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Bio > Chapter 4 > Flashcards

Chapter 4 Flashcards

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Biology 101 flashcards
1
Q

amino acid chains are held together by covalent _____

A

peptide bonds

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2
Q

amino acid sequence

A

the order of the amino acid subunits in a protein chain

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3
Q

polypeptide backbone

A

repeating sequence of the atoms that form the core of a protein molecule and to which the amino acid side chains are attached

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4
Q

N-terminus

A

the end of a polypeptide chain that carries an amino group

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5
Q

C-terminus

A

the end carrying the free carboxyl group, carboxyl terminus

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6
Q

the ____ give each amino acid its identity

A

side chains

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7
Q

the stability of each folded shape is largely determine by the _____

A

noncovalent bonds

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8
Q

_____ has a central role in determining the shape of a protein

A

hydrophobic force

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9
Q

nonpolar, hydrophobic side chains tend to cluster to the ____ of the protein

A

interior

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10
Q

polar side chains ae likely to arrange themselves on the ____ of a protein

A

outside

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11
Q

when polar amino acids are buried within the protein, they are usually ______ to the other polar amino acids or to polypeptide backbone

A

hydrogen-bonded

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12
Q

conformation

A

3-D shape of a protein or other macromolecule, based on the spatial location of its atoms in relation to another

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13
Q

folding process is energetically ______

A

favorable (releases heat, increases disorder)

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14
Q

proteins can be denatured via _____

A

solvents that disrupt the noncovalent bonds

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15
Q

protein folding is generally assisted by ________

A

chaperone proteins
make the folding process more efficient and reliable

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16
Q

______ are the most structurally diverse macromolecules in the cell

A

proteins

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17
Q

backbone model

A

shows the overall organization of the polypeptide chain and provides a straightforward way to compare the structures of related proteins

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18
Q

ribbon model

A

shows the polypeptide backbone in a way that emphasizes the folding patterns

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19
Q

wire model

A

includes the positions of all of the amino acid side chains
useful for predicting which amino acids might be involved in the protein’s activity

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20
Q

space-filling model

A

provides a contour map of the protein surface

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21
Q

two regular folding patterns of proteins

A

alpha helix
beta sheet

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22
Q

alpha helix

A

an elongated structure whose subunits twist in a regular fashion around a central axis (right or left handed)

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23
Q

how are alpha helices generated

A

a single polypeptide chain turns around itself to form a cylinder with a hydrogen bond between every 4th amino acid

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24
Q

coiled-coil

A

alpha helices wrap around each other (have hydrophobic on inside)

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25
Q

how are beta sheets made

A

when hydrogen bonds form between segments of a polypeptide chain that lie side by side
same orientation -> parallel
opposite directions -> antiparallel

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26
Q

beta sheets form the basis of ______

A

amyloid structures

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27
Q

prions

A

amyloid form of the protein can convert properly formed molecules into abnormal conformation

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28
Q

primary structure

A

amino acid sequence of a protein

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29
Q

secondary structure

A

alpha helices and beta sheets

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30
Q

tertiary structure

A

3-D structure of a fully folded protein
heavily influenced by noncovalent bonds

31
Q

quaternary structure

A

structure formed by multiple polypeptide chains to form a larger protein molecule

32
Q

protein domain

A

segment of a polypeptide chain that can fold into a compact, stable structure and that often carries out a specific function
fold independently

33
Q

different domains of a protein are often associated with ______

A

different functions

34
Q

protein family

A

a group of polypeptides that share a similar amino acid sequence or 3D structure, reflecting a common evolutionary origin

35
Q

_____ bond all proteins to bind to each other to produce larger structures

A

noncovalent bonds

36
Q

binding site

A

region on a protein’s surface that interacts with another molecule through sets of noncovalent bonds

37
Q

globular protein

A

any protein in which the polypeptide chain folds into a compact, rounded shape

38
Q

fibrous protein

A

a protein with an elongated, rodlike shape

39
Q

fibrous proteins form the ________ that helps bind cells together to form tissues

A

extracellular matrix

40
Q

elastin (fibrous protein)

A

formed from relatively loose unstructured polypeptide chains that are covalently cross-linked into a rubberlike elastic meshwork

41
Q

disulfide bond

A

covalent cross-link formed between the sulfhydryl groups on two cysteine side chains
reinforce conformation

42
Q

protein molecules that have a quaternary structure will always have two or more of which of the following?
-different primary structure
-disulfide bonds
-protein domains
-alpha helices and beta sheets

A

protein domains

43
Q

what does the primary structure of a protein refer to?

A

the linear amino acid sequence of the protein

44
Q

Is the following statement true or false, and why.
Chaperone proteins provide the energy needed for a protein to fold into the correct conformation.

A

it is false because protein folding is an energetically favorable process

45
Q

ligand

A

term for a small molecule that binds to a specific site on a macromolecule

46
Q

the ability of a protein to bind selectively and with high affinity is due to the formation of _____

A

a set of weak, noncovalent bonds

47
Q

binding site

A

region on the surface of a protein that interacts with a ligands through the formation of multiple noncovalent bonds

48
Q

antibody

A

immunoglobulin protein produced by the immune system in response to foreign molecules and binds to an antigen
Y-shape with 2 antigen binding sites

49
Q

Vmax

A

maximum rate of an enzymatic reaction, reached when the active sites of all of the enzyme molecules are fully occupied by substrate

50
Q

Michaelis constant (Km)

A

concentration of a substrate at which an enzyme works at half its maximum velocity

51
Q

lysozyme

A

enzyme that servers the polysaccharide chains that form the cell walls of bacteria through a hydrolysis reaction
(natural antibiotic)

52
Q

coenzyme

A

small molecule that binds tightly to an enzyme and helps it to catalyze a reaction

53
Q

How do enzymes alter the speed of a reaction without affecting the overall energy?

A

reducing the activation energy of a reaction

54
Q

all of the following are true concerning enzymes except which statement?
-they can bring reactants together in the proper orientation for chemistry to occur
-they usually require an input of energy from ATP for activation
-they can form covalent bonds with their substrates
-they can change the shape of substrates to increase the rate of a particular reaction

A

they usually require an input of energy from ATP for activation

55
Q

what determine the specificity an antibody has for its antigen?

A

polypeptide loops in its variable domains

56
Q

feedback inhibition

A

form of metabolic control in which the end product of a chain of enzymatic reactions reduces the activity of an enzyme early in the pathway

57
Q

negative regulation

A

prevents an enzyme from acting

58
Q

positive regulation

A

enzyme’s activity is simulated by a regulatory molecules rather than being suppressed

59
Q

allosteric

A

proteins can adopt two or more slightly different conformations, and their activity can be regulated by a shift from one to another

60
Q

protein phosphorylation

A

covalent addition of a phosphate group to a side chain of a protein, catalyzed by a protein kinase
form of regulation
create docking sites for other proteins to bind

61
Q

protein kinase

A

enzyme that catalyzes the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein

62
Q

protein phosphatase

A

enzyme that catalyzes the removal of a phosphate group from a protein

63
Q

GTP-binding proteins

A

intracellular signaling protein whose activity is determined by its association with either GTP or GDP

64
Q

scaffold protein

A

protein with multiple binding sites for other macromolecules, holding them in a way that speeds up their functional interactions

65
Q

biomolecular condensate

A

large aggregate of phase-separated macromolecules that creates a region with a special biochemistry without the use of an encapsulating membrane

66
Q

How do most motor proteins ensure that their movements are unidirectional?

A

they couple a conformational change to the hydrolysis of an ATP molecule

67
Q

How does the GTP-bound form of GTP-binding protein switch to a GDP-bound form?

A

it hydrolyzes GTP, releasing a phosphate

68
Q

Which of the following correctly describes phosphorylation of a protein?
-it can increase or decrease the protein’s activity
-it is an irreversible protein modification
-it is catalyzed by a protein phosphate
-it always increases the protein’s activity

A

it can increase or decrease the protein’s activity

69
Q

how does phosphorylation control protein activity?

A

the phosphate group induces a change in the protein’s conformation

70
Q

chromatography

A

use different materials to separate the individual components of a complex mixture into portions based in the properties of the protein

71
Q

electrophoresis

A

a mixture of proteins is loaded onto a polymer gel and subjected to an electric field; the polypeptides will then migrate through the gel at different speeds depending on their size and net charge

72
Q

mass spectrometry

A

determines the exact mass of every peptide fragment in a purified protein

73
Q

Which of the following are methods that can be used for purifying a protein of interest, in other words, isolating it from all other proteins?
-chromatography and electrophoresis
-chromatography and mass spectrometry
-electrophoresis and crystallography
-crystallography and cryoEM

A

chromatography and electrophoresis

74
Q

Which of the following statements is true regarding protein structure determination?
-Mass spectrometry is the fastest way to determine the 3D structure of a polypeptide or protein, regardless of its size
-nuclear magnetic resonance can be used to determine the structure of proteins that are too large to crystallize
-determination of a protein’s structure by x-ray crystallography requires prior knowledge of its amino acid sequence
-cryo-electron microscopy can only be used to determine the structure of proteins that are small enough to avoid freezing

A

determination of a protein’s structure by x-ray crystallography requires prior knowledge of its amino acid sequence

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