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Chapter 4 Flashcards

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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
how are beta sheets made
when hydrogen bonds form between segments of a polypeptide chain that lie side by side same orientation -> parallel opposite directions -> antiparallel
26
beta sheets form the basis of ______
amyloid structures
27
prions
amyloid form of the protein can convert properly formed molecules into abnormal conformation
28
primary structure
amino acid sequence of a protein
29
secondary structure
alpha helices and beta sheets
30
tertiary structure
3-D structure of a fully folded protein heavily influenced by noncovalent bonds
31
quaternary structure
structure formed by multiple polypeptide chains to form a larger protein molecule
32
protein domain
segment of a polypeptide chain that can fold into a compact, stable structure and that often carries out a specific function fold independently
33
different domains of a protein are often associated with ______
different functions
34
protein family
a group of polypeptides that share a similar amino acid sequence or 3D structure, reflecting a common evolutionary origin
35
_____ bond all proteins to bind to each other to produce larger structures
noncovalent bonds
36
binding site
region on a protein's surface that interacts with another molecule through sets of noncovalent bonds
37
globular protein
any protein in which the polypeptide chain folds into a compact, rounded shape
38
fibrous protein
a protein with an elongated, rodlike shape
39
fibrous proteins form the ________ that helps bind cells together to form tissues
extracellular matrix
40
elastin (fibrous protein)
formed from relatively loose unstructured polypeptide chains that are covalently cross-linked into a rubberlike elastic meshwork
41
disulfide bond
covalent cross-link formed between the sulfhydryl groups on two cysteine side chains reinforce conformation
42
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
protein domains
43
what does the primary structure of a protein refer to?
the linear amino acid sequence of the protein
44
Is the following statement true or false, and why. Chaperone proteins provide the energy needed for a protein to fold into the correct conformation.
it is false because protein folding is an energetically favorable process
45
ligand
term for a small molecule that binds to a specific site on a macromolecule
46
the ability of a protein to bind selectively and with high affinity is due to the formation of _____
a set of weak, noncovalent bonds
47
binding site
region on the surface of a protein that interacts with a ligands through the formation of multiple noncovalent bonds
48
antibody
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
Vmax
maximum rate of an enzymatic reaction, reached when the active sites of all of the enzyme molecules are fully occupied by substrate
50
Michaelis constant (Km)
concentration of a substrate at which an enzyme works at half its maximum velocity
51
lysozyme
enzyme that servers the polysaccharide chains that form the cell walls of bacteria through a hydrolysis reaction (natural antibiotic)
52
coenzyme
small molecule that binds tightly to an enzyme and helps it to catalyze a reaction
53
How do enzymes alter the speed of a reaction without affecting the overall energy?
reducing the activation energy of a reaction
54
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
they usually require an input of energy from ATP for activation
55
what determine the specificity an antibody has for its antigen?
polypeptide loops in its variable domains
56
feedback inhibition
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
negative regulation
prevents an enzyme from acting
58
positive regulation
enzyme's activity is simulated by a regulatory molecules rather than being suppressed
59
allosteric
proteins can adopt two or more slightly different conformations, and their activity can be regulated by a shift from one to another
60
protein phosphorylation
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
protein kinase
enzyme that catalyzes the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein
62
protein phosphatase
enzyme that catalyzes the removal of a phosphate group from a protein
63
GTP-binding proteins
intracellular signaling protein whose activity is determined by its association with either GTP or GDP
64
scaffold protein
protein with multiple binding sites for other macromolecules, holding them in a way that speeds up their functional interactions
65
biomolecular condensate
large aggregate of phase-separated macromolecules that creates a region with a special biochemistry without the use of an encapsulating membrane
66
How do most motor proteins ensure that their movements are unidirectional?
they couple a conformational change to the hydrolysis of an ATP molecule
67
How does the GTP-bound form of GTP-binding protein switch to a GDP-bound form?
it hydrolyzes GTP, releasing a phosphate
68
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
it can increase or decrease the protein's activity
69
how does phosphorylation control protein activity?
the phosphate group induces a change in the protein's conformation
70
chromatography
use different materials to separate the individual components of a complex mixture into portions based in the properties of the protein
71
electrophoresis
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
mass spectrometry
determines the exact mass of every peptide fragment in a purified protein
73
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
chromatography and electrophoresis
74
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
determination of a protein's structure by x-ray crystallography requires prior knowledge of its amino acid sequence

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