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Cell Bio > Chapter 4 study guide > Flashcards

Chapter 4 study guide Flashcards

1
Q

The function of a protein depends on the detailed structure of

A

its 3-dimensional
shape

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2
Q

A protein or polypeptide is a long chain of amino acids linked together by

A

covalent peptide bonds

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3
Q
  • The 20 different amino acids differ from one another in the chemical structure of their
A

side chains

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4
Q

Protein folding is influenced by three types of…

A

non covalent bonds: hydrogen bonds, electrostatic interactions, and van der Waals

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5
Q

Protein folding is also influenced by

A

hydophobic interactions (nonpolar side chains cluster together)

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6
Q

Polar side chains tend to be found

A

on the outside surface

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7
Q

The final folded structure or conformation of a polypeptide chain is usually determined
by its

A

lowest free energy state

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8
Q

Proteins can be unfolded or denatured with solvents that

A

disrupt non-covalent
interactions

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9
Q

When proteins fold incorrectly, they often form

A

insoluble aggregates

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10
Q

Many neurodegenerative disorders are associated
with the formation of

A

protein aggregates

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11
Q

Function of Protein aggregates

A

kill cells and tissues

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12
Q

unusual type of neurodegenerative disease that is caused by infectious proteins that stimulate protein misfolding

A

Prion diseases

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13
Q

Relatively easy now to determine a polypeptide sequence by sequencing

A

its gene

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14
Q

The alpha helix and beta sheet are formed by

A

hydrogen bonds between N-H and C=O groups in the polypeptide backbone

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15
Q

-the alpha helix (like a spiral staircase) forms a hydrogen bond between every __ amino acid, forming a regular helix with a turn every __ amino acids.

A

4th, 3.6

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16
Q

alpha helices that span a membrane lipid bilayer typically have __ hydrophobic
amino acids that can contact the hydrophobic lipid tails

A

20

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17
Q

some alpha helices can wrap around each other to form

A

coiled coils

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18
Q

The hydrophobic amino acids on one side of an alpha-helix at positions ___ interact with the hydrophobic amino acids on one side of another alpha helix, whereas the hydrophilic amino acids can be exposed to the aqueous environment

A

a and d

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19
Q

When the polypeptide strands run in the same direction (N to C terminal), they are called

A

parallel

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20
Q

Most proteins contain small stretches of __ amino acids known as __ that can fold __ into a stable, compact structure.

A

100-250, protein
domains, independently

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21
Q

The full three-dimensional structure of a polypeptide chain, with its multiple secondary
structures and domains, is considered its

A

tertiary structure

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22
Q

If a protein molecule contains more than one polypeptide structure, this is known as its

A

quarternary structure

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23
Q

A polypeptide that is n amino acids long would have __ potential amino acid sequences

A

20n

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24
Q

Small changes in a polypeptide sequence (mutations) can disrupt protein structure and
function: what’s an example

A

Sickle cell anemia

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25
Q

Protein families share…

A

both sequence and structural similarities, but differ in functions

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26
Q

__ are a family of proteins that can cleave peptide bonds in a polypeptide
chain.

A

serine proteases

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27
Q

A binding site is any region on a protein surface that interacts with another molecule through

A

non-covalent bonds

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28
Q

In larger protein complexes, each polypeptide chain
is referred to as a

A

subunit

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29
Q

Most proteins are

A

globular

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30
Q

fold up into compact shapes like a ball with an irregular surface

A

globular proteins

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31
Q

Collagen is composed of __ polypeptides that form a __ helix

A

3, triple

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32
Q

The collagen molecules then bind end-to-end and side-to-side to form

A

Collagen fibrils

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33
Q

The interactions between the collagen molecules are stabilized by

A

covalent bonds outside the cell

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34
Q

There are many different kinds of covalent cross-links, but __ between the __ groups of __ are among the most common

A

disulfide bonds (S-S), SH of cytsesines

35
Q

These bonds are formed in the lumen of the ER

A

covalent cross links, S-S bonds

36
Q

Disulfide bonds are found in many

A

extracellular proteins, where they stabilize protein conformation

37
Q

Binding sites depend on the

A

3D organization of the polypeptide

38
Q

an example of proteins that bind their ligands with high affinity and specificity

A

Antibodies (IgG), ligands are antigens

39
Q

IgGs contain how many large and light chains

A

2 large and 2 light

40
Q

IgGs are held together by

A

S-S bonds

41
Q

Most of the polypeptide sequence is conserved between what region

A

constant regions

42
Q

the antigen-binding site is formed by

A

small variable loops in heavy and light chains

43
Q

Changing the length and sequence of the variable loops will alter

A

binding specificities for different antigens without affecting the structure of the rest of the antibody molecule

44
Q

breaks down polysaccharide chains in the cell walls of bacteria

A

Lysozyme

45
Q

Enzymes make and break

A

covalent bonds

46
Q

Many drugs work by blocking the activity of an

A

enzyme

47
Q

How are proteins controlled…

A
  1. Regulate expression of the gene encoding the protein.
  2. Target a protein to a specific cellular compartment
  3. Alter protein degradation
  4. Turn protein activities on and off by ligand bindings
48
Q

second sites where regulatory molecules can bind and alter protein conformation to either inactivate or stimulate a protein (or enzyme).

A

Allosteric regulation

49
Q

Examples of allosteric regulation

A

Feedback inhibition (neg and pos)

50
Q

major mechanism used by cells to control protein activity.

A

phosphorylation

51
Q

Phosphate groups contain

A

2 negative charges and their addition to serine, threonine, or tyrosine side chains alter protein conformation

52
Q

Phosphate addition is catalyzed by a

A

kinase

53
Q

Phosphates are removed from amino acid side chains by a

A

protein phosphatase

54
Q

Phosphorylation may either

A

stimulate or inhibit protein activity

55
Q

molecular switches that are regulated by the cyclic gain
and loss of a phosphate group

A

GTP binding sites

56
Q

Use the energy of ATP binding, hydrolysis, and release to drive the conformational changes needed to move in one direction along a track are done by what proteins

A

Motor proteins

57
Q

Ex of motor proteins

A

myosin moving on an actin filament, kinesin moving on microtubules, DNA polymerase moving on a DNA strand.

58
Q

Proteins often form large machines with

A

10 or more subunits

59
Q

contain binding sites that are recognized by multiple proteins

A

scaffold proteins

60
Q

Binding of several proteins to a scaffold enables formation of

A

protein complex

61
Q

__ modifications of amino acids after __ also control the location and
assembly of protein machines

A

covalent, translation

62
Q

Addition of the __ drives proteins to cell membranes

A

palmitate to cysteines

63
Q

The set of covalent modifications that a protein contains is an important way of regulating the protein’s function and constitutes a

A

regulatory protein code

64
Q

To isolate a protein from a particular cell type, one must break open the cell (poke holes in the cell membrane) to make a

A

cell homogenate or extract that contains all the cell
organelles

65
Q

There are several methods commonly used in cell fractionation and centrifugation

A

a) sonication (high frequency sound)
b) mild detergent treatment
c) forcing cells through small holes under high pressure
d) mechanical shear

66
Q

Once you have your cell extract, you can separate it into crude fractions by

A

differential
centrifugation

67
Q

Less dense components of centrifuge settle at

A

the bottom more quickly

68
Q

Centrifugation: contains whole cells, partially disrupted cells (cell ghosts), and nuclei

A

low speed pellet

69
Q

contains the larger organelles (mitochondria, lysosomes,
peroxisomes)

A

medium speed pellet

70
Q

contains the larger organelles (mitochondria, lysosomes,
peroxisomes)

A

high speed pellet

71
Q

contains large cytoplasmic protein complexes (ribosomes,
virus particles, large macromolecules)

A

very high speed pellet

72
Q

Typically used to separate larger protein complexes based on
the rates that they move through a shallow gradient of sucrose.

A

Velocity sedimentation

73
Q

Larger, denser complexes will move __ than smaller, less dense complexes

A

faster

74
Q

used to separate components based on their buoyant
density, independent of size and shape.

A

Equilibrium centrifugation

75
Q

often used to isolate nucleic acids (DNA, RNA)

A

Equilibrium centrifugation

76
Q

separates proteins according to their size

A

Gel filtration chromatography

77
Q

separate the crude protein mixture on the basis of size, charge, and/or its ability to bind to a particular chemical group

A

Column chromatography

78
Q

contain a matrix that is covalently bound to a molecule that interacts
specifically with the protein of interest

A

Affinity columns

79
Q

This molecule may resemble an enzyme’s substrate, or it might be a specific antibody that recognizes an antigen on the protein surface

A

Affinity columns

80
Q

the proteins are treated with a
negatively charged detergent, sodium dodecyl sulfate (SDS), which denatures the
proteins, and a reducing agent, which breaks disulfide bonds

A

SDS polyacrylamide gel electrophoresis (SDS-PAGE)

81
Q

the gel contains a pH gradient, and the proteins are NOT treated with SDS. Proteins will migrate in the pH gradient until they reach their
individual isoelectric points

A

isoelectric focusing gel

82
Q

mixtures of proteins will be separated in the
first dimension by isoelectric focusing, and then the gel will be treated with SDS and
run in the second dimension using SDS-PAGE

A

two-dimensional gel electrophoresis

83
Q

If you have a complex mixture of proteins, you can sometimes identify what proteins are in
that mixture using

A

mass sepctrometry

84
Q

to determine the structure of large protein complexes, integral membrane proteins and dynamic proteins. This
technique involves rapidly freezing the proteins and exposing them to a beam of
electrons, which projects the images of the molecules onto a detector.

A

Cryoelectron microscopy

Cell Bio (15 decks)

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