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BIOCHEM > Proteins > Flashcards

Proteins Flashcards

1
Q

What is a protein?

A

Linear polymers of amino acids

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2
Q

What is a peptide bond formation?

A

The creation of an amide bond between the carboxyl group (-COO) of one amino acid and the amino group (-NH3) of another amino acid

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3
Q

What is the structure of the backbone of a protein chain?

A

Repeated sequence (N-Ca-C)

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3
Q

Three things that create a peptide bond formation

A
  1. Amide bond
    Between
  2. Carboxyl group (-COO) of amino acid
  3. Amino group (-NH3) of another amino acid
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3
Q

Most proteins use _____ amino acids

A

all

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3
Q

What is Ribonuclease?

A

The enzyme that breaks down RNA molecules

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3
Q

R-side chains (inside) are _____

A

Hydrophobic

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3
Q

The atoms around the peptide bond (CO-NH) are ____________

A

Coplanar

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4
Q

Outside of proteins are __________

A

Hydrophilic

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5
Q

How was the phylogenetic tree constructed?

A

By comparing the amino acid sequences of the protein cytochrome c

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6
Q

What are the two terminal ends of proteins?

A

-Amino terminal end (HOOC)
- Carboxyl terminal end (NH2)

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7
Q

What type of bond are disulfide bonds?

A

Covalent bonds

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8
Q

Do proteins have spaces?

A

No

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9
Q

What is lysosome?

A

An extracellular protein

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10
Q

How many disulfide bonds are in a protein?

A

Any number

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11
Q

List the sizes of proteins from smallest to largest

A

Insulin, cytochrome, ribonuclease, lysosome, myoglobin, hemoglobin, immunoglobin, glutamine sythetase

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12
Q

Shape of insulin

A

A + B chain

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13
Q

Shape of cytochrome

A

Single chain

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14
Q

Shape of ribonuclease

A

Single chain

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15
Q

Shape of lysozyme

A

Single chain

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16
Q

Shape of myoglobin

A

Single chain

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17
Q

Shape of hemoglobin

A

4 chains
(2 alpha)
(2 beta)

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18
Q

Shape of immunoglobulin

A

4 chains

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19
Q

Shape of glutamine synthetase

A

12 chains

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20
Q

Where are the number of amino acid changes listed on the phylogenetic tree?

A

The number of amino acid changes are given on the branches

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21
Q

What is released during a peptide/amide bond formation?

A

Water

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22
Q

A phylogentic tree compares amino acid sequences of the protein ______

A

Cytochrome C

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23
Q

_____ proteins require something bound to them to activate

A

Conjugated

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24
Q

The binding of nonprotein groups affect protein ____

A

Folding

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25
Q

Glycoproteins contain ____

A

Carbohydrates

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26
Q

Lipoproteins contain _____

A

Lipids

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27
Q

Nucleoprotein complexes contain ___

A

Nucleic acid

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28
Q

Phosphoproteins contain _____

A

Phosphate

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29
Q

Metalloproteins contain _____

A

Metal atoms

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30
Q

Hemoproteins contain _____

A

Heme

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31
Q

Flavoproteins contain ____

A

Flavin

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32
Q

Glyco means

A

Carbohydrate

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33
Q

Lipo means

A

Lipid

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34
Q

Nucleo means

A

DNA or RNA

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35
Q

Metallo means

A

Metal ion

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36
Q

Biological functions of proteins:

Enzymes

A

Ribonuclease, trypsin

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37
Q

Biological functions of proteins:

Regulatory proteins

A

Insulin, transcription factor NF -1

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38
Q

Biological functions of proteins:

Transport Proteins

A

Hemoglobin, glucose transporter

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39
Q

Biological functions of proteins:

Storage Proteins

A

Casein, ovalbumin

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40
Q

Biological functions of proteins:

Contractile, Motile Proteins

A

Actin, myosin, tubulin

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41
Q

Biological functions of proteins:

Structural Proteins

A

Collagen, a-keratin
(Hair & fingernails)

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42
Q

Biological functions of proteins:

Protective Proteins

A

Immunoglobulins, fibrinogen
(antibodies)

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43
Q

Biological functions of proteins:

Exotic Proteins

A

antifreeze proteins, glue proteins

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44
Q

Protein Techniques:

Chromatography

A
  • ion exchange chromatography
  • size exclusion chromatography
  • affinity chromatography
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45
Q

Ion exchange chromatography

A

Separates proteins on the basis of their overall charge

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46
Q

Size exclusion chromatography

A

Separates proteins on the basis of size

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47
Q

Affinity chromatography

A

Separates proteins on the basis of affinity (specific binding to small molecules)

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48
Q

Protein Techniques:

Electrophoresis

A
  • SDS-PAGE
  • Isoelectric focusing
  • Two dimensional gel electrophoresis
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49
Q

SDS-PAGE electrophoresis

A

Separates proteins on the basis of molecular weight

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50
Q

Isoelectric focusing

A

Separates proteins on the basis of Isoelectric point (pI)

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51
Q

Electrophoresis

A

The movement in an electric field

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52
Q

Two dimensional gel electrophoresis

A

Separates proteins on the basis of isoelectric point (pl) and molecular weight (a) + (b)

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53
Q

Protein Shape:

Fibrous Proteins

A
  • Linear, serve structural roles
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54
Q

Protein Shape:

Globular Proteins (aq environment)

A
  • Hydrophobic on amino acids on inside
  • Hydrophilic amino acids on outside
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55
Q

Protein Shape:

Membrane Proteins (hydrophobic environment)

A
  • Interact with membrane lipids
  • Hydrophobic amino acids on *outside
  • in entirely different environment than globular proteins
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56
Q

Collagen is an example of what protein shape?

A

Fibrous protein

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57
Q

Myoglobin is an example of what protein shape?

A

Globular protein

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58
Q

Bacteriorhodopsin is an example of what protein shape?

A

Membrane protein

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59
Q

What is primary structure?

A

Amino acid sequence of a protein

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60
Q

What is secondary structure?

A
  • Short range 3D structure in a protein
  • Localized conformation of the polypeptide backbone
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61
Q

What are the two types of secondary structure?

A
  1. a-helix
  2. b-strand
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62
Q

What causes a secondary structure?

A

Due to H-bonding of backbone atoms (-CO-NH-)

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63
Q

What is tertiary structure?

A

Folding of a polypeptide into its 3D shape

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64
Q

What causes a tertiary structure?

A

Due to R-side chain interactions

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65
Q

What are the 4 properties of tertiary structures?

A

1.Hydrophobic
2. H-bonding
3. Charge
4. Disulfide bonds

lots of weak interactions make strong interaction

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66
Q

What are quaternary structures?

A
  • Numbers and kinds of polypeptide subunits in a protein
  • Polypeptide chains in a protein with multiple subunits
67
Q

What are the levels of protein structure?

A

Primary, secondary, tertiary, quaternary

68
Q

What does the sequence of amino acids that go from the amino terminal end to the carboxyl terminal end tell you?

A
  1. What type of protein
  2. Function of protein
  3. Everything you need to know about proteins
69
Q

What causes the a-helix in secondary structure?

A

H-bonding along one strand

70
Q

What causes the b-strand in secondary structure?

A

H-bonding between two or more strands

71
Q

In secondary structure, each C=O is _____ _____ to the N-H group ____ ____ _____ along the chain

A

hydrogen bonded, four amino acids

72
Q

What are the two types of the B-strand in secondary structures?

A
  1. Parallel
  2. Antiparallel
  • Can both exist in the same protein
  • Can form extensive B-pleated sheet structures
73
Q

This type of secondary structure is formed by hydrogen bonding of C=O and N-H groups along the backbone of a single polypeptide chain

A

a-helix

74
Q

How many amino acid residues per turn of the helix?

A

3.6 amino acids per turn of the helix

75
Q

Is the a-helix left or right handed?

A

Right handed

76
Q

What is the pitch of the a-helix?

A

5.4A

77
Q

What is the diameter of the a-helix?

A

6A

78
Q

What stabilizes the a-helix structure?

A

Hydrogen bonds

79
Q

Are the B-strands hydrogen bonding between or within strands?

A

The hydrogen bonding is between strands

80
Q

What is the arrangment of B-strands in the secondary structure?

A

Parallel and antiparallel

81
Q

Are parallel B-strands linear or bent?

A

Bent

82
Q

Are antiparallel B-strands linear or bent?

A

Linear

83
Q

The ______ B-strand is the most common

A

Antiparallel

84
Q

The ____ B-strand is the strongest

A

Antiparallel

85
Q

The four horizontal ______ form an antiparallel B-Plated sheet with _____ strands in _____ directions

A

B-strands, adjacent, opposite

86
Q

B-pleated sheets follow the __ and ____

A

peaks and valleys

87
Q

Antiparallel B-plated sheets are very ____

A

stable

88
Q

B-turn is a ____ _____ in the ______ _____ that allows the strand to _____ its direction

A

sharp bend
polypeptide chain
reverse

89
Q

The B-turn ____ the direction of the strand

A

reverses

90
Q

Tertiary structure is the _______ of a ____ _____ ___ in 3D

A

folding, single polypeptide chain

91
Q

Globular proteins contain segments of both ____ and ____, while fibrous proteins have _____ ____ ____

A

a-helix, b-strand, specialized tertiary structure

92
Q

What three things make up fibrous proteins?

A
  1. Collagen
  2. a-keratin
  3. Fibroin and B-keratin
93
Q

The special collagen helix consists of three interwined polypeptide chains

A

Collagen

94
Q

Formed by the coiling of a-helices

A

a-keratin

95
Q

Consists primarily of B-sheet

A

B-keratin

96
Q

What is tropocollagen?

A

A triple helix

97
Q

What is the main protein of connective tissue?

A

Collagen

98
Q

Makes up 25-35% of the whole body

A

Collagen

99
Q

How many common types of collagen are there?

A

28 types

100
Q

Type l collagen -

A

Most abundant, found in tendons, ligaments, skin, blood vessels, bone

101
Q

Type ll collagen -

A

Cartilage, found in joints between bones, rib cage, nose, ears

102
Q

What is the sequence of formation of tropocollagen and collagen?

A
  1. Procollagen
  2. Tropocollagen
  3. Cross-linked fiber
103
Q

Amino & carboxyl terminal ends - peptides DO NOT twist together

A

Procollagen

104
Q

Protein component of skin, hair, fingernails are made up of _____

A

a-keratin

104
Q

Cute amino & carboxyl terminal ends of procollagen

A

Peptidases

104
Q

2 coiled coils (4 a-helices)

A

protofilament

105
Q

4 protofibrils (32 a-helices)

A

intermediate filament

105
Q

2 protofilaments (8 a-helices)

A

protofibril

106
Q

Two a-helices

A

coiled coil

107
Q

Pair of coiled coils

A

protofilament

108
Q

Four right hand twisted protofibrils

A

filament

109
Q

Disulfide bond formation creates ____ in hair

A

curls

110
Q

Main silk protein

A

Fibroin

111
Q

B-sheet of _____

A

Fibroin

112
Q

Component of bird feathers, beaks, claws

A

B-Keratin

113
Q

Antiparallel arrangement of B-sheet

A

Strands in opposite directions

114
Q

Parallel arrangement of B-sheet

A

Strands in same direction

115
Q

Antiparallel or parallel arrangment most stable?

A

Antiparallel

116
Q

Globular proteins can be classified according to the type and arrangement of secondary structure:

A
  • All a-helix proteins
  • All b-strand proteins
  • a/B proteins
  • Proteins with little secondary structure
117
Q

What are the four classes of globular protein structures? (ABBA LSS)

A
  • All a-helix proteins
  • All b-strand proteins
  • a/B proteins
  • Proteins with little secondary structure
118
Q

A typical globular protein is _____

A

ribonuclease

119
Q

Example of a-helix

A

growth hormone

120
Q

Example of a b-strand

A

yB-crystallin (lens cornea of eye)

121
Q

Example of a/B proteins

A

Flavodoxin (bacteria)

122
Q

Example of protein with little secondary structure

A

Tachystatin (antimicrobial peptide)

123
Q

What type of globular protein is ribonuclease?

A

a/B protein

124
Q

Protein domains are also known as ____

A

modules

125
Q

Protein domains or modules are ___ ____ ____ that are used repeatedly in the same protein or that are found in different proteins

A

amino acid sequences

126
Q

How main amino acids does a protein domain typically contain?

A

40-100

127
Q

Produced by the duplication of DNA segments within a gene or by the insertion of a copy of DNA segment into another gene

A

Protein domains

128
Q

Protein domains are produced by the _____ of DNA segments within a gene

A

protein domains

129
Q

Protein domains can be produced by the ____ of a copy of a DNA segments into another gene

A

insertion

130
Q

Protein domains are produced by _____ or _____ of DNA segments

A

duplication or insertation

131
Q

___ ____ are amino acid sequences used repeatedly in a single protein or that are found in different proteins

A

Protein domains/modules

132
Q

What type of protein domain is unusual and less common?

A

different proteins

133
Q

Domains in the ____ occur from faulty DNA replication

A

same protein

134
Q

Domains in ____ occur after the insertion of a copy of a DNA segment into another gene

A

different proteins

135
Q

Some domains are ___ and their function is unknown

A

neutral

136
Q

Domains ___ over time and become unrecognizable to the original

A

mutate

137
Q

Protein folding is the process of folding a _____ ___ into a ___ ___ with a precise 3D structure

A

polypeptide chain, globular protein

138
Q

Step 1 of protein folding

A
  1. newly synthesized polypeptide first forms segments of secondary structure (a-helix & B-sheet)
139
Q

Step 2 of protein folding

A
  1. These coalesce into a globular structure, primarily through hydrophobic interactions
140
Q

Step 3 of protein folding

A
  1. The final stable tertiary structure is generated by small adjustments to the folded structure
141
Q

Step 4 of protein folding

A
  1. In the cell, protein folding may require the assistance of molecular chaperones
142
Q

In general the #D of folding of extended protein chain is dependent upon the ___ ___ ___ of that protein chain

A

amino acid sequence

143
Q

(1) protein folding: A newly synthesized protein first forms segments of ___ ___

A

secondary structure

144
Q

(2) protein folding: secondary structure of polypeptides arrange into a ____ shape by _____ interactions

A

globular, hydrophobic

145
Q

(3) protein folding: final stable tertiary structure is generated by ____ _____ to the folded structure

A

small adjustments

146
Q

Secondary structure of polypeptide arrange into a globular shape by _____ ____

A

hydrophobic interactions

147
Q

(4) protein folding: Protein folding may need the assistance of ___ ___

A

molecular chaperones

148
Q

Amyloid deposits

A

misfolded, insoluble, and aggregated proteins in brain cells

149
Q

Two examples of amyloid deposits

A

Alzheimer’s disease
Parkinson’s disease

150
Q

What protein is misfolded in Alzheimers disease?

A

amyloid-B

151
Q

What protein is misfolded in Parkinson’s disease?

A

a-synuclein

152
Q

(1) step globular protein folding

A

rapid and reversible formation of local secondary structure (a-helix, B-strand)

153
Q

(2) step globular protein folding

A

establishment of partially folded intermediates

154
Q

(3) step globular protein folding

A

final tertiary structure

155
Q

The association of protein subunits to form multi-subunit complexes is ____

A

quaternary structure

156
Q

Do all proteins have quaternary structure?

A

NO

157
Q

Proteins with quaternary structure are composed of ____ subunits or ____ types of ____ ____

A

identical , different, protein chains

158
Q

The ____ producing quaternary structure are the same as those responsible for tertiary structure

A

forces

159
Q

What four forces are involved in tertiary and quaternary structures?

A
  • hydrophobic int
  • hydrogen bonding
  • ionic int
  • disulfide bons
160
Q

Quaternary structure allows for ___ ____ between protein subunits

A

cooperative behavior

161
Q

In hemoglobin, there are ___ subunits

A

4

162
Q

How does hemoglobin exhibit cooperative behavior?

A

The binding of the first O2 molecule makes it easier for three other O2 molecules to each bind to a subunit

163
Q

Hemoglobin aides in what physiological function?

A

rapid release of O2 into the lungs

164
Q

What are the two types of quaternary structure?

A
  • fixed number of subunits
  • open structure of microtubules
165
Q

What are microtubules?

A

long, hollow tubes

166
Q

Where are microtubules found?

A

cytoskeletion (cell structure)
mitotic spindles (cell division process)

167
Q

Tubulin dimers ___ to form microbtubules

A

polymerize

168
Q

Microtubules are dynamic and can easily ___

A

increase or decrease in length

169
Q

Microtubules have ___ quaternary structure

A

open

BIOCHEM (16 decks)

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