Exam 1 Notes PDF

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Notes from the first session of lectures during the summer semester
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Chapter 1 A. Cell theory 1. Living things are made from cells, - Cells are the basic unit of structure and function, - All cells come from other cells B. Timeline 1. ~ 3900-2500 MYA prokaryotes appeared a) Used CO2 as C source and inorganic molecules for energy 2. ~ 1800-1500 MYA eukaryotes appeared C. Domains of Life: Bacteria, Eukarya, Archaea 1. Bacteria and Archaea are prokaryotic cells, -Eukarya are eukaryotic a) Eukaryotes and archaea are more closely related D. Universal Characteristics of Life: 1. Genetics info is stored as DNA 2. DNA is used as a template for copying the genome 3. A plasma membrane surrounds the cell and creates a barrier 4. RNA is an intermediate 5. Proteins act as a catalyst for all Rx 6. Free energy must be absorbed a) Q: are viruses alive? Debatable, some follow these rules more closely E. Eukaryotes vs Prokaryotes 1. Prokaryotes - Smaller, simpler, most have cell membrane and cell wall, have region called nucleoid, NO membrane bound organelles. 2. Eukaryotes - Larger, more complex, have membrane bound organelles, compartmentalized, “true nucleus” F. Mitochondria and chloroplasts 1. Mitochondria – may at one time have been a bacteria that was consumed by eukaryote. Instead of being digested the mitochondria became an organelle symbiotic relationship (Endosymbiosis // endosymbiotic theory) 2. Chloroplasts have the same theory II. Chapter 2: Chemistry Review A. Atoms and their Electrons 1. MEMORIZE: a) Hydrogen – has 1, can make 1 b) Carbon – has 4, can make 4 c) Nitrogen – has 5, can make 3 d) Oxygen – has 6, can make 2 B. Covalent Bonds: equal and unequal sharing 1. Non-polar - equal sharing due to similar electronegative a) Have greater potential energy, electrons are more available to bond (ex. Fats). 2. Polar - unequal sharing due to different electronegativities a) Form dipole moments (electrons spend more time around negative atoms) b) O>N>C=H C. Ionic Interactions- occur when atoms have a full or partial charge, opposites attract, a) These have litter importance due to the amounts of water in the cell

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D. Hydrogen bonding - occur under specific conditions: 1. Need a H covalently bonded to an electronegative atom, giving it a partial positive charge. 2. Also need an atom with a partial negative charge a) Strength depends on the length and orientation of the bond. E. The hydrophobic effect - forming hydration shells is NOT favorable 1. Like dissolves like, non polar molecules will associate with themselves before other polar molecules 2. ENTROPY- disorder, more disorder is FAVORABLE, a) Forming hydration shells around the non polar substances would be very unfavorable. It is even more unfavorable to form several smaller shells, so one large one is preferred, if needed (1) This is because it required more atoms of H2O to form those several small ones than a single large one (a) Increase disorder. F. Van der Waals forces - weakest of the non covalent interactions, between two covalent bonds there is SOME attraction 1. Q: Why do we need these weak interactions? They are weak and therefore reversible. 2. protein interactions are not through covalent bonds but through (however covalent bonds do hold the actual molecules together). G. Complementarity - two sides have matching shape and opposite or matching bonds. H. Redox Reactions - the gain or loss of electrons, can also be a gain or loss of TIME with electrons. -> OILRIG I. Building Blocks 1. Sugars - polysaccharides 2. Amino acids - protein 3. Fatty acids - fats, lipids, proteins 4. Nucleotides - nucleic acids a) All of these are polymers EXCEPT lipids J. Monosaccharides 1. Simple sugars, go on to form polysaccharides 2. Have the general formula CH2O 3. 2 main groups a) Aldoses (1) C=O on the end of the sugar b) Ketoses (1) C=O in the middle of the sugar 4. Named based on how many carbons are present a) 3 - trioses, 5 - pentoses, 6 - hexoses 5. In aqueous solutions these sugars often form RINGS K. Disaccharides and polysaccharides 1. Forming di/polysaccharides depends on if the molecule are alpha or beta, or what side the hydroxyl group is compared to the left out carbon group a) Alpha - carbon and hydroxyl are on OPPOSITE sides b) Beta - carbon and hydroxy are on the SAME side (1) The formation of branched polysaccharides depends on the alpha beta form L. Common Reactive Groups with pH

1. Zwitter ion - when a protein has charges within, but is overall neutral. M. Polymerization Uses Condensation Reaction 1. Anabolic = Building of molecules a) Produces H20 (condensation) 2. Catabolic = Breaking Down molecules a) Needs H20 (hydrolysis) N. Chemical Reaction Rate and Equilibrium 1. The amount of reactants and products is the same / constant / equal. a) Equilibrium is easy to achieve in test tubes but hard to do in cells. O. Energetics of Reactions: Gibbs Equations [ ∆G = ∆H - T∆S ] 1. ∆G = Gibbs free energy, a) Exergonic - energy of the products is lower than the reactants, ∆G < 0 , spontaneous, FAVORABLE b) Endergonic - energy of the products is higher than the reactants, ∆G > 0, non-spontaneous, NON FAVORABLE 2. ∆H = Enthalpy a) Endothermic = takes in heat / energy b) Exothermic = releases heat / energy 3. ∆S = Entropy, disorder a) To have something that is orderly requires energy (1) To go from order to disorder is FAVORABLE, (+) ∆S (2) To go from disorder to order is UNFAVORABLE, (-) ∆S P. Enzymes and reaction rates 1. All enzymes are proteins, but not all proteins are enzymes a) Only are if they catalyze a reaction b) Not all reaction use enzymes because RNA can act as a enzyme, this is called Ribozyme 2. Enzymes lower the activation energy of a reaction 3. Lots of non-spontaneous Rx occur in our body all of the time. How do these Occur? a) Coupling- using the energy released from an exergonic reaction to kick start the reaction of and endergonic one. Q. Enzymes as catalysts and reaction rate 1. For a reaction there are usually 2 enzymes, 1 for the forward and 1 for the reverse reaction 2. This is due to complementarity. The enzymes is attracted to the initial molecule, once it has carried out the reaction it is not as attracted to the the products and they leave. III. Chapter 3: Proteins A. Anatomy of a protein 1. Side chains can go up or down 2. Amino acids have a three and 1 letter code 3. Proteins are polar (have different ends, N terminus or C terminus) B. Rotation - constrained around a peptide bond 1. C⍺ is attached to the side chain 2. Rotation is possible around these bonds a) ( C⍺ — N ) bond is phi b) ( C⍺ — C = O ) bond is psi

3. NO rotation is possible around the peptide bound due to partial double bond character ( C = O — N ) C. Amino Acids (1) What makes amino acids different? The side chains (2) 20 common side chains, know the three letter codes 2. Charged Side Chains - all of these will have a charge at physiological pH and like to interact with other polar molecules. a) Positive (+) Side Chains (1) Lysine - lys (2) Arginine - arg (3) Histidine - his (a) Histidine can have a (+) or neutral charge b) Negative (-) Side Chains (1) Aspartic Acid - asp (2) Glutamic Acid - glu 3. Non-polar Side Chains a) Alanine - ala b) Valine - val c) Leucine - leu d) Proline - pro (1) Proline has a cyclic side chain which causes kinks, glycine is usually found next to proline. e) Phenylalanine - phe f) Methionine - met g) Glycine - gly (1) Only amino that is not chiral (has H for an R group), smallest amino, usually paired with proline h) Tryptophan - trp i) Cysteine - cys (1) Can form covalent disulfide bridges with other cysteines. Sensitive to REDOX environments (a) Reducing environments = separation (b) Oxidizing environments = bridge formation 4. Polar (uncharged) Side Chains - these polar molecules form most of the molecular complementarity. (1) Interactions that determine how 1 protein fold are the same for determining how multiple proteins interact b) Asparagine - asn c) Glutamine - gin d) Serine - ser e) Threonine - thr f) Tyrosine - tyr (1) These last THREE all have an OH group attached, important for phosphorylation. D. Molecular Complementarity - protein tries to bury the non polar groups inside the protein, a) Q: will chawed aminos always be on the outside? (1) Depends. Not always, if they have a buddy (opposite charged molecule). “the Buddy system”, b) Q: will there always be polar on the outside? (1) Depends on the buddy system again

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c) Q: what bout hydrophobic on the outside? (1) Usually but not always, ex. In the cell membrane, or if the face of the protein is meant to bond to the face of another Protein structure 1. Primary - just the sequence of aminos 2. Secondary - folding of localized areas of aminos that are close interact 3. Tertiary - folding and interactions of multiple secondary structures, may be distant in the primary sequence 4. Quaternary - two or more protein interacting with each other, not all proteins reach this level. a) Still secondary structures interaction, but they are from different proteins. Secondary Structure 1. Alpha Helices - form when backbone twists into helix. Stabilized by vertical H bonding in the backbone. a) UP & DOWN 2. Beta strand - backbone in kinked. When they are together they form a beta sheet. Stabilized by H bonding in the backbone 3. Beta turn - hairpin turns, involve 1 or more proline molecules, glycine is probably nearby 4. Random coil - just a lack of structure Intrinsically disordered proteins - almost completely made of random coils, function by having no structure, ex. Elastin 1. Binding - gain structure by binding to a specific partner 2. Signaling - unfolded = off, folded = on 3. Tethering - keep two proteins close 4. Diffusion barrier - NPC (nuclear pore complex), Matt of structures block diffusion General rules for protein binding 1. Models a) Backbone trance - bare minimum, shows only the backbone, not very useful b) Ball and stick - show backbone and atoms of side chains, hard to interpret c) Ribbon diagram - doesn’t show side chains, does show backbone, shows what types of secondary structures are present, simple but informative d) Space filling model - shows backbone and side chains, but also show how much space is taken up (1) Looks blobby, gives good surface view Structure and Function - structure determines function 1. The 3D structure of a protein matters more than the primary sequence Domains of protein and quaternary structure 1. In a tertiary protein there may be areas that are distinctly folded = DOMAIN 2. Each protein (the whole) is tertiary and each domain is also tertiary 3. What makes something Quaternary? a) The number of backbones 4. Quaternary - multiple polypeptide chains interacting that are always necessary for that proteins function. Assemblies 1. The same subunits = assembly 2. Named by the number of proteins in a complex a) Quaternary protein complex made of 3 proteins = trimer b) “ “ 2 proteins = dimer c) Etc.

3. Homodimer - two polypeptide chains that are identical 4. Heterotrimer - three polypeptide chains that are different (AT LEAST one is different) L. Assistance with folding - chaperones : some proteins end up in the intermediate state and can’t get out ( just stable enough to not be able to unbind) —> need a chaperon 1. Chaperones must: a) help proteins that are hydrophobic and subject to hydrophobic effect. b) stabilize a short segment and allow the rest to fold correctly c) hydrolyze ATP 2. Mechanism a) Unfold protein binds to substrate binding domain at region made of non polar amino acids. b) Binding causes chaperone to clamp down on the unfolded protein (1) To clamp, the chaperone needs to hydrolyze ATP to form ADP. When clamped the protein folds c) Chaperone sense the protein is folded correctly, then gives up ADP, gets a new ATP and chaperon opens releasing the correctly folded protein 3. Hsp70 and it’s family are chaperones M. Chaperonins 1. Help with folding but also can unfold proteins that are in the intermediate form and help them unfold and try again 2. Mechanism: a) Misfolded protein goes into the barrel b) The chaperoning uses ATP to bind GroES cap c) Chaperonin shakes protein around, producing energy and helps to break apart and form the correct foldings d) The chaperoning detects when it is folded right e) It then hydrolyzes ATP to ADP f) Lid comes off and folded protein comes out N. Regulating proteins - post-translational modification 1. Phosphorylation - phosphate group added via covalent bond, phosphate usually comes from ATP a) Protein Kinases - move phosphate group from ATP and put in on the protein b) Protein phosphotases - remove phosphate group (1) Why is phosphorylation needed? Some molecules become activated when they have a phosphate group added OR removed, and vise versa O. Activation by a G protein 1. Some proteins become activated by GTP hydrolysis a) These proteins hold a GTP nucleotide (ON state), then internally hydrolyzes them loosing a phosphate group. Now we have GDP (OFF state). b) To turn back on it needs to first get ride of the GDP molecule and then gets a new GTP (ON again). P. Cofactor Binding 1. To be active proteins have to fold into native confirmation, some need another molecule to become active (ex. Hemoglobin) a) Co-Factor - can be a lot of thing but ARE NOT proteins b) Co- Enzymes - small proteins Q. Proteolytic Activation / cleavage - some proteins need to be CUT before they become active (ex. Insulin) 1. Useful when a very fast response is needed

R. Polyubiquidation - adding a small molecule (ubiqutin) to the protein of interest, lysine likes to get ubiquitin 1. Add 1 ubiquitin = monoubiquidation 2. Add multiple ubiquitin (that aren’t attached) = multiubiquidation 3. Add a long chain of ubiquitin = polyubiquidation a) {{ Polyubiquidation —> degradation at the proteasome }} (1) Proteasome - garbage disposal, barrel shape, degrades proteins and recycles them (a) Damages or worn out proteins will get a polyubiquitin chain attached which directs them to be destroyed at the proteasome S. Protein ligand interaction: not all proteins are enzymes, 1. Substrate - bind to an enzyme, when it leaves it is changed 2. Ligand - bind to proteins, but then they leave they are still the same a) When a protein bind to a ligand the ligand will go into the binding pocket and bind using several non-covalent methods T. Rates of binding 1. Kd - binding affinity or strength of bond between R and L, a) The more stable/ tight RL is the smaller Kd will be (1) Small Kd - (10-100 nanoM) (2) Large Kd - (1-10 microM) U. Binding Curve - used to study affinity between L + R (Kd = binding affinity) 1. Calculating Kd a) Find maximal binding level (vertical) b) Find 1/2 max binding level c) Draw a line from 1/2 max binding to the curve (horizontal line) d) Drop straight down V. Enzymes 1. Q: if only 4 amino acids fit in the active site, why do I need a protein with hundreds them? STRUCTURE. Those hundred other ones fold to the protein so that the active site is correctly structured. W. Enzyme rates and constant 1. Enzymes dont usually reach Vmax 2. At low [S] the rate depends on S 3. At high [S] the rate depends on E a) Vmax depends on [E] 4. Km - how efficient is the enzyme, find it with the same process you find Kd a) Chaining [E] will change Vmax, NOT Km b) Changing [S] will NOT change Vmax, but WILL change Km. IV. Chapters 4-7 A. Nucleotides - has a phosphate groups, sugar group and nitrogenous base B. Nitrogenous Bases - 5 common bases 1. 3 based off of Pyrimidine a) Cytosine b) Uracil c) Thymine

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(1) CUT 2. 2 based off of Purine a) Adenine b) Guanine 3. Pairing a) A > T ( sometimes U In RNA) b) G > C Phosphodiester bonds covalently bond nucleotides: 1. Nucleotides combine via condensation reaction to form a dinucleotide a) A nucleotide initially has 3 phosphates but only 1 remains in the final molecule b) Holding a nucleotide near a nucleic acid causes a lot of tension (repulsion of the negative phosphate groups) which leads to a lot of PE c) We add nucleotides to the 3’ end ( the 3’ end attacks the phosphate group of the nucleotide) d) The other 2 phosphate groups leave as result of this, releasing a lot of energy 2. DNA is complementary and antiparallel a) polar (5’ & 3’ ends) b) Complementary - pairing rules (1) GC bond are made up of 3 H bonds, AT bonds are made of 2, so GC are slightly stronger Nucleic acid strand polarity 1. Nucleotides are added at the 3’ end. We write nucleic acids 5’ to 3’ as that is the way they are synthesized DNA double helix - major and minor grooves 1. Minor Groove - shorter distance between the helix curve 2. Major Groove - longer distance between the helix curve a) This Is functionally important as there are some proteins that interact with the minor group and some that interact with the major group 3. Minor Groove Proteins - the are is so small that the binding protein cannot access the sequence information. There are a lot of non specific binders 4. Major groove proteins - area is large enough that most binding proteins can access the sequence. Specific binding DNA Replication 1. Replication starts at the BUBBLES a) Each side of the replication bubble has a replication fork b) Free nucleotides are added to the 3’ end of the strand 2. General sequence: a) Specific sequences (replication origins) mark where replication should begine (1) Each chromosome has many of these b) Replication origin will be bound by proteins allowing a replication bubble to form c) Short RNA primers are added to DNA (1) Necessary for beginning DNA synthesis d) DNA is synthesized by the enzyme DNA polymerase e) Replication bubbles continue to replicate until they run into each other Leading and Lagging strand

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1. Leading strand - synthesizes DNA in the same direction the fork is moving. CONTINUOUS 2. Lagging Strand - synthesizes DNA in short fragments opposite the direction the fork is moving, OKAZAKI FRAGMENTS 3. DNA synthesis is semiconservative - DNA is 1/2 new and 1/2 old 4. To be replicated DNA myst be accessible, it is usually tightly bound in chromosomes so it needs to be unwound Chromatic Structure - chromosomes are very long and must be compacted, LINEAR 1. It is compacted by histone proteins to form DNA / Histone complex called chromatin a) These help to fit genome in nucleus but also to regulate gene expression (1) All cells have the same DNA but that genes re expressed differently Chromosome Structure (in order of increasing compaction) 1. Naked DNA - not stored this way because it is more vulnerable, usually like this when it is being used 2. “Beads on a Thread” model - the beads are histone proteins with DNA wrapped around it 3. 30 nm Fiber - twisting of the bead on a thread model give this form, if it continues to twist it forms the… 4. 700 nm structure - wraps even more tightly to form 5. Mitotic Chromatin Euchromatic vs Heterochromatic 1. Euchromatic - less tightly packed, accessible for use 2. Heterochromatic - genes stored this way are tightly packed and being expressed Histones and Neucleosomes - each nucleosome has 8 histones a) 2 each of H2A, H2B, H3 and H4 b) How do you fom euchromatin or heterochromatin? By modifying the histone tails (1) Acetylation = addition of acetyl group opens up the chromatin - favors euchromatin (a) HDAC - (histone deacetylase) pulls acetyl group off of which makes the chromatin get tigher and less accessible, favors heterochromatin (b) HAT - (histone acetyl transferase), put acetyl group on which makes the chromatic get loose which favors euchromatin. Transcription factors, promoters and euchromatin 1. Basal Transcription Factors - (BTF) bind to a region all genes have (promoter region) a) Bind all available promoters nonspecifically in euchromatin, GENERAL 2. Regulatory Transcription Factors - (RTF) are more specific, regulate only certain genes, do not bind to promoter region. They bind to a ENHANCER and SILENCER regions of DNA 3. Transcription sequence: a) Put desired gene in euchromatin form (use HAT) b) Open gene has promoter region which has region called the TATA BOX which is bound by the BTF. c) BTF bind to promoter and then recruit RNA polymerase (1) Only ...