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)
2
Q
What is 1Da the equivalent weight to?
A
1 hydrogen atom
3
Q
What unit of distance is used to measure protein distances?
A
The Angstrom, 1A=1*10^-20m (0.1nm)
4
Q
Give examples of structural proteins
A
Collagen, keratin, amelogenin
5
Q
Give examples of movement proteins
A
Actin, myosin
6
Q
Give examples of enzyme and catalyst proteins
A
Trypsin, DNA polymerase
7
Q
Give examples of transport proteins
A
Haemoglobin, transferin
8
Q
Give an example of hormone proteins
A
Insulin
9
Q
What protein is reponsible for chromosome sorting?
A
Tubulin
10
Q
How do proteins fold?
A
Spontaneously from linear chains of amino acids
11
Q
What covalent forces stabilize protein structure?
A
Disulphide bridges (not all proteins have them)
12
Q
What non-covalent forces stabilise protein structure?
A
Hydrogen bonds, electrostatic interactions, Van der Waals forces and hydrophobic effect
13
Q
What is protein primary structure?
A
Sequence of aa in peptide chain, including disulphide linkages
14
Q
What is secondary structure?
A
Local regions of folding/coiling of peptide chain (usually a helix or b sheet)
15
Q
What is tertiary structure?
A
Overall conformation of peptide chain, chain folds upon itself
16
Q
What is quaternary structure?
A
Folded peptide chains join together
17
Q
What name is given to the directionality of polypeptides?
A
Polarity
18
Q
In what direction is the order of residues read from?
A
Amino (N) terminal to carboxy (C) terminal
19
Q
What is a protein?
A
Linear polymer of amino acids (1 or more polypeptide chain)
20
Q
What bonds join amino acids?
A
Peptide bonds (called Amide bonds too)
21
Q
What groups are found at the N terminal?
A
First amino acid has free NH3+ group
22
Q
The last amino acid in a chain has what free group?
A
COO- group (C terminal)
23
Q
The peptide bond is a ____ bond with ____ bond characteristics
A
Single bond
Double bond characteristics
24
Q
How long is the distance between CO and NH groups in a peptide bond?
A
1.32Angstrom
25
Why is the distance between CO and NH groups shortened in a peptide bond?
Resonance structures: electron is skipping between C and N, bringing them closer together
26
What is the consequence of the peptide bond resonance strucutre?
Rotation cannot occur (planar orientation) which restricts chain conformation
27
In which two forms can a peptide bond exist?
Cis or trans
28
What form of peptide bond almost always exists?
Trans form (because of steric hinderance)
29
In what aa is trans form not always seen and why?
Proline, because of ring strucutre
30
Where is proline often found and why?
Corners and junctions due to steric hinderance in cis & trans orientation
31
Name an example of a dipeptide
Aspartame (Asp-Phe) artifical sweetner
32
Name an example of a tripeptide.
Glutathione: natural antioxidant
33
Name a short polypeptide hormone
Glucagon
34
Name a short polypeptide neurotransmitter
Substance P
35
Name a large protein
Dystrophin
36
What is a proteins backbone?
A regular repeating part called the main chain
37
Give an example of a protein where intrachain disulfide bridges link subunits
Insulin
38
In sickle cell anaemia, which BP change occurs which leads to primary structure change (and thus functional change)
Glutamic acid to valine
39
Amino acids are read in a _ to _ direction
N
| C
40
Define secondary structure of a protein
The spatial arrangement of amino acids near to each other in the linear sequence
41
How does hydrogen bonding occur in proteins to give rise to the secondary strucutre?
Polar backbone (N donates H, O on C accepts H bond)
42
How is rotation is peptide backbone possible?
Around non-peptide bonds in the chain (2 possible angles)
43
Who proposed the alpha helix and beta pleated sheet?
Linus Pauling and Robert Corey (1952)
44
How are alpha helix formed?
H-bonds in the same polypeptide chain (backbone)
45
Where do the H bonds form in the alpha helix?
Peptide bond carbonly O and H of NH every 4th peptide
46
What direction is the alpha helix?
Right hand helix
47
What does the rigid cylinder shape of the alpha helix act as?
Architectural support for protein
48
How much rotation is there between residues in the alpha helix?
100 degrees
49
How many residues are there per turn on the alpha helix?
3.6
50
How far is the rise between each residue in an alpha helix?
1.5 angstrom
51
What is the diameter of the alpha helix coil?
around 5 angstrom
52
LH alpha helices possible but why do these no exist?
RH helices are more energetically favorable
53
What motif do many DNA binding proteins have?
Helix-turn-helix
or
Helix-loop-helix
54
What % of haemoglobin is an alpha helix?
60%
55
Why does proline end an alpha helix?
No H atom bound to nitrogen, no H bonding, structure resists rotation
56
What does the B sheet consist of?
2 or more strands of polypeptide called beta-strands
57
How are beta sheets different to alpha helix?
residues in beta sheets are almost fully extended
58
What are the two possible forms of beta sheet?
Antiparallel (opposite direction)
| Parallel (same direction)
59
Which form of beta sheet lines up more neatly and so has a more regular structure?
Parallel
60
What occurs in antiparallel beta sheet?
Beta-hairpin bend (widespread in globular proteins)
61
Which type of beta sheet is more stable?
Antiparallel (H-bonding not distorted)
62
What is the distance between adjacent residues in a beta pleated sheet?
3.5 angstrom
63
Where are the side chains in the beta-pleated sheet?
Alternate above and below plane of strand
64
What type of protein consist largely of beta-sheet?Give an example.
Transmembrane proteins
| e.g. porin
65
Typically how many strands are b-sheet formed from?
5 but up to 10
66
beta sheets are often ____.
Twisted
67
What properties do high % of beta sheet give?
High tensile strength, no elasticity
68
Name proteins with high % of b sheet
Fibrillar proteins (silk fibres fibroin)
69
Define tertiary structure of a protein
The spatial arrangement of amino acids usually far apart from each other in the primary sequence
70
Where is myoglobin found?
Muscles (act as oxygen reserve)
71
Myoglobin is made of how many polypeptide chains?
1
72
Define quaternary structure of a protein
The spatial arrangement in a protein made up from more than one polypeptide chain
73
Subunits can be the same (____) or different (____) polypeptides
Homo
| Hetero
74
Give an example of a homo polypeptide
Restriction enzymes
75
Haemoglobin is a ____ protein with 2 identical alpha subunits and 2 identical beta subunits
Tetrameric
76
What configuration foes haemoglobin have?
alpha 2 beta 2 configuration
77
What does quaternary structure allow?
Smaller quantities of genetic material to create larger proteins and structures
78
Give an example of quaternary structure allowing larger proteins/structures
Human rhinovirus uses 60 repeats of 4-unit structure to produce coat
79
How does quaternary structure allow co-operative regulation of enzymes?
Allosteric effects (change in one subunit induces change in another)
80
Name 4 types of post-translational modification
Acetylation, hydroxylation, glycosylation, phosphorylation
81
Where are most proteins acetylated at?
Their N terminal amino acid
82
Why are proteins acetylated?
Protects proteins (stabilises the protein) from degredation by aminopeptidases
83
What residues within a protein can be acetylated within proteins?
Lysine
84
In what organisms is acetylation found?
Eukaryotes only (not seen in mitochondria or chloroplasts)
85
What % of proteins in the cytoplasm are acetylated?
60-90%
86
What molecules are involved in acetylation?
Acetyl Coenzyme A
| N-acetyl tranferase enzymes (NATS)
87
Proteins that are N-terminally acetylated are often what type of proteins?
Structural
| e.g. keratin
88
How long can acetylation increase half-life of proteins by?
From seconds to hours or days
89
How does acetylation protect proteins from degredation?
Proteases can't bind to acetylated amino acids so can't cleave them as well
90
Lysine acetylation is associated with ?
Histones bound to transcriptionally active DNA
91
How does acetylation help DNA get transcribed?
Reduces net + charge between histones and DNA, more open conformation, more transcriptional activity
92
What enzymes remove acetyl modification on histones?
Histone deacetylases (HDACs)
93
Chronic obstructive pulmonary disease is linked to what?
Decreased HDAC activity
94
What is the effect of cigarette smoke deactivating histone deacetylases that causes the symptoms of COPD?
Inflammatory response cannot be turned off (HDAC2 is lost), permanent inflammatory response leads to lung breakdown
95
What name is given to the protein modification that is the addition of an OH group?
Hydroxylation
96
Which two residues can become hydroxylated?
Proline and lysine
97
What name is given to hydroxylated proline and lysine?
(4 or 3)- Hydroxyproline
| 5-Hydroxylysine
98
What is hydroxyproline a major component of?
Collagen
99
Why is hydroxyproline key for the structural stability of collagen?
Hydroxyproline involved in H-bonding (OH is charged) within collagen fibre
100
What repeat is found in the collagen sequence?
G-X-Y
| G for glycine
101
In what position is proline/hydroxyproline found in the G-X-Y repeat of collagen sequences/
Y position
| 15-30% is the hydroxyproline form
102
What enzyme converts proline to hydroxyproline?
prolyl hydroxylase
103
What does prolyl hydroxylase require to convert proline to hydroxyproline?
Cofactor ascorbic acid (vitamin C)
104
What does a lack of Vit. C cause?
Scurvy
105
What symptoms characterise scurvy?
Poor wound healing, easy bruising, loss of teeth, eventual death (due to weaker collagen)
106
Who introduced the idea that the addition of fresh fruit and veg, particularly citrus fruit, could prevent scurvy?
James Lind
107
What name is given to the modification of proteins in which sugar molecules are attached to specific residues in proteins?
Glycosylation
108
In what organisms does glycosylation occur?
Eukaryotes only
109
Where does glycosylation occur within eukaryotic cells?
Lumen of the ER and Golgi
110
What are the two forms of glycosylation?
N-glycoslation
| O-glycoslation
111
What residue is glycoslated in N-glycoslation?
Asparagine (N)
112
In what sequence does N-glycosylation occur?
N-X-S/T
| Aspargine-any amino acid except proline-serine or threonine
113
Are all possible glycosylation sites used for N-glycoslation?
No, not always modified
114
What does the initial oligosaccharide involved in N-glycoslation consist of?
2 molecules glycosamine, 9 molecules mannose, 3 molecules of glucose
115
What can happen to the initial oligosaccharide involved in N-glycoslation once attached?
Can be trimmed/undergo further elaboration
| In the ER or golgi
116
What does O-glycoslation involve?
Attachment of sugar to O groups of threonine and serine
117
How is O-glycoslation different to N-glycoslation (other than residues being glycoslated)
No characteristic sequence involved
118
What effect does glycoslation have on the solubility of proteins?
Makes them more soluble (easier to be secreted)
119
What other effects can glycoslation have on proteins?
Some types can make them more prone to degredation
120
Proteins that are secreted from cells often have what type of modification?
Glycosylated (e.g. immunoglobins, ABO blood system)
121
What reversible form of post translational modification occurs in both pro and eukaryotes?
Phosphorylation
122
What effect does phosphorylation often have on proteins?
Turns them on and off, such as in cascades
123
Which residues can be phosphorylated?
Threonine, serine, tyrosine
124
What part of the side chain of threonine, serine and lysine is phosphorylated?
OH group
125
The phosphate group is ______ charged, so transfers this charge to the protein
Negatively
| carries 2 negative charges
126
What enzymes attach phosphate groups to proteins?
Kinases
127
What enzyme removes phosphate groups from proteins?
Phosphotases
128
Phosphotases are key in what regulation?
Enzyme regulation
129
Kinases are highly selective, targeting particular residues in certain proteins. True or false?
True
130
What sequence does protein kinase A modify?
R-R-X1-S/T-X2
X1 is a small residue
X2 is a large hydrophobic residue
131
What two other types of PTM makes a protein a target for degredation?
Ubiquitination (adds ubiquitin)
| Sumolation (ubiquitin-like modifier)
132
Give an example of the PTM nucleotide addition.
Charging tRNA's
133
Name 4 more PTM examples
Nitrosylation
Sulfonylation
Cabonylation
Biotinylation
134
Define protein cleavage
The process by which specific peptide bonds between amino acid residues are hydrolyzed
135
What proteins perform cleavage between of peptide bonds?
Proteases
136
Why are proteases required to cleave peptide bonds?
Proteins are very stable, unlikely to break down on their own
137
What do different proteases have
Different specificities and functions
138
Name three examples of families of proteases
Metalloproteases
Serine proteases
Aspartyl proteases
139
Give an example of a metalloprotease
Carboxypeptidase A
140
Give an example of a serine protease
Chymotrypsin
141
Give an example of an aspartyl protease
HIV protease
142
What are metalloproteases?
Proteases with metal ion in the active site of the enzyme
143
What metal group is found in the active site of carboxypeptidase A?
Zinc (Zn2+)
144
What is carboxypeptidase A?
A digestive enzyme found in the gut, break down proteins from the C terminal
145
When does carboxypeptidase A function best?
When the residue is aliphatic
146
Which are the three aliphatic residues that carboxypeptidase A works best on?
Val, Leu, Ile, Ala
147
What characterises serine proteases?
Serine reisude in the active site
148
What is chymotrypsin?
Digestive enzyme found in the gut
149
What peptide bonds does chymotrypsin cleave?
Peptide bonds on carboxyl side of aromatic or large hydrophobic residues
150
In what way does chymotrypsin break down a protein?
Starts in the middle of the chain, breaks it into smaller fragments which can be hydrolysed by other proteases
151
What is the first role of HIV protease?
To cleave itself out of a large polypeptide chain produced from viral genetic material
152
What does HIV protease do once it has cleaved itself out of the chain?
Chops up remaining bits of polypeptide into functional polypeptide
153
Why is HIV protease a good drug target?
It is critical to viral replication
154
What characterises aspartyl proteases?
Aspartic acid in the active site
155
Why are proteins modified to turn them into their functional state?
Native state may need to be modified for protein to get its active state
156
Why can't proteins that have been cleaved renature after being denatured?
Primary sequence has changed, refolds differently once denatured
157
Why are many proteins synthesised in a longer from than native chain and thus require cleaving?
- Transit peptides
- Longer chains assist in folding
- Longer chains render protein inactive
158
What type of proteases in particular are synthesized in their proprotein form?
Gastric proteases (shouldn't be active until in stomach)
159
What are pro-form gastric proteases called?
Zymogens
160
Both carboxypeptidase S and chymotrypsin are initially synthesized as zymogen. These are cleaved by what?
Protease trypsin into active forms
161
Define pro-protein
Any protein that is cleaved by a convertase to form a smaller protein or biologically active polypeptide
162
Define pre-protein
A protein precursor that contains a signal peptide sequence
163
What is a signal peptide sequence?
A nonpolar sequence at the head of the growing peptide chain required for transfer into cistern of ER
164
What happens once a pre-protein is in the cistern of the ER?
Cleaved to from the protein or proprotein
165
List bond types in order of strength
```
Ionic (400-800)
Covalent (150-950)
Hydrogen (20-30)
Van der Waals (2-15)
kJ/mol
```
166
Turns in proteins are primarily composed of _____ residues
Hydrophilic
167
What residues are most commonly found in protein turns?
Glycine and proline
168
What are most common turns called?
Beta-turns
169
What are beta turnsformed from?
4 residues with glycine in 3rd position
170
What are turns often involved in?
Interactions with other proteins (thus are often on protein surface)
171
What bonding occurs in beta turns between residues?
CO group on 1st residue in turn hydrogen bonds to NH group in 4th residue
172
What is myoglobin?
Red pigment in muscle, oxygen store for intense activity
173
What molecule is found in the hydrophobic centre of myoglobin?
Haem
174
Haem has a ____ oxygen affinity
High
175
What is the structure of collagen?
```
Triple superhelix (tropocollagen)
Left-handed
```
176
How long is collagen and how wide?
3000Angstrom
| 15 Angstrom
177
How is collagen held together?
Every third residue in helix is glycine, held together by electrostatic forces, H bonding occurs between strands (not within)
178
Why is glycine localised to the interior of the helical bundles of collagen?
Only residue that fits due to steric hinderance
179
Collagen is made in the ER as?
Procollagen (preprotein)
180
How are collagen fibrils folded and assembled?
Help of chaperones
181
Where is collagen cleaved to tropocollagen?
in the ECM
