Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

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

Exam 1: Ch 3 Flashcards

You may prefer our related Brainscape-certified flashcards:
AP® Biology flashcards Biology 101 flashcards
1
Q

conformation

A

closely related 3-D shape a protein folds into

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what determines a protein’s function

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

how are structural proteins formed

A

assembly of multiple protein subunits into large structures

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

scaffold proteins

A

bring other proteins together in ordered arrays to perform specific functions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

enzymes

A

proteins that catalyze chemical reactions without being altered or consumed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

membrane transport proteins

A

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

called integrated membrane proteins (channels/pumps)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

regulatory proteins include _______ proteins

A

signaling

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

signaling proteins

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

motor proteins

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

protenome

A

entire protein complement of an organism

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

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

A

aa sequence (primary structure) and intramolecular noncovalent interactions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

protein

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

how is size of a protein expressed

A

daltons (1 AMU) or MW

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

random coil

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

tertiary structure

A

overall conformation of a polypeptide chain

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

disulfide bonds

A

formed by cysteine residues

covalently link regions of proteins reducing flexibility

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

globular protein

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

leucine zipper

A

a structural motif that looks like a zipper made of leucine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

protein domains

A

distinct regions of protein structure

structural, functional, or topological

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

functional domain

A

region of a protein that exhibits a particular activity characteristic

ex. some region of a protein is specifically responsible for its catalytic activity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

protease

A

enzyme that cleaves peptide bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

structural domain

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

topological domain

A

region of protein defined by its location in the protein

ex. integrated membrane proteins have an extracellular domain, membrane spanning domain, and cytoplasmic domain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

protein homolog

A

proteins that have a common ancestor

determined by sequence similarity

30
Q

native state

A

most stable folded form of the protein that permits normal function

conformation with lowest delta G

31
Q

denaturation

A

process by which a protein’s structure is disrupted

32
Q

chaperones

A

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
Q

functions of chaperones

A

fold newly proteins into functional conformations

refold misfolded or unfolded proteins

disassemble toxic protein aggregates

assemble or dismantle large multiprotein complexes

34
Q

molecular chaperone

A

bind to a short segment of protein substrate and stabilize unfolded or partly folded states

prevents these proteins from aggregating and being degraded

35
Q

chaperonins

A

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
Q

alzheimers

A

aggregation of improperly folded proteins into plaques in the brain

37
Q

affinity

A

tightness or strength of a protein binding its ligand

expressed by Kd (dissociation constant)

higher affinity = lower Kd

38
Q

how does a catalyst work

A

lowers Ea by lowering energy of the transition state (stabilizes it)

39
Q

active site regions

A

substrate-binding site: recognizes (specificity) and binds substrate

catalytic site: carries out chemical reaction

40
Q

michaelis menten kinetics

A

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
Q

michaelis constant Km

A

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
Q

turnover number

A

max number of substrate molecules converted to product at a single enzyme active site per second

43
Q

metabolic coupling

A

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
Q

3 ways proteins can be regulated

A

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
Q

rate of protein synthesis determined by…

A

rate of transcription, steady state of mRNA in the cell, rate of translation

46
Q

protein degredation

A

chaperones

lysosomes

cytoplasmic

47
Q

proteasomes

A

large protein degrading macromolecular machines

influence cell cycle, transcription, DNA repair, apoptosis, recognition and response to foreign organisms, removal of misfolded proteins

48
Q

proteasome structure

A

30,000 in a mammalian cell

~50 protein subunits

cylindrical barrel like core with caps

49
Q

partial proteasome inhibition for short intervals has been introduced as an approach to…

A

cancer chemotherapy

cells die by apoptosis, can target cancer cells and not normal cells in multiple myeloma

50
Q

how do cells mark proteins that should be degraded?

A

covalently attaching them to multiple copies of the 76 residue polypeptide ubiquitin

51
Q

3 steps of ubiquitination

A

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
Q

overall picture of ubiquitination

A

target protein gets 4 ubiquitins attached, which signals degradation in a proteasome

53
Q

Dubs

A

enzymes that deubiquitinate targeted proteins in the proteasome

54
Q

cyclins

A

proteins that control the cell cycle

after phosphorylation, become targets of ubiquitination

55
Q

allostery

A

any change to a protein’s tertiary or quaternary structure that is induced by noncovalent binding of a ligand

56
Q

do allosteric proteins have more than one binding site?

A

yes

at least 1 for the allosteric effector

at least 1 for the other molecules the protein interacts with

57
Q

what happens when a ligand binds an allosteric protein?

A

conformation change, which affects the activity of a different binding site

58
Q

allosteric effector

A

the ligand that induces a conformational change in an allosteric protein

59
Q

is allosteric change in activity positive or negative?

A

it can be either

60
Q

negative allostery

A

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
Q

cooperativity

A

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
Q

do michaelis menten proteins exhibit cooperativity?

A

no

63
Q

importance of Ca2+

A

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
Q

calmodulin

A

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
Q

GTPase superfamily

A

group of intracellular switch proteins that hydrolyze GTP to GDP

ex. Ras or G alpha

66
Q

functions of GTPase superfamily

A

bind to cell membrane for cell signaling

cell proliferation & differentiation

protein synthesis, transport

67
Q

2 forms of GTPases

A

1) active when bound to GTP

2) inactive when bound to GDP

68
Q

covalent modification

A

phosphorylation (kinase) and dephosphorylation (phosphatase)

changes a protein’s charge, which can induce conformational change

69
Q

proteolytic cleavage activation/deactivation

A

irreversible mechanism for protein regulation

70
Q

zymogen

A

inactive precursor enzyme

cleaved via proteolytic cleavage to become active

ex. trypsinogen cleaved to trypsin, which can activate other zymogens
ex. clotting cascade

71
Q

protein self-splicing

A

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
Q

compartmentation

A

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)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions