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Cell Biology Exam 2
Chpt: 5-7 Cell biology USD Fall 2018 Dr. Karen Koster
| Question | Answer |
|---|---|
| What is GFP? | green fluorescent proteins |
| Structure is a function of _____. | proteins |
| What gives the extracellular structure of cells? | proteisn in the extracellular matrix |
| What is an example of a protein that provides structure in the extracellular matrix? | collagen |
| What provides structure to the intracellular portion of cells? | cytoskeleton |
| Communication is a function of _______. | Proteins |
| What are 4 forms of communicaton in proteins? | Receptors, antibodies, hormones, and transport |
| What provides transport across membranes? | channels and pumps |
| what provides transport along cytoskeletons? | myosin and kinesin |
| Catalysis is a function of ______. | enzyme proteins |
| Regulation is a function of ______. | proteins |
| How do proteins use regulation? | proteins can regulate gene expression |
| how do proteins physically regulate gene expression? | with histones |
| How do proteins physiologically regulate gene expression? | by enzymes that control transcription |
| Do proteins provide regulation for other proteins? | yes |
| Adhesion is a function of ________. | proteins |
| how do proteins use adhesion? | glycoproteins at cell surface |
| Storage and Transport are functions of ______. | proteins |
| How do proteins use storage and transport? | seed storage proteins, albumins, and hemoglobin |
| What are the 6 functions of proteins? | structure, communication, regulation, adhesion, catalysis, storage and transport |
| What is the monomer of proteins? | amino acids |
| What is the sterioisomer of amino acids in nature? | L |
| How many amino acids are used in protein synthesis? | 20 |
| What is a residue? | term used to indicate a monomer within a polymer |
| What makes an amino acid non-polar? | the r-group being mostly hydrocarbons |
| What type of amino acids are usually structural residues? | non-polar amino acids |
| What are the 9 nonpolar amino acids? | glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, and proline |
| What makes an amino acid polar? | r groups with polar groups (charged or uncharged) |
| What are the 6 polar uncharged amino acids? | serine, threonine, cysteine, tyrosine, asparagine, glutamine |
| What links amino acids together? | peptide bonds |
| What is the characteristic of peptide bonds and why? | they have a partial double bond charactersitic due to mobility of the electrons from the carbonyl |
| Where are peptide bonds added? | to the c-terminus of the peptide |
| What limits rotation of amino acids? | peptide bonds |
| What is the primary structure of proteins? | sequence of amino acids linked together by peptide bonds to from a polypeptide |
| What is the secondary structure of proteins? | polypeptides being coiled into alpha helix, beta strands, or random coils |
| What is the tertiary structure of proteins? | regions of secondary structure associated in a particular manner |
| What is the quaternary structure of proteins? | associaton of two or more polypeptides to form a multimeric protein |
| What structural level is the last folding of the polypeptide? | tertiary strucure |
| How are amino acids added in the primary structure of proteins? | from N terminus to c terminus |
| What are the three most common patterns of secondary protein structures? | alpha helix, beta strands, and random coil |
| What stabilizes alpha helix? | hydrogen bonds between carboxyl and amino of one amino acid to one 4 mino acids down in each direction |
| What stabilizes the beta sheets? | hydrogen bonds between carboxyl and amno group in adjacent polypeptide |
| What is the difference in hydrogen bonding between the alpha helix and beta strands? | Alpha helix hydrogen bonds form between functional groups of the same polypeptide while beta strands form between an adjacent polypeptide |
| Approximately how may amino acids per turn | 3.6 amino acids per turn |
| Where do side chains point in an alpha helix? | the side chains point outward |
| Where do the side chains point in beta strands? | up and down perpendicular to the strand |
| Is random coil random? | no |
| What is a random coil? | stretch of amino acid chains that allows alpha and beta structures to fold together within themselves |
| What amino acid allows for random coil? | proline |
| What are intrinsically unstructured proteins? | abundant proteins that are primarily random coil, but gain structure when the environment changes |
| What is an example of an intrinsically unstructured protein? | alpha synuclein |
| What does alpha synuclein do? | can unfold and aggregate to form fibrils |
| What are alpha synuclein fibrils associated with? | neurodegenerative diseases and lewy bodies |
| What level of structure in proteins forms the 3D arrangement? | tertiary structures |
| What level of structure in protiens depends on the primary and secondary structures? | tertiary |
| Besides structures, what do tertiary structures of proteins depend on ? | the solution: pH, salts, temperature |
| What is a motif? | pattern of secondary structures |
| What stabilizes tertiary structures? | disulfide bridges |
| What is the only amino acid that can form disulfide bridges? | cystein |
| What is the difference between unfolding and denaturation? | denaturing disrupts the function of the protein while the unfolding changes the 3D structure |
| What is a domain | stable region within the protein structure |
| True or False: Protein domains are not functionally distinct | false |
| How many domains can a protein have? | one or many |
| What level of protein structure are domains? | tertiary |
| How many amino acids are typically in a domain/ | 50-350 |
| True or False: Proteins with multiple functions usally have separate domains for each | true |
| What holds tertiary structures together? | hydrogen bonds, ionic bonds, vanderwalls, disulfide bridges |
| What holds quaternary structures of proteins together? | hydrogen bonds, ionic bonds, VDW, disulfide bridges |
| What is the common number of subunits in a protein? | 10 to 12 |
| What do you call a protein with the same subunits within? | homopolymer |
| What do you call a protein with different subunits within? | heteropolymer |
| What is an example of a homopolymer? | microfilaments |
| What is an example of a heteropolymer? | ATP synthase |
| What is the first law of thermodynamics? | Conservation of energy |
| What does the first law of thermodynamics mean? | energy is neither created nor destroyed but rather transferred and transformed |
| What are the two types of energy? | potential and kinetic |
| What is potential energy? | energy due to position or chemical composition |
| What is kinetic energy? | energy due to movement |
| What is the second law of thermodynamics? | law of entropy |
| What does the second law of thermodynamics mean? | every energy transfer/transformation increases the entropy of the universe |
| What is entropy? | measure of disorder/randomness |
| What is often used to measure entropy? | heat |
| What is free energy? | portion of system's energy that can perform work |
| What is free energy represented by? | G |
| What is the equation to determine free energy? | delta G=delta H-TdeltaS |
| What is the delta H in the free energy equation? | Enthalpy |
| What is hte delta S in the free energy equation? | change in entropy |
| What does negative delta G mean? | a reaction is exergonic |
| What does a positive delta G mean? | a reaction is endergonic |
| What is a spontaneous reaction? | occurs if there is a net loss of free energy |
| What type of delta G does a spontaneous reaction have? | negative |
| What determines the amount of product yielded in an exergoinic reaction? | the larger the change in free energy the larger the yield of products |
| What is Keq a measure of? | directionality |
| How do you calculate Keq? | ratio of product concentrations to reactant concentrations at equilibrium |
| What happens to change at equilibrium? | there is no net change of concentrations of products and reactants |
| True or false: the more negative the delta G the farther the net reaction goes to products | true |
| True or fase: delta G tells us the rate of a reaction | false |
| What does delta G tell us? | if a reaction will occur |
| True or false: if a reaction isspontaineous, the reactio will occur at any time | false |
| What is a catalyst? | something that speeds up a reaction |
| Does a catalyst affect delta G? | nope |
| Does a catalyst affect equilibrium? | nope |
| Does a catalyst allow a reaction to reach equilibrium faster? | yes |
| Does a catalyst add energy to a reaction? | no |
| Does a catalyst lower activation energy? | yes |
| What is an enzyme? | a protein that acts as a biological catalyst |
| What is a ribozyme? | RNA molecule that acts as a biological catalyst |
| What is believed to be the first biological catalyst? | ribozyme |
| What catalyzes peptide bond formation in ribosomes? | ribozymes |
| What is activation energy? | energy barrier that must be overcome for a reaction to occur |
| What can activation energy represent? | energy needed to bring substrate to transition state, physical separation of reactants, unfavorable chemical environment, other factors |
| For uncatalyzes reactions, what does activation energy come as? | random thermal energy (heat) |
| Why do biological reactions need to be catalyzed rather then the use of heat to overcome activation energy barrier? | because heat can denature cellular structures by destroying hydrogen bonds |
| What does a catalyst do? | overcomes the activation energy without large inputs of heat |
| What are the four ways that catalysts can work? | bring reactants together, alter chemical environment, bring substrate into transition state, other things to remove obstacles |
| What are the three basic properties of catalysts? | they can increase reaction rates by lowering activation energy, form transient, reversible complexes with substrate molecules nad they can change the rate at which equilibrium is reached |
| Do catalysts change the positon of the equilibrium | no |
| What is a coupled reaction? | use of an exergonic reaction to provide energy for an endergonic reaction |
| What is an example of a couple reaction? | glucose phosphorylation is endergonic, ATP hydrolysis is exergonic, when coupled there is enough energy for the endergonic reaction to take place |
| What is an enzyme? | protein catalyst |
| What does an enzyme do? | decreases the activation energy of biological reactions |
| True or false: enzymes are reusable | true |
| What is the turnover number of an enzyme? | rate of catalysis |
| Waht is the average turnover number? | 1000/sec |
| What is the range of turnover numbers of enzymes? | .5 -40000000/sec |
| What is the lock and key model? | a model representing enzyme catalysis where the substrate fits into the enzyme like a key and when released forms the products |
| What is the induced fit model? | a model representing enzyme catalysis where the substrate bonds are distorted when in the active site of an enzyme which forms the products |
| Where are charged polar amino acids found in an enzyme? | they are found in the active site |
| Where are nonpolar amino acids found in an enzyme? | often structural units in the hydrophobic environment |
| What is enzyme specificity? | each enzyme catalyzes a specific type of reaction for a single type of substrate or similar shaped substrates |
| How do enzymes reacognize substrates? | by their shape and chemical properties |
| What does amylase break? | alpha (1->4) bonds |
| Where are alpha (1->4) bonds found? | between glucose monomers in amylose |
| Where are beta (1->4) bonds found? | in cellulose |
| Why can't amylase break b(1->4) bonds between glucose monomers of cellulose? | alpha and beta bonds differ in orientation of the bond, so they ahve different shapes. the alpha (1->4) bond is the shape that amylase recognizes and therefore can catalyze the breaking of |
| What other properties to enzymes recognize on substrates? | molecular shape, charge, polarity |
| What helps contribute to enzyme activity? | cofactor |
| What are inorganic cofactors? | Metal ions such as magnesium, zinc, calcium |
| What is an organic cofactor? | coenzymes and prosthetic group |
Created by:
kenzigustafson
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