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Cell Biology Exam 2

Chpt: 5-7 Cell biology USD Fall 2018 Dr. Karen Koster

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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