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Cellular and Molecular Biology > Exam 1: Ch 3 > Flashcards

Exam 1: Ch 3 Flashcards

(72 cards)

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1
Q

conformation

A

closely related 3-D shape a protein folds into

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2
Q

what determines a protein’s function

A

its conformation combined with the chemical properties of its aa side chains

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3
Q

structural protein

A

determine the shapes of cells and their extracellular environments

guide wires or rails to direct intracellular movement of molecules or organelles

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4
Q

how are structural proteins formed

A

assembly of multiple protein subunits into large structures

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5
Q

scaffold proteins

A

bring other proteins together in ordered arrays to perform specific functions

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6
Q

enzymes

A

proteins that catalyze chemical reactions without being altered or consumed

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7
Q

membrane transport proteins

A

permit the flow of ions & molecules across the cell’s membrane

called integrated membrane proteins (channels/pumps)

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8
Q

regulatory proteins

A

act as signals, sensors and switches to control activities of cells by altering the functions of other proteins and genes

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9
Q

regulatory proteins include _______ proteins

A

signaling

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10
Q

signaling proteins

A

hormones and cell-surface receptors that transmit extracellular signals to the cell interior

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11
Q

motor proteins

A

move other proteins, organelles, cells, or even whole organisms

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12
Q

protenome

A

entire protein complement of an organism

humans have 20,000-23,000 genes that code for proteins

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13
Q

what is a protein’s 3-D structure determined by

A

aa sequence (primary structure) and intramolecular noncovalent interactions

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14
Q

peptide bond

A

planar bond formed between the amino group of one aa and the carboxyl group of another

dehydration rxn to form

hydrolysis to break

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15
Q

protein

A

a polypeptide that has a well-defined 3D structure and function

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16
Q

how is size of a protein expressed

A

daltons (1 AMU) or MW

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17
Q

random coil

A

a type of secondary structure that is highly flexible and has no fixed 3D structure

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18
Q

tertiary structure

A

overall conformation of a polypeptide chain

the 3D arrangement of aa residues stabilized by hydrophobic interactions and h-bonds

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19
Q

disulfide bonds

A

formed by cysteine residues

covalently link regions of proteins reducing flexibility

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20
Q

globular protein

A

water soluble, compact spheroidal structures made of a mix of secondary structures

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21
Q

fibrous proteins

A

large, elongated and stiff molecules with repeat units

usually play a structural role or participate in cellular movements

ex. collagen

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22
Q

structural motif

A

combination of 2 or more 2ndary structures that form a distinct 3D structure with a specific function

ex. coiled coil (heptad repeat) - transcription factor

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23
Q

leucine zipper

A

a structural motif that looks like a zipper made of leucine

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24
Q

protein domains

A

distinct regions of protein structure

structural, functional, or topological

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25
functional domain
region of a protein that exhibits a particular activity characteristic ex. some region of a protein is specifically responsible for its catalytic activity
26
protease
enzyme that cleaves peptide bonds
27
structural domain
a region ~40 aa or more that represents a single, stable and distinct structure usually has one or more 2ndary structures that can fold independently from rest of protein
28
topological domain
region of protein defined by its location in the protein ex. integrated membrane proteins have an extracellular domain, membrane spanning domain, and cytoplasmic domain
29
protein homolog
proteins that have a common ancestor determined by sequence similarity
30
native state
most stable folded form of the protein that permits normal function conformation with lowest delta G
31
denaturation
process by which a protein's structure is disrupted
32
chaperones
a set of protein that facilitate proper folding of proteins use ATP binding, hydrolysis, and exchange of ATP for ADP to induce conformational changes to assist protein folding ATP also enhances binding of protein substrates
33
functions of chaperones
fold newly proteins into functional conformations refold misfolded or unfolded proteins disassemble toxic protein aggregates assemble or dismantle large multiprotein complexes
34
molecular chaperone
bind to a short segment of protein substrate and stabilize unfolded or partly folded states prevents these proteins from aggregating and being degraded
35
chaperonins
form small folding chambers where all or part of an unfolded protein is gathered, giving it time and the appropriate environment to fold correctly
36
alzheimers
aggregation of improperly folded proteins into plaques in the brain
37
affinity
tightness or strength of a protein binding its ligand expressed by Kd (dissociation constant) higher affinity = lower Kd
38
how does a catalyst work
lowers Ea by lowering energy of the transition state (stabilizes it)
39
active site regions
substrate-binding site: recognizes (specificity) and binds substrate catalytic site: carries out chemical reaction
40
michaelis menten kinetics
rate (kinetics) of enzyme is proportional to substrate concentration at low [ ]s, but reaches Vmax at Vmax the rate is directly proportional to how much enzyme is present in rxn mixture (all enzyme sites occupied)
41
michaelis constant Km
Km = substrate concentration required for the reaction to occur at 1/2 Vmax Low km means higher affinity b/c less substrate needed to get enzyme to 1/2 vmax
42
turnover number
max number of substrate molecules converted to product at a single enzyme active site per second
43
metabolic coupling
enzymes participating in a common metabolic pathway are sometimes physically associated with each other products of one rxn are passed to next enzyme without leaving the complex
44
3 ways proteins can be regulated
cells inc or dec steady-state level of the protein by altering its rate of synthesis, degradation or both cells change the intrinsic activity distinctly from the amount of the protein change in location or [ ] within the cell of the protein itself, the protein's substrate, or a molecule required for the protein's activity
45
rate of protein synthesis determined by...
rate of transcription, steady state of mRNA in the cell, rate of translation
46
protein degredation
chaperones lysosomes cytoplasmic
47
proteasomes
large protein degrading macromolecular machines influence cell cycle, transcription, DNA repair, apoptosis, recognition and response to foreign organisms, removal of misfolded proteins
48
proteasome structure
30,000 in a mammalian cell ~50 protein subunits cylindrical barrel like core with caps
49
partial proteasome inhibition for short intervals has been introduced as an approach to...
cancer chemotherapy cells die by apoptosis, can target cancer cells and not normal cells in multiple myeloma
50
how do cells mark proteins that should be degraded?
covalently attaching them to multiple copies of the 76 residue polypeptide ubiquitin
51
3 steps of ubiquitination
activation of ubiquitin activating enzyme by adding ubiquitin (uses ATP) transfer of ubiquitin molecule to cysteine in ubiquitin-conjugating enzyme form covalent bond btw lysine of target protein and glycine 76 of ubiquitin by ubiquitin-protein ligase
52
overall picture of ubiquitination
target protein gets 4 ubiquitins attached, which signals degradation in a proteasome
53
Dubs
enzymes that deubiquitinate targeted proteins in the proteasome
54
cyclins
proteins that control the cell cycle after phosphorylation, become targets of ubiquitination
55
allostery
any change to a protein's tertiary or quaternary structure that is induced by noncovalent binding of a ligand
56
do allosteric proteins have more than one binding site?
yes at least 1 for the allosteric effector at least 1 for the other molecules the protein interacts with
57
what happens when a ligand binds an allosteric protein?
conformation change, which affects the activity of a different binding site
58
allosteric effector
the ligand that induces a conformational change in an allosteric protein
59
is allosteric change in activity positive or negative?
it can be either
60
negative allostery
often found in biochemical pathways when end product builds up, it reduces the activity of the enzyme to prevent excess buildup of product (feedback inhibition)
61
cooperativity
influence that ligand binding has on the other subunits of the protein amplifies sensitivity of a system to [ ] changes in its ligands (imparts a selective evolutionary advantage) ex. hemoglobin
62
do michaelis menten proteins exhibit cooperativity?
no
63
importance of Ca2+
concentration in cell's cytosol is low, extracellular higher cytosolic [ ] can increase 100 fold by channels, which is sensed by binding proteins binding proteins alter cellular behavior by switching other proteins on or off
64
calmodulin
Ca2+ binding EF hand protein (monomeric or multimeric) binding Ca2+ causes a conformational change that turns activity of other proteins on or off (switch protein)
65
GTPase superfamily
group of intracellular switch proteins that hydrolyze GTP to GDP ex. Ras or G alpha
66
functions of GTPase superfamily
bind to cell membrane for cell signaling cell proliferation & differentiation protein synthesis, transport
67
2 forms of GTPases
1) active when bound to GTP | 2) inactive when bound to GDP
68
covalent modification
phosphorylation (kinase) and dephosphorylation (phosphatase) changes a protein's charge, which can induce conformational change
69
proteolytic cleavage activation/deactivation
irreversible mechanism for protein regulation
70
zymogen
inactive precursor enzyme cleaved via proteolytic cleavage to become active ex. trypsinogen cleaved to trypsin, which can activate other zymogens ex. clotting cascade
71
protein self-splicing
rate form of proteolytic processing in bacteria and some eukaryotes middle portion of polypeptide removed, and ends rejoined ex. hedgehog: membrane bound signal that does this
72
compartmentation
separation allows competing rxns to take place simultaneously in different parts of the cell allows control of substrate delivery and product exiting

Cellular and Molecular Biology (34 decks)

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