Exam 1: Ch 3 Flashcards Preview

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Flashcards in Exam 1: Ch 3 Deck (72):
1

conformation

closely related 3-D shape a protein folds into

2

what determines a protein's function

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

3

structural protein

determine the shapes of cells and their extracellular environments

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

4

how are structural proteins formed

assembly of multiple protein subunits into large structures

5

scaffold proteins

bring other proteins together in ordered arrays to perform specific functions

6

enzymes

proteins that catalyze chemical reactions without being altered or consumed

7

membrane transport proteins

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

called integrated membrane proteins (channels/pumps)

8

regulatory proteins

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

9

regulatory proteins include _______ proteins

signaling

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signaling proteins

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

11

motor proteins

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

12

protenome

entire protein complement of an organism

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

13

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

aa sequence (primary structure) and intramolecular noncovalent interactions

14

peptide bond

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

dehydration rxn to form

hydrolysis to break

15

protein

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

16

how is size of a protein expressed

daltons (1 AMU) or MW

17

random coil

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

18

tertiary structure

overall conformation of a polypeptide chain

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

19

disulfide bonds

formed by cysteine residues

covalently link regions of proteins reducing flexibility

20

globular protein

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

21

fibrous proteins

large, elongated and stiff molecules with repeat units

usually play a structural role or participate in cellular movements

ex. collagen

22

structural motif

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

ex. coiled coil (heptad repeat) - transcription factor

23

leucine zipper

a structural motif that looks like a zipper made of leucine

24

protein domains

distinct regions of protein structure

structural, functional, or topological

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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

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protease

enzyme that cleaves peptide bonds

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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