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chapter 4 Flashcards

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Biology 101 flashcards
1
Q

The shape of a protein is specified by its

A

amino acid
sequence

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2
Q

Amino acids are connected together by

A

covalent peptide
bonds

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3
Q

Proteins fold into

A

3D shapes

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4
Q

Proteins fold into a conformation of

A

lowest energy

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5
Q

An amino acid contains an

A

amino group (NH2), a carboxyl group (COOH),
an a-carbon atom and a side chain

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6
Q

covalent link between carboxyl group of one amino acid and amino group of next amino acid

A

Peptide bond

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7
Q

Linking amino acids together through peptide bonds forms the

A

polypeptide backbone

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8
Q

polypeptide backbone

A

a repeating sequence of the core atoms (N-C-C) in
every amino acid

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9
Q

Denature proteins with solvents that

A

disrupt non-covalent bonds (urea, detergent)

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10
Q

When you remove the solvents from proteins, the proteins will

A

refold

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11
Q

Protein folding depends on

A

non-covalent bonds and
hydrophobic interactions

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12
Q

Protein folding occurs in the

A

aqueous environment of the cell interior

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13
Q

Although chaperones make the folding process more efficient and reliable, the final
3-D shape of the protein is specified

A

only by its amino acid sequence

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14
Q

What proteins can assist with protein folding

A

chaperone

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15
Q

Two common secondary structures for folding proteins are

A

the alpha helix and beta sheet

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16
Q

Amino acid side chains are not or are involved in secondary structure formation

A

are not

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17
Q

The alpha helix is formed by

A

by hydrogen bonds in the polypeptide backbone as it
twists, amino acid side groups project out

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18
Q

How many amino acids can form an alpha helix

A

many

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19
Q

20 __ amino
acids can span a lipid
bilayer, interact with fatty
acids in phospholipids

A

hydrophobic

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20
Q

Hydrophobic side chains in __ position every __
amino acids form a hydrophobic “stripe”

A

1st and 4th, seven

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21
Q

Two or more alpha-helices with hydrophobic stripes can
interact to form a

A

coiled coil

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22
Q

Beta sheets are formed by

A

by hydrogen bonds
between polypeptide
backbones of adjacent strands

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23
Q

In the beta sheet, the amino acid side chains project…

A

above & below the
b-sheet

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24
Q

regions of 40-350 amino acids that can fold independently into a stable structure

A

Protein domains

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25
Q

There are more than __ recognized protein domains

A

2000

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26
Q

what is the first protein level of organization, primary structure?

A

amino acid sequence

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27
Q

what is the second protein level of organization, secondary structure?

A

simple folding patterns (a-helix, b-sheet)

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28
Q

what is the third protein level of organization, tertiary structure?

A

3-dimensional shape of the polypeptide

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29
Q

what is the fourth protein level of organization, quaternary structure?

A

multiple polypeptide subunits in a protein complex

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30
Q

Where are protein domains located, what structure?

A

tertiary

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31
Q

Protein subunits can assemble to form

A

larger macromolecules

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32
Q

Depending on the location of __ on
the surface of a protein, a single protein subunit
can assemble into a wide variety of shapes

A

binding sites

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33
Q

Fibrous, elongated proteins are common in the

A

Extracellular matrix

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34
Q

Elastin and collagen are

A

ECM proteins

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35
Q

Fibrous, elongated proteins are often stabilized by

A

disulfide bonds

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36
Q

The binding sites of antibodies are

A

versatile

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37
Q

All proteins bind to

A

ligands

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38
Q

powerful and highly specific catalysts

A

enzymes

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39
Q

bind substrates and hold them in conformations that promote a particular reaction

A

enzymes

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40
Q

Binding sites for proteins are usually a pocket near

A

the surface of the folded protein

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41
Q

Binding usually involves many __ bonds

A

non-covalent

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42
Q

Heme group binds

A

iron

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43
Q

Heme group facilitates

A

O2 binding to hemoglobin

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44
Q

Aberrant conformation causes

A

polymerization

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45
Q

Enzymes are often regulated by other molecules
that bind at a

A

second site, allosteric control

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46
Q

controls the location,
assembly, stability and activity of protein complexes

A

covalent modification

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47
Q

can control protein activity by
triggering a conformational change

A

phosphorylation

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48
Q

regulated by cyclic
gain and loss of a phosphate group

A

GTP binding proteins

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49
Q

allows motor proteins to
produce large movements in cells

A

Nucleotide hydrolysis

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50
Q

Z binds to a __ on enzyme and exerts __ control

A

second, allosteric

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51
Q

As concentration of Z increases, it feeds back to the enzyme that

A

converts B to X to shut down the pathway

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52
Q

Allosteric control can also provide what feedback

A

positive feedback

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53
Q

When the concentration of ATP is low, the concentration of ADP is

A

high

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54
Q

can bind the enzyme, changing its conformation so it favors the
active form

A

ADP

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55
Q

What protein use ATP to phosphorylate amino acid side chains

A

Kinases

56
Q

remove the phosphate group (Pi)

A

Phosphatases

57
Q

Pi adds what charge

A

negative

58
Q

The __ charge on Pi results in a

A

conformational change

59
Q

Phosphorylation can either

A

activate or inactivate a protein

60
Q

Ubiquitination stimulates

A

degradation

61
Q

Palmitoylation on cysteine targets…

A

the protein to a membrane

62
Q

G-proteins with bound
GTP are

A

active

63
Q

G-proteins with bound GDP
are

A

inactive

64
Q

GTP hydrolysis switches
G-protein

A

off

65
Q

GDP-GTP exchange
switches G-protein

A

on

66
Q

Many cell signaling
pathways use what protein

A

G-proteins

67
Q

what drives
directional movement

A

NTP (nucleotide hydrolysis)

68
Q

NTP is observed with

A

motor proteins

69
Q

s enables the protein to
bias its conformational
changes in one direction

A

Nucleotide (NTP) hydrolysis

70
Q

Amino acids only differ by their

A

Side chains

71
Q

breaks holes in cell membranes

A

Homogenization

72
Q

Spin the homogenate to enrich for your protein or cellular
component of interest

A

Centrifugation

73
Q

2 centrifugation techniques:

A

Velocity Sedimentation and
Equilibrium Sedimentation

74
Q

Take advantage of your protein’s unique size, shape, charge or binding properties

A

Column chromatography

75
Q

3 chromatography methods:

A

Gel filtration, Ion exchange and Affinity chromatography

76
Q

Overview of protein purification

A
  1. Centrifugation
  2. Column chromatography
  3. Analysis
77
Q

Assess the purity and identity of your protein sample

A

Analysis

78
Q

Assesses the number and sizes of protein in your sample

A

Gel electrophoresis

79
Q

Bigger organelles sediment more __ at lower speeds

A

quickly

80
Q

1st step differential Centrifugation allows one to make a

A

Crude, enriched fraction

81
Q

separates components based on the rate at which they
move through a gradient

A

Velocity sedimentation

82
Q

Used to isolate large protein complexes like ribosomes

A

Velocity sedimentation

83
Q

separates components based on buoyant density

A

Equilibrium sedimentation

84
Q

In equilibrium sedimentation, Components migrate in gradient until their

A

Density matches that of the surrounding medium

85
Q

2nd step of Centrifugation

A

Velocity vs equilibrium sedimentation

86
Q

Often used to purify DNA, RNA, different membranes

A

Equilibrium sedimentation

87
Q

Most soluble proteins are too __ to purify by Centrifugation

A

Small

88
Q

Column chromatography can separate

A

Protein mixtures

89
Q

Gel filtration separates proteins based on

A

Size

90
Q

Beads for gel filtration contain

A

Small proes

91
Q

In gel filtration,
__ proteins flow around beads and out the column first.

__ proteins enter the beads and flow out more slowly.

A

Larger, Smaller

92
Q

Ion exchange separates proteins based on

A

Charge

93
Q

What do yo use for ion exchange

A

Positively or negatively charged beads and add proteins

94
Q

In ion exchange,

Positively charged beads will bind

A

Negatively charged proteins

95
Q

Positively charged proteins in ion exchange will flow

A

Through without binding

96
Q

Increase __ of buffer to elute the protein

A

ionic strength

97
Q

In ion exchange, negative ions in buffer….

A

Displace negatively charged proteins

98
Q

Affinity chromatography separates proteins
based on

A

Specific binding

99
Q

In affinity chromatography, buy beads with a

A

Covalently attached substrate

100
Q

Add a protein mixture, wash away proteins that can’t bind t substrate occurs in

A

affinity chromatography

101
Q

Analyze protein mixtures by

A

Gel electrophoresis (SDS PAGE)

102
Q

How to analyze proteins by gel electrophoresis

A
  1. Treat the protein sample with two chemicals
  2. Load treated protein sample onto gel with electric field
  3. Proteins migrate towards positively charged anode
  4. Smaller proteins migrate through the gel faster than larger ones
103
Q

What two chemicals are used to treat the protein sample in gel electrophoresis

A

Beta-mercaptoethanol and SDS

104
Q

What chemical breaks disulfide bonds

A

Beta mercapotethanol

105
Q

What chemical denatures proteins & coats them with negative charges

A

SDS

106
Q

SDS-PAGE separates proteins by

A

Size

107
Q

In SDS PAGE, larger proteins are at the

A

Top, smaller at bottom

108
Q

Protein complexes composed of four subunits (2 Heavy Chains, 2 Light Chains)

A

Antibodies

109
Q

Small variable __ in antigen binding site recognize and bind antigens in antibodies

A

loops

110
Q

In an antibody, Each light chain and heavy chain contains

A

One variable domain and one or more constant domains

111
Q

Each antibody contains __ antigen binding sites, which are made up of __
that have variable amino acid sequences

A

2, loops

112
Q

These loops in antibodies are located in the ___ of the heavy chain and the light chain on each side of the antibody

A

variable domains,

113
Q

To make an antibody, Host animal degrades protein and presents fragments to
antibody-producing cells called

A

B cells

114
Q

Binding of antigens stimulates

A

B cells to divide and secrete antibodies

115
Q

Use for protein purification

A

Immunoaffinity chromatography

116
Q

Use antibodies to detect a particular protein
within a mixture of proteins

A

Biochemical chromatography

117
Q

Use antibodies to locate a protein inside a cell

A

Microscopic detection

118
Q

In biochemical detection, antigen A is separated from other molecules by

A

Electrophoresis

119
Q

In biochemical detection, Incubation with labeled antibodies that bind to antigen A allows…

A

the position of the antigen to be determined

120
Q

Flourescent tags of DNA, microtubules, and Actin

A

DNA= blue
Microtubules= green
Actin=red

121
Q

Smaller and less dense components

A

Supernatant

122
Q

Larger and more dense components

A

Pellet

123
Q

1st step differential Centrifugation can’t make what into a pellet

A

Most proteins

124
Q

After running the protein through the gel in SDS PAGE..

A

Stain the gel with dye specific for proteins

125
Q

common assay for analyzing column fractions

A

SDS PAGE

126
Q

Separate denatured proteins according to their size (molecular weight)

A

SDS PAGE

127
Q

Separate native (folded) proteins according to their size and shape

A

Gel filtration chromatography

128
Q

Separate native proteins according to their ability to bind a specific substrate

A

Affinity chromatography

129
Q

Separate native proteins according to their charge

A

Ion exchange chromatography

130
Q

Separate proteins according to the rate at which they move through a gradient

A

Velocity sedimentation

131
Q

Separate proteins according to their buoyant density

A

Equilibrium sedimentation

132
Q

Flourescent microscopy allows you to

A

Detect specific components

133
Q

What parts of amino acids are involved in peptide bonds

A

Amino group on one amino acid and carboxyl group on the other

134
Q

How do most motor proteins make their movements unidirectional

A

They couple a conformational change to hydrolysis of an ATP molecule

135
Q

Binding site of protein structure is located

A

Inside cavity on protein surface

136
Q

Variable domains are located near the

A

Antigen binding site

Cell Bio (15 decks)

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