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Cell Phys > Lec 2: Proteins > Flashcards

Lec 2: Proteins Flashcards

1
Q

proteins are essentially

A

macromolecules

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2
Q

Macromolecules: 4 1* categories:

A

Proteins
Nucleic Acids
Polysaccharides
Lipids

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3
Q

Proteins: 9 Major Classes & Functions:

& based on…

A
  1. ) Enzymes: selective catalysis
  2. ) Structural Proteins: support of cell structures
  3. ) Motility Proteins: movement of cells and cell parts
  4. ) Regulatory Proteins: regulation of cell functions
  5. ) Transport Proteins: transport of substances across membranes
  6. ) Hormonal Proteins: communication between distant parts of an organism
  7. ) Receptor Proteins: response of cells to chemical stimuli
  8. ) Defensive Proteins: protection against disease
  9. ) Storage Proteins: storage and release of amino acids

…based on function

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4
Q

All proteins are initially…

which =

A

…made as linear polymers of amino acids

= polypeptide chain

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5
Q

Amino acids =

A

= monomers

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6
Q

Polypeptide chain =

A

= polymer

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7
Q

proteins are encoded by:

A

DNA –(transcription in nucleus)–>
mRNA –(translation at ribosome)–>
polypeptide chain –> (folding) –> protein

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8
Q

Approximately __ different amino acids contribute to

A

20

proteins (thousands of different proteins in each cell)

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9
Q

(AA’s)

Always use the…

A

…L-form amino acid (l-alanine, etc.)

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10
Q

(AA’s)
Some are…
usually…
& 3 examples:

A

…modified
(usually via post-translational modification)
ex 1.) proline → hydroxyproline (collagen, plant cell walls)
ex 2.) lysine → hydroxylysine (collagen)
ex 3.) cysteine → cystine (many proteins, dimer of 2 cysteines via disulfide bridge)

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11
Q

(AA’s)

General Features: (4)

A
  1. ) central a-carbon
  2. ) amino group
  3. ) carboxyl group
  4. ) R-group
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12
Q

Most amino acids in proteins are

A

L-amino acids

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13
Q

(AA structure)
Because the a-carbon is…
it is a…
this gives rise to…

A

…asymmetric (4 different groups attached to it) in most amino acids,
…chiral carbon
…stereoisomers (D and L)

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14
Q

Enantiomer =

A

= one of 2 optical isomers

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15
Q

Because amino acids differ only at…

it is what determines…

A

…R-Group,

…determines its specific chemical properties

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16
Q

(AA’s)
3 main categories of R-Groups:

The R-groups then determine things like…

A
  1. ) Nonpolar (R is mostly hydrocarbon)
  2. ) Polar, Uncharged (R contain sulfhydryl, hydroxyl, or carboxamide)
  3. ) Polar, Charged (R contains carboxyl or amino group)

…charge state, hydrophobicity, possibility for hydrogen bonding, etc.

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17
Q

non polar AA’s Side groups are highly

hydrophilic or hydrophobic?

A

organic (hydrocarbon-based)

= hydroPHOBIC

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18
Q

polar, charged AA’s contain side groups that have

hydrophilic or hydrophobic?

A

…carboxyl, amino groups or imidazole ring, which are either negatively (acidic) or positively (basic) charged.

= hydroPHILIC

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19
Q

polar, uncharged AA’s contain side groups that have…
capable of…
hydrophilic or hydrophobic?

A

…Hydroxyl, sulfhydryl, and amino carbonyls (carboxamide)
…hydrogen bonding
= hydroPHILIC

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20
Q

Proteins are formed by

A

successive linkages of amino acids into a polypeptide chain (via the peptide bond)

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21
Q

The _______ bond links two successive amino acids via …

A

peptide

…the carboxyl group of one amino acid binding to the amino group of the other amino acid

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22
Q

Peptide Bond forms via

A

Condensation Reaction

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23
Q

(Peptide Bond Formation)

catalyzed by

A

enzyme peptidyl transferase

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24
Q

(Peptide Bond Formation)
occurs at…
during…

A

…at the ribosome

…during translation

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25
Q

(Peptide Bond Formation)

Initially forms a

A

dipeptide → tripeptide… → polypeptide chain

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26
Q

(Peptide Bond Formation)

Protein =

A

= final folded version of the polypeptide

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27
Q

(Peptide Bond Formation)

Always starts at…

A

…the N-terminus proceeds to C-terminus

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28
Q

(Peptide Bond Formation)

cost =

A

= 4 ATP (or GTP) per peptide bond formed during translation at ribosome

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29
Q

Monomeric proteins =
Multimeric proteins =
Homomeric =
Heteromeric =

A

= proteins composed of a single polypeptide chain
= proteins composed of multiple polypeptide chains
= all subunits are the same polypeptide (ex: LDH-1 & LDH-5)
= different polypeptide chains assemble together (ex: Myosin, hemoglobin, LDH-2, LDH-3, LDH-4)

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30
Q

Dimer, trimer, tetramer represents

A

of subunits

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31
Q

What causes the polypeptide to fold in a certain way?

A

Due to the R-group interactions:

  1. ) with other R-groups
  2. ) or with surrounding cellular components
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32
Q

Polypeptide Folding Possible R-Group Interactions: (5)

A
  1. ) Disulfide bonds (bridges)
  2. ) Hydrogen Bonds
  3. ) Ionic Bonds
  4. ) van der Waals Interactions (forces)
  5. ) Hydrophobic Interactions
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33
Q

Disulfide bridge =

what type of bond is this?

A

= The sulfhydryl (aka thiol) side groups of 2 cysteine combine to form a cystine
= (covalent bond between the two sulfur atoms)

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34
Q

Intramolecular disulfide bridge forms a

A

cross-link

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35
Q

Disulfide bridges help to…

A

…stabilize overall protein folding

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36
Q

Hydrogen Bonds involve: (2)

A
  1. ) uncharged, polar interactions
  2. ) R–groups with:
    - OH
    - SH
    - C=O
    - C-NH2
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37
Q

Ionic Bonds Involve…

making…

A

…amino acids with charged R-Groups

…Opposite charges attract, like charges repel

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38
Q

van der Waals Interactions =

A

= Transient interactions due to transient (+) and (-) charged regions in nonpolar molecules.

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39
Q

van der Waals Interactions strength

A

Very weak and transient electrical based forces between nonpolar molecules.

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40
Q

(Hydrophobic Interactions)
Hydrophobic R-groups will tend to…
In contrast, hydrophilic R-groups (charged or polar) will tend to…

A

…“push” away from charged and strongly polar R-groups and polar molecules (including water)
…be attracted to water and charged R-groups of the opposite charge.

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41
Q

2* Protein Structure: (2)

A
  1. ) a-helix

2. ) B-sheet

42
Q

a-helix Polypeptide chain forms

A

a spiral

43
Q

(a-helix)

R-Groups generally point to…

A

the outside of the spiral

44
Q

(a-helix)

Approximately…

A

four (~3.6) amino acids per complete ‘turn’ of the spiral

45
Q

c

Small distance between

A

every 4th peptide bond

46
Q

(a-helix)

________ bonding between…

A

Hydrogen

…every 4th peptide bond –strengthens the overall structure (coil)

47
Q

(a-helix)
“MALEK” =
& all have…

A

= Methionine, alanine, leucine, glutamate, and lysine

…especially high helix-forming propensities

48
Q

B-(pleated) sheet =

A

Extended sheet like conformation with successive peaks and troughs “pleats”
(Like the pleats in a curtain or skirt)

49
Q

(B-sheet)

involves

A

two sections of polypeptide positioned side by side

50
Q

(B-sheet)

________ bonding between…

A

Hydrogen

…the peptide bonds of the side by side regions helps to stabilize the configuration (not fold)

51
Q

A single section of beta sheet =

A

= a beta strand

52
Q

2* Structural “Motifs” aka

examples:

A

“Combinations”

  1. ) B-a-B (parallel)
  2. ) Hairpin Loop (anti-parallel)
  3. ) Helix-turn-helix
53
Q

Arrow of b-sheet points to

A

the C-terminus

54
Q

Motifs based on =

Domains based on =

A

= structure

= function

55
Q

3* Structure =

A

= Overall complex 3 dimensional folding pattern

56
Q

3* Structures are not as well

A

understood compared to 2* structures (which can be predicted based on AA sequence)

57
Q

(3* Structure)

Native conformation =

A

= most stable pattern of folding (under in vivo conditions)

58
Q

2 Main types of 3* structure:

some proteins have…

A
  1. ) Globular proteins (amorphous) [Many enzymes]
  2. ) Filamentous (rod-like) [Collagen, elastin]

…both regions
ex: Myosin heavy chain (has a globular head & filamentous tail)

59
Q

4* Structure =
which leads to…
example:

A 
= Subunit Interactions
...multimeric proteins
ex: (Myosin) 
- 2 Myosin heavy chains
- 4 Myosin light chains
60
Q

Protein Domains (sites) result from

A

3* and 4* structure

61
Q 
Protein Domains (sites) involve...
& have...
A

…portions of the overall protein

…a specific function

62
Q

Many types of domains (examples) (5)

A 
DNA binding domain
Substrate binding domain
Regulatory domains
Ligand binding domains
Catalytic domains
63
Q

Insulin =

A

= A protein hormone that is synthesized by the Beta-cells in the Islets of Langerhans in the Pancreas

64
Q 
(Insulin)
secreted in...
acts as... 
without it...
if it becomes ineffective...
A

…the blood
…a chemical signal to cause other cells to take up glucose.
…people suffer diabetes
…leads to insulin resistance

65
Q

(Calcineurin)

is a…

A

…Heterodimeric protein
A-subunit = Catalytic subunit
B-subunit = Ca2+ binding subunit

66
Q

(Calcineurin)

A-subunit Domains:

A

Catalytic domain
B-subunit binding domain
Calmodulin binding domain
Autoinhibitory domain

67
Q

(Calcineurin)

B-subunit Domains:

A

Four EF hand domains

EF hand dom fun = bind Ca2+

68
Q

Beyond Quaternary Structure, proteins can have…

Example =

A

…even higher level multi-protein complexes

= Thick Filament in skeletal muscle

69
Q

Most (all?) proteins…

A

…bind to (or at least interact with) other molecules (at least transiently)

70
Q

What ever proteins bind to is called a

& type of bond?

A

ligand

& NON-COVALENT BONDS

71
Q

types of ligands: (6)

A
  1. ) Other proteins (structural, receptors)
  2. ) Substrates (enzymes)
  3. ) Membranes or membrane components (integral membrane proteins)
  4. ) Ions (ionic pumps, Ca2+ activated proteins, etc)
  5. ) Infectious agents (antibodies)
  6. ) DNA (transcription factors)
    etc. ..
72
Q

The portion of a protein that binds something is usually called a

A

binding domain (or binding site)

73
Q

The ________ of the binding domain for the ligand is dependent on…

A

affinity

…the amino acid composition of that region

74
Q

Binding strength is measured as

A

the Kd (dissociation constant)

75
Q

(Kd)
The formation of a ligand-protein complex (C) can be described by…

For this reaction, Kd =

A

… a 2-state process (P = Protein, L = Ligand):
C ↔ P + L

Kd = [P] x [L] / [C]

76
Q

(Kd)
If the reaction tends to favor the bound state (C), then…
If the reaction tends to favor the unbound (dissociated) state, then…

A

…the Kd will be small = Strong binding

…Kd will be large = Weak binding

77
Q

(Kd)
High Affinity =
Low Affinity =

*Note: Do not confuse Kd with

A

= Low Kd
= High Kd

*the equilibrium constant, Keq

78
Q

Kd is important for understanding…

Kd has units of…

A

…the functional properties of several types of proteins, including:

  1. ) Receptor proteins
  2. ) Enzymes
  3. ) Transporters

…M (Molarity)

79
Q

(Kd Example)
Protein P and drug D1 have a Kd = 0.1
Protein P and drug D2 have a Kd = 0.01
*Which drug has a stronger interaction with protein P?

A

drug D2

since it has a lower Kd = higher affinity

80
Q

At neutral pH the carboxyl and amino groups are…

A

…charged = Zwitterion (hybrid ion with 1 + and 1 - charge)

81
Q

Zwitterion =

A

= molecule with formal positive and negative charges on 2 different atoms and a net charge = 0

82
Q

@ pH 1 (acidic)

A

Low pH
High [H+]
Positive (+) charge

83
Q

@ pH 7 (neutral)

A

Neutral pH
Neutral [H+]
Net neutral charge
Zwitterion state

84
Q

@ pH 11 (basic)

A

High pH
Low [H+]
Negative (-) charge

85
Q

The electrical charge on the amino acid is dependent on

A

the pH

86
Q

However, in a polypeptide most of the carboxyl and amino groups are used for…
What can be charged?
Several R-groups can also be…

A 
...the peptide bonds and cannot be ionized
The carboxy (C-) and amino (N-) termini can be charged
...charged (we saw these previously), but the pH will influence their charges in the same way.
87
Q

(Aspartate & Glutamate (acidic))

@ low pH:

A

high [H+]
R-group carboxyl saturated with H
R-group uncharged

88
Q

(Aspartate & Glutamate (acidic))

@ neutral or high pH:

A

low [H+]
R-group carboxyl unsaturated with H
R-group (-) charged

89
Q

(Lysine & Arginine (basic))

@ neutral or low pH:

A

high [H+]
R-group amino(s) saturated with H
R-group (+) charged

90
Q

(Lysine & Arginine (basic))

@ high pH:

A

low [H+]
R-group amino(s) unsaturated with H
R-group uncharged

91
Q

(Histidine (imidazole ring))

  • The charged state of the imidazole ring has a pKa =
  • Which means that…
  • Therefore a small change in…
  • Also, because the pKa is…
  • Protein charge depends on…
  • Mainly due to…
A

= 6.8
…at pH 6.8 (near neutral) 1/2 of the histidines will be (+) and 1/2 neutral
…pH (in this range) will have a large influence on the charge of the imidazole ring
…near neutral, imidazole (histidines in proteins) can help “buffer” small changes in [H+]
…pH!
…Asp, Glu, Lys, Arg, (His)

92
Q

Each protein will have: (3)

However, at some pH, the positive and negative charges will…

The pH at which the protein is neutral is called…

A
  1. ) One Amino Terminus
  2. ) One Carboxyl terminus
  3. ) Variable number of charged amino acids

…cancel each other out and the protein will have no net charge

…the Isoelectric Point (pI)

93
Q

Different proteins have different

A

isoelectric points

94
Q

You can use pI to…

& 2 methods:

A

…isolate proteins

  1. ) Electrophoretically (isoelectric focusing)
  2. ) Solubility
95
Q

(pI)

The solubility of a protein in an aqueous environment will be lowest when…

A

…it has no net charge

96
Q

Isoelectric Focusing allows for

A

the separation of proteins based on their inherent pI’s

97
Q

*Note: At pH of 9 (high pH, low [H+]) carboxyl groups will be… Thus, the proteins will tend to…

A

…negative and amino groups uncharged

…be negatively charged and move to the positive pole

98
Q

You can also separate proteins based on their…

by using…

A

…size (molecular mass)

…SDS-PAGE

99
Q

Proteomics =

“proteome” is derived from…

A

= refers to all the proteins produced by an organism (or cell or tissue or even cell component)
…proteins expressed by a genome

100
Q

(Proteomics)

The identification of all the proteins in a specific proteome has largely depended on…

A

…knowing the pI and MW of each of the constituent proteins

101
Q 
Traditional method = 
Separate proteins based on...
Then separate them in a second dimension based on...
Allows for...
And allows for...
A

= 2D gel electrophoresis
…pI (isoelectric focusing)
…their molecular mass
…identification of a tremendous number of specific proteins in any one sample
…the identification of changes in any one component of the proteome under any experimental condition

102
Q

Other methods for studying proteins: (7)

A
  1. ) Native gel electrophoresis
  2. ) Western blotting
  3. ) Immunohistochemistry
  4. ) ELISA
  5. ) Capillary electrophoresis
  6. ) Mass Spectrometry
  7. ) Protein Arrays

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