembled in a 5’ to 3​’ direction - Phosphodiester bonds - release energy - Required for replication: - Free hydroxyl group - DNA template - Primer - Leading​ (aka. continuous) strand​ -5’→3’ >>primer attached to 3’ adds hydroxyl, much easier than lagging strand to replicate - Lagging​ (aka. discontinuous) strand​ - 5’→ 3’ creates antiparallel synthesis away from the original strands, there are areas missing, but once the replication bubble is opened enough to replicate another big enough segment, it will be copied and will not be completely missed - Topoisomerase​ - cuts phosphate-sugar backbone to release tension in the strand as helicase​ is unzipping the strand per kinking that occurs if not Chapter 15 continued Central Dogma: DNA Replication Needed for replication: - Primer - 3’ hydroxyl group - Template DNA runs in an antiparallel direction​ (meaning 5’ → 3’ on one of the two helixes and 3’ ← 5’ on the other that connects to it) Enzymes used in the process of replication: - Topoisomerase:​ enzyme to release the tension in DNA strand while it’s getting unzipped, cuts the backbone of DNA- Helicase:​ unzips the double helix - Primase:​ creates primer - SSBP:​ stabilize the base pairs so the DNA doesn’t come back together - DNA polymerase: ​makes DNA by reading strand & bringing in complementary base pairs (and much more than this… read on.) Lagging strand-​ the opposite side of the “leading” that is being copied 5’ → 3’ which is much harder to copy than leading Replisome- DNA folding - lagging loops around complex End of replication -​ leading has no problem, primase falls off and all is good in the world, lagging has unreplicated end, chromosomes shorten throughout life and therefore slowly by slowly shorten your life. Telomerase:​ comes with it’s own template full of repeated nucleotides, it extends original length of DNA and makes the complementary strand What if there’s a mistake in the matching of base pairs? - Proofreading ​- 3’ ← 5’ exonuclease activity of DNA polymerase (polymerase above) removes MOST mismatches, but not all - Mismatch repair​ - template strand is methylated, new isn’t so new one is fixed - Nucleotide excision repair Causes of DNA damage - Sun, chemicals, etc. - Common mutation​ - thymine dimer when T bonds with another T that causes a kink in DNA and when this happens DNA is cut, nucleotides excised & nucleotides are replaced - Xeroderma Pigmentosum -​ caused by mess ups in multiple genes, they cannot be exposed to sun that will directly damage their cells Chapter 16 Central dogma : dna​(storage) -​(transcription)→​ RNA​ (transfer) -​(translation)→​ protein​(function) - Mutations in DNA - effects everything, sometimes death. - What do genes do? Code for proteins and gene products - One gene, one enzyme polypeptide hypothesis - Genotype determines your phenotype - If first enzyme in a chain of enzyme reactions doesn’t work, the following enzymes will not perform. Codons: - mRNA -​ the messenger, it brings information for every 3 nucleotides, this is called a codon, and each triplet codes for one amino acid with a ribosome as a decoder - This code is nearly universal- 64 possible codons - 20 amino acids used in biology means we have a redundancy - The first 2 letters in the codon are essential, and last letter can be any of the 4 making codons redundant but also unique. - AUG is the start codon, and polymerase cannot start translation until ribose finds it. How we get from amino acids → proteins - Transcription: ​RNA polymerase makes mRNA from DNA, translation: ribosomes make proteins from mRNA - A mutation in DNA → transcription → translation → mutation in protein - A change in genotype can cause a change in phenotype (but isn’t always detrimental) - When a mistake in DNA replication isn’t fixed, the next time the original strand isn’t affected, mutated strand will ALWAYS have a mutation also called a stable mutation Point mutations (4 main mutations) Silent​- NO CHANGE in amino acid (no phenotypic change) Missense​ - CHANGES in amino acid (can be bad, or fine, or benefit the organism to be more fit) Nonsense ​- change to STOP CODON (detrimental, in most cases) Frameshift​ - altered reading frame (off one by one), 1,2, deletions bad, but 3 (think about how many nucleotides are in a codon:3) can sometimes be completely ok Gene duplication Chromosome inversion​(flipped) Review​ - 2 alleles for every gene - So this means that if there is a mutation there is a chance, and a high one, that your body will use the unaffected allele to compensate for the mistake - This happens all the time There are 200 forms of cancer 40% population, karyotype will have many mutation making it obvious to spot in a human body Many RNAs that never need to become/become into proteins Chapter 17 Transcription : 1st step to gene expression Only 1 of 2 DNA strands is transcribed by RNA polymerase - The other is “non-template” or “coding strand” - RNA polymerase adds ribonucleotides (rNTPs) to 3’ end of RNA chain Bottom strand is template and top strand is coding strand RNA polymerase​ - core enzyme is catalysis of RNA synthesis - Sigma​ - initiate transcription process by connecting to strand, DNA recognition RNA polymerase​ - opens helix for transcription, moves upstream to downstreamPromoter region​ - upstream of strand Elongation​ - bubble continues down strand Termination​ - that hairpin turn that we talked about way back when, RNA hairpin turns on itself to terminate at the end of transcription Repressors​ - binding proteins that blocks the attachment of RNA polymerase to the promoter, which prevents transcription​ to mRNA Activators: THESE ARE THE MAIN PRODUCTS OF TRANSCRIPTION! - rRNA​ - central component of the ribosome, helps mRNA bind to the right spot, sometimes acts as an enzyme which then is called ribozymes - tRNA​ - acts as carriers in synthesis of proteins, they bring amino acid to ribosome as specified by mRNA one strand of RNA to make total of 2 - mRNA ​- between protein coding gene and protein product (of the diagram in red/blue/purple above), it’s a copy of the dna (with ‘U’s in place of ‘T’ in nucleotides)or transcript. Its next step once created is to associate with a ribosome (which creates aor assemble proteins of nucleic acids) and makes a codon and a particular amino acid for each one Bacteria -​ 4 subunits Eukaryote and archaea ​- 10 subunits Eukaryotic transcription Interruptions​ - exons - expressed segments, introns - non-coding interruption/intervening segments - mRNA transcripts both exon/introns - Spliceosome excise introns and joins exons into mature RNA - This splicing creates diversity (variable splicing) - All RNA based - Snurps ​-small nuclear ribonucleoproteins (snRNP) - “Post - transcriptional Mods”​ - poly(A) tail protects from RNAse degradation Transcription : Bacteria vs. Eukaryotes  Bacteria  Eukaryotes - 1 rNA polymerase - promoter : -10 & -35 - Sigma for initiation - NO rna processing - 3 RNA polymerases - TATA box (sometimes) - TBP + other factors - 5’ cap, splicing, poly(A)


- Where do the exons go?




What if there’s a mistake in the matching of base pairs?




What if we wanted to find TWO moles of H2O molecule?



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TranslationmRNA → amino acid sequence Ribosome binds to mRNA​ - in E interacts w/CAP, B-complementary base pairing between mRNA and rRNA Bacteria - TRANSLATION AND TRANSCRIPTION are coupled together Adapter molecule hypothesis tRNA always ends in CCA at 3’ end Aminoacyl tRNA​ synthetase - enzyme that attaches appropriate amino acid to tRNA Chapter 17 cont’d Translation Somewhat of review stuffs: (Eukaryotes) - Know use of TATA box! - mRNA transcript is the primary transcript - Snurps​ are what make up the spliceosome​ which cuts​ through and takes out intros​ and skips over exons so that the exons will be “expressed”​ in the polypeptide. - 5’ CAP, poly(A) tail in mature mRNA - this is for stability At this point, it goes to a ribosome which binds to mRNA and active sites are properly aligned. 2 different splice products of Tropomyosin (her jumpyness not mine) - Skeletal muscle​ (aka. striated) #1-13 - Smooth muscle​ (involuntary - heart, organs) #1-10, 13, 14 Ribosome​ is made primarily out of rRNA, but also protein and tRNA - The active site​ isn't a protein, it IS RNA Know these 3 sites!! (of the ribosome): - A:​ site “acceptor site” ​- hold aminoacyl tRNA - P:​ site “peptide bond”​ - holds tRNA w/growing polypeptide - E:​ site “exit site”​ not bound START/STOP signals​ (in translation) - “Shine-dalgarno” site ribosome binding code - Start signal coded by AUG - KNOW THIS - Stop signal coded by one of 3 nonsense codons - UAA, UAG, UGA Translation initiation mRNA codon adjacent to the initiating codon is positioned w/another amino acid bearing tRNA molecule Translocation Ribosome moves down mRNA one codon at a time Termination Nonsense codons are recognized by release factors that release the newly made peptide from the ribosome - ribosome, protein & mRNA dissociateChapter 18 Bacteria E.coli are an excellent source of gene expression (as we saw in lab) Post translational control - changing final shape, which is a rapid response, and efficient Transcriptional control - slowest response, but most efficient Translational control - in between post and transc. In speed and efficiency Lactose - made of glucose and galactose - So E. coli cannot matabolize lactose! - She goes onto a E.Jacob & J. Monod example and totally butchers it, search on Khan Academy or Crash Course if you want a more exciting explination Classes of Mutants: (with regard to lactose) Side note:​ Khan has an amazing video on this. Go to their bio section and look up lac operons. - lacZ: no beta galactosidase - lacY: lactose won’t and can’t make it into the cell - lacI​: beta galactosidase is constantly made, Induction​ is unnecessary - If lacI has a mutation, it’s ALWAYS on, transcribing away - They are in this order in the cell, but were discovered at different times. “Negative control”: Transcription blocking by use of a protein repressor, when the repressor is turned on per lactase present, it will fail to bind to the DNA. “Positive control”: A protein known as an activator binds to the dNA, changing it’s shape in order for the transcription to take place. - Think of TATA box (in Eukaryotes) Operon​- a suite of genes, 1 promoter per operon AND almost never found in Eukaryotes, safe to think of this as a bacteria thing. So when you are thinking of the lac operon, think of E. coli, think of bacteria. Chapter 19 Gene expression in Eukaryotes Gene expression changes: - By responding to environment - Depending on age - cell/tissue type - Are important!4 steps for gene expression - Step 1: Chromatin Remodeling - A signal is received that turns on a gene or set of them; “remodeling complex” - regulatory factors induced - Methylation of DNA - Acetylate proteins - Histone deacetylases (HDAC) Step 2: Expose DNA - DNA is exposed by being stretched out - Core promoter (aka promoter on Khan or Crash Course) - closest to the gene sequence, is highly conserved, has a sequence COMMON to most genes - Start site +1 of gene sequence - Promoter proximal element - have a unique sequence per THAT gene - regulatory transcription factors - major/minor grooves in DNA - chemical interactions! Step 3: Assembly RNA Polymerase II - Activators bind to the enhancer, mediator binds to enhancers - Recrute basal transcription operators - Used and required for initiation (general transcription factor) - TBP (TATA binding proteins) - DNA loops Step 4: Transcription - Gtfs & RNA Polymerase II assemble at the Mediator - RNA polymerase II binds to core promoter and the gene is transcribed RNA interference (RNAi) control of mRNA stability - miRNA microRNA - RISC- RNA induced silencing complex or the “kiss of death” which is potentially useful in gene therapy Post translational Control in Eukaryotes - Where do the exons go? Well those exons are put together in multiple ways creating combo and alternative splicing - RNA will be broken down if it needs to be by RNAi- mRNA can be stored - Depending on what the cell needs, ribosome mods can happen, like phosphorylation which slow/speed up translation - Protein “activation ” - lots of proteins are inactive until phosphate group attaches to it, and this happens AFTER translation making it a post transl. Mod. - Folding - Degradiation yb proteasomes Mutagens: ​carcinogens - Smokers - causes DNA mutation, UV light, radiation exposure - Can affect expression of proto-oncogenes or tumor suppressors which causes proliferation or uncontrolled cell cycle progression Tumor-​ a local expansion of growth Metastasis​ - cancer cells leave the tumor Proto​ - oncogenes - cell division “on”/gas pedal Tumor suppressors​ - cell division “off”/gas break p53​ - tumor suppressor prevents cell division in 50% of cancer and if the gene is mutated, cancer can take over :( - Blocks G1 checkpoints in mitosis Cancer remission​ - a point in time where cancer is responding to treatment with no new cancer cell growth Complete remission​ - all signs of cancer are gone Partial remission​ - cancer is shrunk but still present Chapter 20 Biotechnology Genomics​ - genetic engineering Indirectly ​- has been done for centuries, think of mendell or dog breeding Directly​ - by altering genetic material with specific modifications Vectors​- DNA vehicles for genetic engineering - Plasmids​ - less than 10,000 base pairs, circular, bacteria and easily maintained - Viruses​ - easy to add new DNA since some only have RNA - CUT/PASTE method -Uses restriction enzyme which cuts the DNA EcoR1 palindrome Stages of Cloning experiment​: - Isolation​ - gets DNA alone - Cleavage​ - restriction endonuclease cleaves to the source of DNA into pieces - Production of Recombinant DNA​ - these are pieces of DNA put into vectors or plasmids - Cloning​ - recombinant is propagated - Screening​ - clones that have the vector are identifiedPituitary dwarfism - deficiency of growth hormone (GH1) - Clone gene of interest into “Expression vector” which is an engineered bacterial plasmid Steps of PCR: 1. Denaturation​ - mixture is created and is at 94 degrees celsius the DNA splits apart 2. Annealing​ (around 50 degrees) because the DNA is cooler, the primers anneal to the template 3. Extension​ (around 72 degrees) DNA polymerase uses dNTPs to synthesize the complementary DNA strand, beginning at the primerMT 2 Review Chapter 6:​ NOT SURE if the entire chapter 6 will be on the exam, however, I wanted it included juuuust in case. Lipids - 3 kinds (fats, steroids, phospholipids) - not very soluble in water - Major component in membranes - Hydrophobic or Amphipathic - some of it is hydrophobic and some of it is hydrophilic - Beeswax is a lipid - 6 carbon rings with a 5 carbon ring - think steroid - Cholesterol is a steroid and is essential for life! - store energy, provide insulation, make up cell membranes, form water-repellent layers on leaves, and provide building blocks for hormones like testosterone Fats​ (are one type of lipid molecule) - molecule consists a glycerol backbone and three fatty acid tails and lack a polar end which makes them insoluble in water. - 2 types of fats - Triglyceride (three fatty acids attached) - Glycerol is a small organic molecule with three hydroxyl (OH) groups vs. fatty acid consists of a long hydrocarbon chain attached to a carboxyl group - hydroxyl groups on the glycerol backbone react with the carboxyl groups of fatty acids in a dehydration synthesis reaction - three fatty acid tails bound to the glycerol backbone via ester linkages (linkages containing an oxygen atom next to a carbonyl, or C=O, group - Yield more energy per gram than carbs (think of candy vs. bread) First type (of fat)​: - Saturated fatty acids​ (also lipids)- think single bonds between neighboring carbons in the hydrocarbon chain - Straight configuration chain - Solid at room temp Second type (of fat): - Unsaturated fatty acids​ (also lipids) - when there’s at least one double bond in the hydrocarbon chain (monounsaturated) but can have more than one double bond (polyunsaturated) - cis configuration - two hydrogens associated with the bond are on the same side - Generates a kink in the fatty acid molecule - Oils - low melting point- ​trans configuration - two hydrogens associated with the bond are on opposite sides - When two amino acids combine, the carboxyl group of one amino acid reacts with the amino group of the other amino acid to form a peptide bond. - The R group is a side chain (group of atoms) specific to each amino acid. The identity and chemical properties of an amino acid are determined by its R group. Most large biological molecules are polymers, long chains made up of repeating molecular subunits, or building blocks, called monomers - If you think of a monomer as being like a bead, then you can think of a polymer as being like a necklace, a series of beads strung together. - lipids are one of the four main types of large biological molecules, but that they don’t generally form polymers Waxes - Cover bird’s wings - that’s how they don’t get wet in the rain! - Contain long fatty acid chains connected by alcohol and ester linkages Phospholipids​ -amphipathic - Similar to fats, they have usually 2 fatty acid tails, instead of 3 tails which are connected to a glycerol backbone, with the third carbon connected to a phosphate group. - Polar head - Nonpolar tails Osmosis-net movement of h2o across membrane Diffusion ​of moving water from high -> low concentration - This continues until what we call dynamic equilibrium is obtained - Water and solute in diffusion of high to low aka down a concentration gradient - Solutes will generally not be lipid-soluble - Water passes thru the phospholipid bilayer - Random net movement from high to low - Dynamic equilibrium - Water membranes are selectively permeable - Water moves towards lower concentration from higher concentration of solution Aquaporins​ - the protein that allows water through membrane, but stops unwanted molecules from entering and most ions. - Can be found in all domains of life Osmotic Concentration - ​the total concentration of solutes in solution Hydrostatic pressure - ​pressure that is exerted by a fluid at equilibrium at a given point within the fluid, due to the force of gravityOsmotic pressure ​- driving osmosis of water AT LEAST ONE QUESTION ON EXAM 2: One cell is placed in solution of… In isotonic​ (water moving in and out of cell at equal rates) - both solutions have same osmotic concentration Hypertonic​ (shriveled looking) solution - high concentration of solutes Hypotonic​ solution (big and swollen) - low concentration of solutes Clicker question: (not verbatim) Net movement of sugar molecules from 0.5 molar sugar to 0.4 molar sugar Why? Ions can move - everything can move! High to low, concentration, and because of this factor it is the correct answer. C is wrong because it’s going from a high concentration of water to a low concentration of salt… why is she so fucking tricky??? Fluid Mosaic Model - cell membrane - “Floating” of proteins in a fluid lipid bilayer - Represents an actual mosaic. Seeing just one phospholipid doesn’t tell you anything but when you see the entire you can tell what the molecule is doing - TRANSMEMBRANE PROTEIN - Transmembrane proteins aka.peripheral membrane protein - allow certain molecules through the phospholipid bilayer into the cell. They are often in the shape of alpha helices. - Hydrocarbon tails nonpolar covalent bonds - Hydrophobic tails - Hydrophilic heads on either ends - Are usually alpha helices - Glycolipid - Extracellular fluid carbs - Glycoproteins - Peripheral protein - Filaments - Cytoplasm - Proteins can move laterally across the bilayer, or across the mosaic Transport in general:Facilitated diffusion - polar molecule transport via own type of channel through the plasma membrane and ions move in ion channels through… charged ions move according to their charge. If charge is positive, it moves high to low areas of positive charge. Note: ​Membranes are selectively permeable, polar molecules that transport across plasma membrane has it’s own specific type of channel; ions can also move across the membrane in their own channel, called an ion channel. PASSIVE TRANSPORT PROTEINS Down electrochemical gradients - # of channels help the movement go quicker, requires no energy GATED CHANNELS (passive, selective channels) Open and close at gates ex) POTASSIUM CHANNEL (K+) When (-) charged relative to outside channel is closed, however if membrane is (+) it will be allowed in the cell! No ATP used TRANSPORT (aka. CARRIER) PROTEINS Change shape by changing bonds to assist in diffusion of SPECIFIC MOLECULES No ATP used Concentration gradient determines the movement of this protein. Steps for GLUT-1 or Glucose diffusion: 1. Unbound protein 2. Glucose binding 3. Conformational change 4. Release FACILITATED DIFFUSION 3 main take-aways…. Specific- Each is unique Passive - movement (high to low) Saturates - concentration of diffusing molecule increases and will increase the rate of diffusion until channels are all saturated. Active Transport:When substances move against their concentration gradients. This REQUIRES ENERGY. Remember: Active = use of ADT ie) Sodium-potassium pump 1) Unbound protein 2) Sodium binding (to Na+) 3) Shape change 4) Release Na+ outside of cell 5) Unbound protein 6) Potassium binding (to K+) 7) Shape change 8) Release K+ into cell - This creates a chemical and electrical gradient across the membrane Side Notes/Review: Cells made of phospholipid bilayers. These are made of a hydrophilic/phobic areas depending on where you are in the bilayer. In a solution the bilayer becomes selectively permeable. Bilayers are EASIER TO permeate when it is filled with SHORT, and UNSATURATED hydrocarbon tails vs. a bilayer with long, saturated hydrocarbon tails are harder to permeate. Not covered in class: - Omega fatty acids - 3 & 6 - Human body needs these, but we don’t produce them ourselves. - Aka - essential fatty acids - Found in : chia seeds, flax seeds, salmon - Lower blood pressure, prevent heart attacks and blood clots Dehydration synthesis reactions​- in which one monomer forms a covalent bond to another monomer releasing a water molecule in the process. Dehydration (losing water) synthesis (bringing together 2 things) makes 2 monosaccharides into disaccharide, or many monosaccharides into polysaccharides. Hydrolysis reactions​ - Polymers are broken down into monomers in a hydrolysis reactions, in which a bond is broken, or lysed, by addition of a water molecule. A molecule composed of multiple subunits splits in 2: one of the new molecules gains a hydrogen atom, while the other gains a hydroxyl (-OH) group, both of which are donated by water. Water molecule splits maltose to release two glucose monomers. This reaction is the reverse of the dehydration synthesis reaction.Carbohydrates, proteins, and nucleic acids go through dehydration synthesis to be built up and experience hydrolysis to be broken down. Glucose​ - aka dextrose, aka blood sugar - means sweet in Greek! - how energy is stored and transported in your body. - Photosynthesis uses glucose. - Cellular respiration uses it to make ATP. - Chains become glycogen. - Building block for more complex sugars and carbohydrates. - isomers, make different forms of glucose, it changes the look of the molecule (or  In other words, it’s arrangment - Sugars form in straight lines, or in rings! - β glycosidic linkages in cellulose can't be broken by human digestive enzymes, so humans are not able to digest cellulose - Enzymes - end with -ase: - DNA - four types of nucleotide monomers - Monosaccharide (aka monomer) polysaccharide (aka polymer) - Starch - in plants (polysaccharide) - Glycogen - in humans (polysaccharide) - Twenty types of amino acid monomers commonly found in the proteins of your body - Starch, glycogen, and cellulose are all carbohydrates made up of glucose monomers, but they have different bonding and branching patterns. Carbohydrates​ are biological molecules made of carbon, hydrogen, and oxygen, 1:2:1 ratio If the sugar has an aldehyde group​, meaning that the carbonyl C is the last one in the chain, it is known as an aldose​. If the carbonyl C is internal to the chain, so that there are other carbons on both sides of it, it forms a ketone group​ and the sugar is called a ketose​. Phospholipid bilayer - Cell membrane - Low permeability - Made of a “mosaic” transmembrane proteins, network of supporting fibers, exterior proteins and glycolipids Chapter 7All cells share four key components: The plasma membrane​ is an outer covering that separates the interior. Cytoplasm​ is has cytosol​ inside the cell, and cellular organelles in it. DNA​ is the genetic coding of the cell. Ribosomes​ are organic molecular machines that synthesize proteins. Procaryotic cells: - Have a rigid cell wall called peptidoglycan - Have a capsule that helps it stick to it’s environment - flagella are whip-like structures that act as rotary motors to help bacteria move - Single circular chromosome Eukaryotic cells Organelles- ​the compartments that allow biochemical processes which are often times happening simultaneously Lysosomes​ - act as recycling centers which maintain an acidic pH, break down old unnecessary structures to be reused - Plants cells do not have lysosomes but instead, they have vacuole,​ another type of organelle which is much like a lysosome Peroxisomes​ - carry out chemical reactions called oxidation reactions and produce hydrogen peroxide Nucleus​ - dna, nuclear envelope which has 2 phospholipid bilayer membranes. Those are linked to the endoplasmic reticulum Mitochondria​ - break down fuel molecules and capturing energy during cellular respiration Cytosol​ - fluid between the organelles within the cell Cytoplasm​ - everything within the cell Paranuclear, inner and outer membrane​ - of nucleus - just like it sounds Ribosomes-​ make proteins from mRNA - structure : rRNA connected to several different proteins assembled at the nucleolus within the nucleus - Translation in the cytoplasm (in the cytosol) and associates with ER - Subunits assembled at nucleolus and then exported out of the nucleus through nuclear pores Peroxisomes - ​a container for oxidation reactions and catalyze specialized reactions Endoplasmic reticulum​ - its internal membrane of phospholipid bilayer and proteins and makes channels w/in the cell, 2 types. Rough endoplasmic reticulum​ - in protein synthesis - rough because of ribosomes on the outside of it. mRNA find ribosomes and as they are translated, they are translated inside of the rough ER. Make phospholipids for cell membranes. These are transported when vesicles are formed, in short, they synthesize proteins to be secreted. Vesicles​ - used for transport to Golgi apparatusSmooth endoplasmic reticulum​- no ribosomes - functions include synthesis of carbohydrates/lipids/steroid hormones, detox of medications and poisons, stores calcium ions. Found in muscle tissue! Used for fatty acid and phospholipid synthesis Golgi Apparatus​ - tags, modifies and routes proteins, it packages proteins cis face receives packages, cells involved with secretion such as ones found in your mouth for saliva have lots of golgi bodies Chloroplasts​ are only found in plants and algae Signal hypothesis: 1. ER signal sequence synthesizes in the cytosol. This oncoming organelle is a signal cell 2. The signal sequence binds to a SRP (signal recognition particle) 3. The SRP binds to the receptor found on the membrane of the rough ER 4. From the signalling cell, the protein enters into the ER through the translocon 5. Protein is then released into the cell, and the ER signal sequence breaks off of the Lumen of the rough ER Endocytosis​ - engulfing of something - phagocytosis ​- when a foreign body is taken into the cell - Receptor mediated endocytosis - when macromolecules initiate the engulfing of the foreign body - Pinocytosis​ - when extracellular liquid enters the cell Cytoskeleton​ - continues shrinking, and growing throughout the life of the cell. - Actin filaments​ - these are actin monomers, which create cell movement and transport of organelles - Ie: actin and myosin in muscle tissue move muscles! - Microtubules​ - these are tubulin​ monomers, which transport organelles​ as well they are also responsible for cilia and flagella movement - Separate chromosomes in cell division but started off as centrosomes - Intermediate filaments​ - which are keratin and the nuclear lamin which play structure roles for the cell and its compartments - Transport: - Short distances - golgi - Long - vesicle, motor molecules, microtubule Chapter 8 Chemical reactions Gibbs free energy​ - a thermodynamic quantity equal to the enthalpy minus the product of the entropy and the absolute temperature Exergonic​ - releases energy and that energy gets pushed into an endergonic reaction which needs that energy. This requires the exchange of electrons between reactions.Oxidation- reduction​ - also electron transfer during chemical bond transfers of potential energy Oxidation ​- losses an electron and energy Reduction​ - gains an electron and energy Redox reaction​ - electrons transferred from one atom to another Redox reaction steps: 1. Enzymes harvest H have a binding site for NAD+ near the substrate binding site 2. Oxidation-reduction reaction H transferred to NAD+ forming NADH (notice added H and loss of + charge) 3. NADH diffuses and is ready for use by other molecules Note: accompanied by a proton usually ATP: energy center (potential) - Consists of 3 phosphate groups and 4 neg charges - Energy released when hydrolyzed - This is highly exergonic - ATP drives endergonic reactions and activity within the cell - enzymes have 2 binding sites - reactants and ATP - Protein fns: enzyme catalysis, cell receptors and signals, transport, motion and gene expression regulation Enzymes - Catalyze one reaction typically - Bring substrates together - Change shape Affectors of Enzymes​: - Temperature and pH affect enzyme activity - Cofactors: function of the enzyme is assisted by additional chemical components - Coenzyme: a cofactor that is not a protein but that is organic - Prosthetic Group: this group is permanently attached to the enzyme Enzyme control: - Non-covalent modification - inhibitors/activators bind to the enzyme reversibly and affect reactions, 2 types: - Competitive inhibition - binds to active site and disallows substrate binding to occur - Higher concentration of reactants can prevent inhibition - Allosteric inhibition - binds far from the active site and changes shape of enzyme to also disallow substrate binding - Because the shape has changed, no number of reactants can prevent inhibition- Covalent modification - change to structure - Irreversible, such as peptide bond broke - Reversible, such as phosphate group bonds to enzyme Typical Enzyme Action Steps: 1. Initiation - substrates find an enzyme to bind to at the activation site, this forms an enzyme-substrate complex 2. Translation state facilitation - the enzyme and substrates are interacting and the enzyme lowers activation energy 3. Termination - products are released and are released, the enzyme also loses it’s charge after the enzyme action Competitive inhibition​ - takes place on an enzyme, which it’s active site gets blocked by some other substrate. In a chemical reaction it facilitates it by lowering the activation energy ie) caffeine, cocaine, antidepressants Allosteric inhibition​: inhibitor binds distant from the active site, changes the enzyme shape to prevent substrate binding Endothermic (inside heat) /endergonic (input of energy) Exothermic (outside heat)/ Feedback Inhibition - ​3 chemical reactions that turn an enzyme substrate into an intermediate that binds to another enzyme then the same process happens again until there’s a product which is the feedback inhibition process. Quality control​ - one enzyme, one catalyst. If there’s a problem, you can stop it. Ability to capture & harness energy Chapter 9 Cellular Respiration & Fermentation 3 major components of cell respiration & then fermentation Glycolysis - (SUGAR, TO BREAK APART) Use sun to convert CO2 and H2O into sugar. Know what goes in and what goes out and where it takes place. Metabolism Electrons give up energy as bonds break and fall. It’s harnessed by something, and if it isn’t they are called “free radicals”. NADH is energized ​but only stores energy short term. Is much like a battery. Is oxidized in order to use that energyTerminal Electron Acceptors Aerobic Respiration Fermentation​ - ie) lactic acid in muscles Aerobic Respiration - 4 steps 1. Glycolysis - breaking of sugar - substrate - level phosphorylation. Adds phosphate. - For every 1 molecule of glucose we get 2 ATP molecules out of it. - Glucose has more energy than ATP. - Everything that’s alive can go through glycolysis. - 2 main steps (book has 10) - Priming (2 ATP) - Consumes ATP - Is not always necessary - Phosphofructokinase = you need to know this. - Substrate-Level Phosphorylation - Oxidation makes ATP 2. Pyruvate processing - Making energy storing molecule - Gets rid of a carbon, makes NADH (used in electron transport chain), - Inside of mitochondria - Each pyruvate makes one 3. Krebs cycle aka citric acid cycle - Tap into NADH and ATP (energized electrons) - Generates 2 ATP - Starts as a 4 carbon molecule and after the cycle it also has a 4 carbons - PRODUCTS: 1 ATP, 2 Co2 waste product, 3 NADH, 1 FADH2 - All the steps are to regulate the process (by ATP or NADH) 4. Electron transport and oxidative phosphorylation - Takeaway: high free energy (48 kilocalories/mole) to low potential energy - 29 ATP/glucose Fermentation - happens if no oxygen is available! - After glycolysis, if there’s no oxygen, fermentation happens and makes much less ATP - 2 ATP per sugar molecules - Much less efficient way to make ATPChapter 10 Photosynthesis​ - 40-50 chloroplast per inner membrane 1) Capture a photon of light 2) chemical energy in the form of ATP 3) CO2 reduction Pigments are there… for why? Chlorophyll​ - to absorb light, from red to blue, then they transmit or reflect GREEN. Green is transmitted because they don’t use that wavelength of light Carotenoids ​- absorb blue and green and then transmit yellow orange, red. Think of carrots. These are not absorbed by chlorophyll, and carotenoids stabilize free radicals Accessory pigment​ - protect plant, act as a sunscreen, stabilize free radical Chloroplasts ​are in the mesophyll - ​chloroplasts have stroma(free fluid) ​with thylakoids ​that are arranged in stacks called grana. Stomata​: a closeable pore that allows permit of CO2 entry. Need to close their pores (stomata) so they don’t lose water or oxygen C4 plants - capture carbon dioxide in mesophyll cells, this become “bundle sheath” cells. - corn is a good C4 example CAM plants​ - cacti open stomata during the night (run calvin cycle during that time) when it’s less hot. During this time, they take in CO2 - still a C4 cycle and store the 4 carbon compound and wait for the sun Why are plants green? Atoms and electron state and chlorophyll molecule itself, when sunlight is hitting the plant, and get excited (electrons) they get bumped to a higher energy state. Pigments cluster and become complexes. Photosystem (Two acts first and then One acts second)​ : 2 components: Antenna complex -​ chlorophyll (carotenoid) held together by membrane/protein matrix, these chlorophyll pigments capture photon light energy from the sun Reaction center - ​where molecules get excited and transfer energy. Loose electrons Photosystem Two - acts much like mitochondria - Light reactions: 4 stages 1) Primary photoevent 2) Charge separation - passing energy to “reaction center” 3) Electron transport - generate electron gradient4) Chemiosmosis - like in mitochondrial - proton gradient - Pheophytin​ - like chlorophyll in structure but instead of being a pigment it acts as an electron acceptor - Oxygen is a byproduct - Thylakoid Lumen is acidified - Proton gradient powers ATP synthase - This powers the electron transport chain (gradient) 2nd stage of photosynthesis Calvin Cycle: - 3 phases: - Fixation​: RUBISCO attaches to CO2 to RuBP - this is called carbon fixation - Reduction​: 3-PGA molecules phosphorylated requiring ATP and reducing power by NADPH to produce G3P - G3P is used in plates to create carbs - Regeneration​ - G3P used to recreate RuBP which starts the cycle again. After every 3 turns, you get 1 G3P, 5 other G3P goes back into the cycle Photosynthesis vs. cellular respiration: They are almost complete opposites. We’d love for it to be as easy as saying that photosynthesis is cellular respiration in reverse, but it unfortunate;y is not that easy Chapter 11 Cell surface - Protection - Adhesion - Identity - Communication Plants: Cell wall: - Cellulose - this is a fiber composite and also pectin - Turgor pressure is maintained without the cell approaching a point of potential to burst - Middle lamella (pectin) are what make cell-to-cell connections Animals​ : - have no cell wall - they have an extracellular matrix (shortened to ECM) - Collagen - (instead) which is not easily regenerated - Directly linked to cytoskeleton thru:- Fibronectins - Integrins - Disconnections happen (from cytoskeleton) for movement - Cell-cell connections: (3 kinds) - Water-tight seal via tight junctions - much like a quilted comforter - Desmosome - Cadherin - anchor thru intermediate filament interaction, are important in tissue cell-cell interactions Intercellular adhesion and junctions - Communicating junctions - passages, signals (one cell -> another cell) - Animals have gap junctions/protein pores - found in your heart - Plants have plasmodesmata which have membranes which allow water, ions, and proteins through them and have no protein pores. - Allows for networking Cell signaling Signal Molecule: 1. Receives a signal outside of the the cell wall OR inside of the cell. 2. Processes signal INSIDE the cell, and will be interpreted through a second messenger molecule 3. Something about the cell is then changed 4. SIGNAL DEACTIVATES - Examples of signal cells: nitric oxide, ethylene, insulin, estrogen Receptor proteins - These are transmembrane proteins - Very specific, and have a very specific signal molecule that will cue it - blockable Cell surface receptors - Initiates diffusible signal (GTP-binding protein, or G-protein)within the cytoplasm - Largest family of surface receptors found within the cell - GTP(on) GDP (off) Initiating and amplifying the signal/Intracellular receptors - Inside cell signal molecules - cAMP - KNOW STEPS FOR cAMP - Calcium - will change per the level of cation which affects protein activity What happens when a signal cell doesn’t deactivate?​ Cell division signals will go through transmembrane kinase and continue growing and phosphorylate Ras which causes a cascade of cell dividing, cancer is the result per uncontrolled cell division.Chapter 12 - Mitosis Procaryotes: binary fission (one cell becomes 2) Eukaryotes Vocab Diploid - ​2n Haploid - ​1n Centromere -​ regions of DNA where sister chromatids are most tightly connected Nucleosome - ​structural unit for eukaryotic chromosome Kinetacore - ​patch of protein found at the centromere Kinetacore tubules​- microtubules that are bound to chromosomes, they pull chromosomes toward centromere poles in anaphase IPPMAT + Cytokinesis Interphase - G1 -cell growth - S - chromosome replication - G2 - sister chromatid chromosomes condense and centrosomes divide phases Prophase - mitotic spindle forms - Chromosomes condense Prometaphase - Nuclear envelope is broken and starts breaking down - Spindle fibers connect to chromosomes at the kinetochore Metaphase - Chromosomes line up in the middle of the cell Anaphase - Poles start moving away from each other and elongating the cell - Centromeres move in that direction pulling the sister chromatids with them Telophase - Nuclear envelope reappears (2 instead of one) - Spindle apparatus (and spindle fibers) disintegrate - Centromeres are free floating again Cytokinesis Animals - cleavage furrow forms via actin ring between 2 nuclear envelopes formed Plants - cell plate forms between nuclear envelopes More important notes:- G phases are important, they ensure the cell can live and continue replicating. G1 checks for DNA eligible and ready to replicate for S phase, and G2 checks for completed replication. - M check point prior to dividing - looks for spindle apparatus and properly segregated chromosomes and that the MPF is gone MPF-Mitosis promoting factor - Creates 2 phosphorylation events when on: - Activates kinase - both : inactivation - Off: in anaphase, enzyme will degrade cyclin subunit Kinases​ regulates checkpoints which are activated by cyclin (Cdk) which change during the cell cycle and activate proteins which are needed for a successful cell division cycle Social control​ - signals from other cells the frequency of cell division E2F ​- specific activator of the S-phase, Rb becomes phosphorylated which E2F then activates target genes Proliferation - When cells lose control over cell cycle, usually during G1 checkpoint, and may continue replication which causes tumors to form - which is the loss of social control. 3 types: - Benign - ​non-invasive - Malignant ​- invasive - Metastasis​ - when a tumor leaves the site it was formed in - 2 kinds of genes impacted when cancer happens: - Tumor suppressors​ - these usually stop the cell cycle - Example: Rb (inhibits E2F) - Mutations in genes are recessive - Proto-oncogenes​ - normally start the cell cycle - Stimulators of cyclin synthesis - Examples: myc (increase in Cdk), Ras Chapter 13 - Meiosis - reduction division Vocab: Chromosome​ (think: Chromo-SOME​) - giant long sequence of DNA that codes for a gene and its proteins Chromatid​ (Think: Chrorm - ATID​) - 1 or 2 identical strands of replicated DNA, or more simply, chromosomes connected by a centromereChromatin​ (Think: Chrom - ATIN​) - DNA and proteins Homologous chromosomes ​- chromosomes that have the same types of genes at the same location on the chromosome (making them eligible to pair) Ploidy​ - number of chromosome sets Gene ​- physical traits, ie) eyes Allele​ - versions or variations of genes, ie)brown eyes (from dad) blue eyes (from mom) Diploid -​ 2 copies of each gene in a chromosome Haploid​ - 1 copy of each gene in a chromosome Chiasmata - this indicates that the crossing over of chromatin has occurred which happens 2-3 times per chromosome. This ONLY happens in MEIOSIS Independent Assortment - 2 genes that fall on two different chromosomes Meiosis 1 & Meiosis 2 Meiosis 1 Interphase 1​ - start where telophase from mitosis left off Early prophase 1​ - non sister chromatids condense Late prophase 1​ - crossing over of chromatids (this is where genetic variation happens!!) Metaphase 1​ - chromosomes migrate toward poles Telophase 1​ - each chromosome has 2 non identical sister chromatids, cytokinesis happens during this stage, and the cell becomes 2 cells RESULT: 2 haploid cells Meiosis 2 Prophase 2 ​- start where meiosis left off and spindle apparatus is forming Metaphase 2​ - chromosomes line up in the center of the cell at the metaphase plate Anaphase 2​ - sister chromatids separate and begin moving toward poles Telophase 2 ​- chromosomes move to opposite sides of the cell and it divides, cytokinesis happens in this stage as well, so there are now 2 cells instead of one. RESULT: ​4 haploid cells More important notes: Asexual reproduction - binary fission: bacterial reproduction - Low mutation rates Sexual reproduction - Meiosis adds to “survivability” by increasing changes of increased fitness “Purifying selection” hypothesis - Asexual - live/die fast - Sexual - will not carry deletions“Changing environment” - Asexual - all/non die - Sexual - unique so random who lives/dies Nondisjunction - increases with age especially for women - Chromosomes fail to separate - aneuploidy - Failure to fertilize 10% - missing /extra chromosome - Zygote - trisomy, monosomy, autosome, chromosome sex - Miscarriages - 38% (not accurate per persons tested does not include everyone) Humans always need X chromosome to survive - Y is not required Turner’s syndrome (XO) Xnot - 1/5000 births - Present as female - Shows usually during puberty - Interfle - X linked recessive trait Trisomy X (XXX) - 1/1000 women - Fertile XX & XY children Klinefelter's Syndrome (XXY) - 1/1000 males - Tall males and high testosterone levels Missing/extra autosomes - Usually a birth failure/miscarriage Trisomy 21 - More commonly known as down syndrome - 1/900 births Chapter 14 - Mendel & Genes Trait ​- characteristic of some living thing Heredity​ - characteristics (traits) inherited by offspring from their mother/father Blending inheritance​ idea during Mendel’s time supposed that traits blended together evenly Inheritance of Acquired character​ - traits that during the parental lifetime are modified with age then passed to their offspring - Blending and Inheritance of Acquired character were both obviously totally wrong.- Mendel used peas per self-fertilization & cross fertilization (fertilized by another plant) - Parental generation: P (capitalization matters) First generation: F1 generation - Seed shape: round - No wrinkled seeds Second generation: F2 generation - Round seed shape of 3:1 which is a famous Mendelian ratio - Dominant alleles will have a Capital letter while recessive alleles will have a lower case letter KNOW PUNNETT SQUARES Mendelian Model for Heredity: 1. Peas have 2 alleles for each gene a. Homozygous alleles - same b. Heterozygous alleles - different 2. 2 alleles do not change each other 3. Gamete contains one version of the allele for each gene 4. M/F contribute equally to offspring 5. Alleles have dominance over other alleles. Mendel’s First Principle of Heredity​ - MEIOSIS 1/2 - Says that each allele for a gene is present on a homologous chromosome since we are diploid organisms Mendel’s Second Principle of Heredity - the Principle of Independent Assortment​ - MEI - Genes in parents are distributed to offspring assorted in different chromosomes Chromosome Theory - Pairs - One from each gamete - Segregation of chromosomes happens independently from others, just like genes ‘Sex-Linked’ Traits - X chromosome - diploid in females and haploid in males - Patterns of inheritance for X linked genes are not the same in males and females, because males do not pass their X chromosome to their sons - Autosomal Incomplete Dominance - which is called an intermediate phenotype - heterozygotes could have an intermediate trait that is expressed - Often enzymes Codominance​ - heterozygous organism with phenotype of both alleles - Structural genesPleiotropic Effects​ - genes can affect many phenotypes at once - Example: Cystic Fibrosis - Your environment can affect the phenotype - Epistasis​ - when a gene affects what another gene can do - “Quantitative traits” - determined by how many genes are influencing a trait - 22 pairs autosomal chromosomes - 1 pair sex chromosome - Pedigrees​ - family trees - Sperm - 50% contain X, 50% contain Y
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