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Biomolecules > Week 2 Lecture 3 and 4 > Flashcards

Week 2 Lecture 3 and 4 Flashcards

1
Q

What is the unit of mass used to measure protein mass?

A

The Dalton (Da) (often quoted in KDa)

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2
Q

What is 1Da the equivalent weight to?

A

1 hydrogen atom

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3
Q

What unit of distance is used to measure protein distances?

A

The Angstrom, 1A=1*10^-20m (0.1nm)

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4
Q

Give examples of structural proteins

A

Collagen, keratin, amelogenin

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5
Q

Give examples of movement proteins

A

Actin, myosin

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6
Q

Give examples of enzyme and catalyst proteins

A

Trypsin, DNA polymerase

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7
Q

Give examples of transport proteins

A

Haemoglobin, transferin

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8
Q

Give an example of hormone proteins

A

Insulin

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9
Q

What protein is reponsible for chromosome sorting?

A

Tubulin

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10
Q

How do proteins fold?

A

Spontaneously from linear chains of amino acids

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11
Q

What covalent forces stabilize protein structure?

A

Disulphide bridges (not all proteins have them)

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12
Q

What non-covalent forces stabilise protein structure?

A

Hydrogen bonds, electrostatic interactions, Van der Waals forces and hydrophobic effect

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13
Q

What is protein primary structure?

A

Sequence of aa in peptide chain, including disulphide linkages

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14
Q

What is secondary structure?

A

Local regions of folding/coiling of peptide chain (usually a helix or b sheet)

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15
Q

What is tertiary structure?

A

Overall conformation of peptide chain, chain folds upon itself

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16
Q

What is quaternary structure?

A

Folded peptide chains join together

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17
Q

What name is given to the directionality of polypeptides?

A

Polarity

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18
Q

In what direction is the order of residues read from?

A

Amino (N) terminal to carboxy (C) terminal

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19
Q

What is a protein?

A

Linear polymer of amino acids (1 or more polypeptide chain)

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20
Q

What bonds join amino acids?

A

Peptide bonds (called Amide bonds too)

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21
Q

What groups are found at the N terminal?

A

First amino acid has free NH3+ group

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22
Q

The last amino acid in a chain has what free group?

A

COO- group (C terminal)

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23
Q

The peptide bond is a ____ bond with ____ bond characteristics

A

Single bond

Double bond characteristics

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24
Q

How long is the distance between CO and NH groups in a peptide bond?

A

1.32Angstrom

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25
Q

Why is the distance between CO and NH groups shortened in a peptide bond?

A

Resonance structures: electron is skipping between C and N, bringing them closer together

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26
Q

What is the consequence of the peptide bond resonance strucutre?

A

Rotation cannot occur (planar orientation) which restricts chain conformation

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27
Q

In which two forms can a peptide bond exist?

A

Cis or trans

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28
Q

What form of peptide bond almost always exists?

A

Trans form (because of steric hinderance)

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29
Q

In what aa is trans form not always seen and why?

A

Proline, because of ring strucutre

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30
Q

Where is proline often found and why?

A

Corners and junctions due to steric hinderance in cis & trans orientation

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31
Q

Name an example of a dipeptide

A

Aspartame (Asp-Phe) artifical sweetner

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32
Q

Name an example of a tripeptide.

A

Glutathione: natural antioxidant

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33
Q

Name a short polypeptide hormone

A

Glucagon

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34
Q

Name a short polypeptide neurotransmitter

A

Substance P

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35
Q

Name a large protein

A

Dystrophin

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36
Q

What is a proteins backbone?

A

A regular repeating part called the main chain

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37
Q

Give an example of a protein where intrachain disulfide bridges link subunits

A

Insulin

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38
Q

In sickle cell anaemia, which BP change occurs which leads to primary structure change (and thus functional change)

A

Glutamic acid to valine

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39
Q

Amino acids are read in a _ to _ direction

A

N

C

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40
Q

Define secondary structure of a protein

A

The spatial arrangement of amino acids near to each other in the linear sequence

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41
Q

How does hydrogen bonding occur in proteins to give rise to the secondary strucutre?

A

Polar backbone (N donates H, O on C accepts H bond)

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42
Q

How is rotation is peptide backbone possible?

A

Around non-peptide bonds in the chain (2 possible angles)

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43
Q

Who proposed the alpha helix and beta pleated sheet?

A

Linus Pauling and Robert Corey (1952)

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44
Q

How are alpha helix formed?

A

H-bonds in the same polypeptide chain (backbone)

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45
Q

Where do the H bonds form in the alpha helix?

A

Peptide bond carbonly O and H of NH every 4th peptide

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46
Q

What direction is the alpha helix?

A

Right hand helix

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47
Q

What does the rigid cylinder shape of the alpha helix act as?

A

Architectural support for protein

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48
Q

How much rotation is there between residues in the alpha helix?

A

100 degrees

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49
Q

How many residues are there per turn on the alpha helix?

A

3.6

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50
Q

How far is the rise between each residue in an alpha helix?

A

1.5 angstrom

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51
Q

What is the diameter of the alpha helix coil?

A

around 5 angstrom

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52
Q

LH alpha helices possible but why do these no exist?

A

RH helices are more energetically favorable

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53
Q

What motif do many DNA binding proteins have?

A

Helix-turn-helix
or
Helix-loop-helix

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54
Q

What % of haemoglobin is an alpha helix?

A

60%

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55
Q

Why does proline end an alpha helix?

A

No H atom bound to nitrogen, no H bonding, structure resists rotation

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56
Q

What does the B sheet consist of?

A

2 or more strands of polypeptide called beta-strands

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57
Q

How are beta sheets different to alpha helix?

A

residues in beta sheets are almost fully extended

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58
Q

What are the two possible forms of beta sheet?

A

Antiparallel (opposite direction)

Parallel (same direction)

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59
Q

Which form of beta sheet lines up more neatly and so has a more regular structure?

A

Parallel

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60
Q

What occurs in antiparallel beta sheet?

A

Beta-hairpin bend (widespread in globular proteins)

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61
Q

Which type of beta sheet is more stable?

A

Antiparallel (H-bonding not distorted)

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62
Q

What is the distance between adjacent residues in a beta pleated sheet?

A

3.5 angstrom

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63
Q

Where are the side chains in the beta-pleated sheet?

A

Alternate above and below plane of strand

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64
Q

What type of protein consist largely of beta-sheet?Give an example.

A

Transmembrane proteins

e.g. porin

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65
Q

Typically how many strands are b-sheet formed from?

A

5 but up to 10

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66
Q

beta sheets are often ____.

A

Twisted

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67
Q

What properties do high % of beta sheet give?

A

High tensile strength, no elasticity

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68
Q

Name proteins with high % of b sheet

A

Fibrillar proteins (silk fibres fibroin)

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69
Q

Define tertiary structure of a protein

A

The spatial arrangement of amino acids usually far apart from each other in the primary sequence

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70
Q

Where is myoglobin found?

A

Muscles (act as oxygen reserve)

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71
Q

Myoglobin is made of how many polypeptide chains?

A

1

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72
Q

Define quaternary structure of a protein

A

The spatial arrangement in a protein made up from more than one polypeptide chain

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73
Q

Subunits can be the same (____) or different (____) polypeptides

A

Homo

Hetero

74
Q

Give an example of a homo polypeptide

A

Restriction enzymes

75
Q

Haemoglobin is a ____ protein with 2 identical alpha subunits and 2 identical beta subunits

A

Tetrameric

76
Q

What configuration foes haemoglobin have?

A

alpha 2 beta 2 configuration

77
Q

What does quaternary structure allow?

A

Smaller quantities of genetic material to create larger proteins and structures

78
Q

Give an example of quaternary structure allowing larger proteins/structures

A

Human rhinovirus uses 60 repeats of 4-unit structure to produce coat

79
Q

How does quaternary structure allow co-operative regulation of enzymes?

A

Allosteric effects (change in one subunit induces change in another)

80
Q

Name 4 types of post-translational modification

A

Acetylation, hydroxylation, glycosylation, phosphorylation

81
Q

Where are most proteins acetylated at?

A

Their N terminal amino acid

82
Q

Why are proteins acetylated?

A

Protects proteins (stabilises the protein) from degredation by aminopeptidases

83
Q

What residues within a protein can be acetylated within proteins?

A

Lysine

84
Q

In what organisms is acetylation found?

A

Eukaryotes only (not seen in mitochondria or chloroplasts)

85
Q

What % of proteins in the cytoplasm are acetylated?

A

60-90%

86
Q

What molecules are involved in acetylation?

A

Acetyl Coenzyme A

N-acetyl tranferase enzymes (NATS)

87
Q

Proteins that are N-terminally acetylated are often what type of proteins?

A

Structural

e.g. keratin

88
Q

How long can acetylation increase half-life of proteins by?

A

From seconds to hours or days

89
Q

How does acetylation protect proteins from degredation?

A

Proteases can’t bind to acetylated amino acids so can’t cleave them as well

90
Q

Lysine acetylation is associated with ?

A

Histones bound to transcriptionally active DNA

91
Q

How does acetylation help DNA get transcribed?

A

Reduces net + charge between histones and DNA, more open conformation, more transcriptional activity

92
Q

What enzymes remove acetyl modification on histones?

A

Histone deacetylases (HDACs)

93
Q

Chronic obstructive pulmonary disease is linked to what?

A

Decreased HDAC activity

94
Q

What is the effect of cigarette smoke deactivating histone deacetylases that causes the symptoms of COPD?

A

Inflammatory response cannot be turned off (HDAC2 is lost), permanent inflammatory response leads to lung breakdown

95
Q

What name is given to the protein modification that is the addition of an OH group?

A

Hydroxylation

96
Q

Which two residues can become hydroxylated?

A

Proline and lysine

97
Q

What name is given to hydroxylated proline and lysine?

A

(4 or 3)- Hydroxyproline

5-Hydroxylysine

98
Q

What is hydroxyproline a major component of?

A

Collagen

99
Q

Why is hydroxyproline key for the structural stability of collagen?

A

Hydroxyproline involved in H-bonding (OH is charged) within collagen fibre

100
Q

What repeat is found in the collagen sequence?

A

G-X-Y

G for glycine

101
Q

In what position is proline/hydroxyproline found in the G-X-Y repeat of collagen sequences/

A

Y position

15-30% is the hydroxyproline form

102
Q

What enzyme converts proline to hydroxyproline?

A

prolyl hydroxylase

103
Q

What does prolyl hydroxylase require to convert proline to hydroxyproline?

A

Cofactor ascorbic acid (vitamin C)

104
Q

What does a lack of Vit. C cause?

A

Scurvy

105
Q

What symptoms characterise scurvy?

A

Poor wound healing, easy bruising, loss of teeth, eventual death (due to weaker collagen)

106
Q

Who introduced the idea that the addition of fresh fruit and veg, particularly citrus fruit, could prevent scurvy?

A

James Lind

107
Q

What name is given to the modification of proteins in which sugar molecules are attached to specific residues in proteins?

A

Glycosylation

108
Q

In what organisms does glycosylation occur?

A

Eukaryotes only

109
Q

Where does glycosylation occur within eukaryotic cells?

A

Lumen of the ER and Golgi

110
Q

What are the two forms of glycosylation?

A

N-glycoslation

O-glycoslation

111
Q

What residue is glycoslated in N-glycoslation?

A

Asparagine (N)

112
Q

In what sequence does N-glycosylation occur?

A

N-X-S/T

Aspargine-any amino acid except proline-serine or threonine

113
Q

Are all possible glycosylation sites used for N-glycoslation?

A

No, not always modified

114
Q

What does the initial oligosaccharide involved in N-glycoslation consist of?

A

2 molecules glycosamine, 9 molecules mannose, 3 molecules of glucose

115
Q

What can happen to the initial oligosaccharide involved in N-glycoslation once attached?

A

Can be trimmed/undergo further elaboration

In the ER or golgi

116
Q

What does O-glycoslation involve?

A

Attachment of sugar to O groups of threonine and serine

117
Q

How is O-glycoslation different to N-glycoslation (other than residues being glycoslated)

A

No characteristic sequence involved

118
Q

What effect does glycoslation have on the solubility of proteins?

A

Makes them more soluble (easier to be secreted)

119
Q

What other effects can glycoslation have on proteins?

A

Some types can make them more prone to degredation

120
Q

Proteins that are secreted from cells often have what type of modification?

A

Glycosylated (e.g. immunoglobins, ABO blood system)

121
Q

What reversible form of post translational modification occurs in both pro and eukaryotes?

A

Phosphorylation

122
Q

What effect does phosphorylation often have on proteins?

A

Turns them on and off, such as in cascades

123
Q

Which residues can be phosphorylated?

A

Threonine, serine, tyrosine

124
Q

What part of the side chain of threonine, serine and lysine is phosphorylated?

A

OH group

125
Q

The phosphate group is ______ charged, so transfers this charge to the protein

A

Negatively

carries 2 negative charges

126
Q

What enzymes attach phosphate groups to proteins?

A

Kinases

127
Q

What enzyme removes phosphate groups from proteins?

A

Phosphotases

128
Q

Phosphotases are key in what regulation?

A

Enzyme regulation

129
Q

Kinases are highly selective, targeting particular residues in certain proteins. True or false?

A

True

130
Q

What sequence does protein kinase A modify?

A

R-R-X1-S/T-X2
X1 is a small residue
X2 is a large hydrophobic residue

131
Q

What two other types of PTM makes a protein a target for degredation?

A

Ubiquitination (adds ubiquitin)

Sumolation (ubiquitin-like modifier)

132
Q

Give an example of the PTM nucleotide addition.

A

Charging tRNA’s

133
Q

Name 4 more PTM examples

A

Nitrosylation
Sulfonylation
Cabonylation
Biotinylation

134
Q

Define protein cleavage

A

The process by which specific peptide bonds between amino acid residues are hydrolyzed

135
Q

What proteins perform cleavage between of peptide bonds?

A

Proteases

136
Q

Why are proteases required to cleave peptide bonds?

A

Proteins are very stable, unlikely to break down on their own

137
Q

What do different proteases have

A

Different specificities and functions

138
Q

Name three examples of families of proteases

A

Metalloproteases
Serine proteases
Aspartyl proteases

139
Q

Give an example of a metalloprotease

A

Carboxypeptidase A

140
Q

Give an example of a serine protease

A

Chymotrypsin

141
Q

Give an example of an aspartyl protease

A

HIV protease

142
Q

What are metalloproteases?

A

Proteases with metal ion in the active site of the enzyme

143
Q

What metal group is found in the active site of carboxypeptidase A?

A

Zinc (Zn2+)

144
Q

What is carboxypeptidase A?

A

A digestive enzyme found in the gut, break down proteins from the C terminal

145
Q

When does carboxypeptidase A function best?

A

When the residue is aliphatic

146
Q

Which are the three aliphatic residues that carboxypeptidase A works best on?

A

Val, Leu, Ile, Ala

147
Q

What characterises serine proteases?

A

Serine reisude in the active site

148
Q

What is chymotrypsin?

A

Digestive enzyme found in the gut

149
Q

What peptide bonds does chymotrypsin cleave?

A

Peptide bonds on carboxyl side of aromatic or large hydrophobic residues

150
Q

In what way does chymotrypsin break down a protein?

A

Starts in the middle of the chain, breaks it into smaller fragments which can be hydrolysed by other proteases

151
Q

What is the first role of HIV protease?

A

To cleave itself out of a large polypeptide chain produced from viral genetic material

152
Q

What does HIV protease do once it has cleaved itself out of the chain?

A

Chops up remaining bits of polypeptide into functional polypeptide

153
Q

Why is HIV protease a good drug target?

A

It is critical to viral replication

154
Q

What characterises aspartyl proteases?

A

Aspartic acid in the active site

155
Q

Why are proteins modified to turn them into their functional state?

A

Native state may need to be modified for protein to get its active state

156
Q

Why can’t proteins that have been cleaved renature after being denatured?

A

Primary sequence has changed, refolds differently once denatured

157
Q

Why are many proteins synthesised in a longer from than native chain and thus require cleaving?

A
  • Transit peptides
  • Longer chains assist in folding
  • Longer chains render protein inactive
158
Q

What type of proteases in particular are synthesized in their proprotein form?

A

Gastric proteases (shouldn’t be active until in stomach)

159
Q

What are pro-form gastric proteases called?

A

Zymogens

160
Q

Both carboxypeptidase S and chymotrypsin are initially synthesized as zymogen. These are cleaved by what?

A

Protease trypsin into active forms

161
Q

Define pro-protein

A

Any protein that is cleaved by a convertase to form a smaller protein or biologically active polypeptide

162
Q

Define pre-protein

A

A protein precursor that contains a signal peptide sequence

163
Q

What is a signal peptide sequence?

A

A nonpolar sequence at the head of the growing peptide chain required for transfer into cistern of ER

164
Q

What happens once a pre-protein is in the cistern of the ER?

A

Cleaved to from the protein or proprotein

165
Q

List bond types in order of strength

A 
Ionic (400-800)
Covalent (150-950)
Hydrogen (20-30)
Van der Waals (2-15)
kJ/mol
166
Q

Turns in proteins are primarily composed of _____ residues

A

Hydrophilic

167
Q

What residues are most commonly found in protein turns?

A

Glycine and proline

168
Q

What are most common turns called?

A

Beta-turns

169
Q

What are beta turnsformed from?

A

4 residues with glycine in 3rd position

170
Q

What are turns often involved in?

A

Interactions with other proteins (thus are often on protein surface)

171
Q

What bonding occurs in beta turns between residues?

A

CO group on 1st residue in turn hydrogen bonds to NH group in 4th residue

172
Q

What is myoglobin?

A

Red pigment in muscle, oxygen store for intense activity

173
Q

What molecule is found in the hydrophobic centre of myoglobin?

A

Haem

174
Q

Haem has a ____ oxygen affinity

A

High

175
Q

What is the structure of collagen?

A 
Triple superhelix (tropocollagen)
Left-handed
176
Q

How long is collagen and how wide?

A

3000Angstrom

15 Angstrom

177
Q

How is collagen held together?

A

Every third residue in helix is glycine, held together by electrostatic forces, H bonding occurs between strands (not within)

178
Q

Why is glycine localised to the interior of the helical bundles of collagen?

A

Only residue that fits due to steric hinderance

179
Q

Collagen is made in the ER as?

A

Procollagen (preprotein)

180
Q

How are collagen fibrils folded and assembled?

A

Help of chaperones

181
Q

Where is collagen cleaved to tropocollagen?

A

in the ECM

Biomolecules (3 decks)

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