MGD Sessions 1-6 Flashcards
(379 cards)
1
Q
Why are amino acids classified by their R group?
A
Only part of molecule not disrupted upon formation of peptide bonds
2
Q
Which isomer are naturally occurring amino acids found?
A
L
3
Q
Which group of amino acids do glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine and tryptophan all belong to?
A
Non-polar (hydrophobic)
4
Q
Which group of amino acids do serine, threonine, asparagine, glutamine, tyrosine and cysteine belong to?
A
Polar, uncharged (hydrophilic)
5
Q
Which group of amino acids do lysine, arginine, histidine, aspartate and glutamate belong to?
A
Polar, charged (hydrophilic)
6
Q
Which amino acids have positive R groups?
A
Lysine
Arginine
Histidine
7
Q
Which amino acids have negative R groups?
A
Glutamate
As
Aspartate
8
Q
If pH > pK what happens to the R group on an amino acid?
A
It is deprotonated
9
Q
Which type of peptide bonds only are found in a protein?
A
Trans so side chains aren’t too close together
10
Q
What is the isoelectric point?
A
pH at which a protein has no net charge
11
Q
If pH
A
Protonated
12
Q
If pH > pI what happens to the protein?
A
Deprotonated
13
Q
How many amino acids in length are peptides/oligopeptides?
A
Few
14
Q
Give three examples of basic proteins.
A
Chymotripsinogen
Cytochrome C
Lysozyme
15
Q
Give four examples of acidic proteins.
A
Pepsin
Serum albumin
Urease
Haemoglobin
16
Q
What is the pI of myoglobin?
A
7.0
17
Q
What determines the conformation of the backbone of a polypeptide and hence how the protein folds?
A
Bond angles of peptide bonds
18
Q
Why are not all bind angles available in a polypeptide?
A
Some will cause side group clashes
19
Q
How many amino acids are there per turn in an alpha-helix?
A
3.6
20
Q
What is the distance between amino acids in an alpha helix?
A
0.15 nm
21
Q
What is the height of a turn in an alpha-helix?
A
0.54 nm
22
Q
Is an alpha-helix right handed or left handed?
A
Right handed
23
Q
Where are the side chains on an alpha-helix positioned so they do not affect the alpha-helix structure?
A
On the outside
24
Q
What bonds allow an alpha-helix to be formed?
A
Carbonyl group of one residue H-binding to amine group of the residue 4 a.a. away
25
What type of residues are strong helix formers?
Small, hydrophobic
26
Why are small hydrophobic residues strong alpha-helix formers?
Keep their hydrophobic side chains out of solution
27
Why is proline an alpha-helix breaker?
Rotation around N-C(alpha) is impossible
28
Why is glycine an alpha-helix breaker?
It's tiny R group allows for other conformations
29
How does a beta strand compare to an alpha-helix?
Less compact
| Fully extended
30
What is the distance between amino acids in a beta-strand?
0.35 nm
31
How are the R groups of amino acids arranged in a beta-strand?
Alternate b/w opposite sides of the chain
32
What provides stability in the anti-parallel alignment of beta-strands?
Hydrogen bonds
33
How does a sheet with parallel alignment compare to a sheet with antiparallel alignment of beta-strands?
Less compact
34
What is used to illustrate beta-strands on a diagram?
Flat arrows
35
What is the function of fibrous proteins?
Provide support, shape and protection
36
How many types of repeating secondary structure make up fibrous proteins?
One
37
What is the structure of collagen?
Super helix of three alpha-helix collagen chains wrapped around each other, stabilised by hydrogen bonds
38
How does the structure of collagen allow it to form fibrils?
Superhelices can form covalent cross-links
39
What are globular proteins used for?
Catalysis
| Regulation
40
How many secondary structures do globular proteins contain?
More than one
41
What are motifs?
Globular folding patterns of 1 or more secondary structure elements e.g. Beta-alpha-beta loop or beta-barrel
42
What are domains?
Part of a polypeptide chain that fold into a distinct shape, often with a specific functional role
43
Why do membrane proteins show an 'inside-out' amino acid distribution by having a hydrophobic exterior?
To allow it to sit in the membrane
44
How can covalent bonds in the tertiary and quaternary structure of a protein be broken?
Reducing agent
45
Why are most proteins with disulphide bonds secreted?
They are stable
46
What holds protein structures together?
```
Covalent bonds
Electrostatic interactions b/w charged groups
H-bonds
Van der Waals
Hydrophobic effect
```
47
How can proteins be denatured?
Heat
pH
Detergents/organic solvents
48
How does pH denature a protein?
Alters ionisation state of a.a. and disrupts ionic/H-bonds
49
How do detergents/organic solvents cause denaturation?
Disrupt hydrophobic interactions
50
What determines how a sequence is folded?
Primary structure
51
What may be required for a protein to fold?
Chaperone
52
What happens when mis folding occurs?
Molecules cluster to form accumulations of denatured proteins which disrupt cell and its function
53
Give three examples of degenerative neurological disorders caused by misfolded proteins.
BSE (mad cow disease)
CJD
Kuru
54
What can happen when soluble proteins misfold?
Create insoluble form
55
What causes Alzheimer's disease?
Amyloid beta-protein tail misfolding to form a highly ordered structure w/a high degree of beta-sheet which disrupts the rest of the protein formation
56
What is the inter-chain assembly in Alzheimer's disease stabilised by?
Hydrophobic interactions b/w aromatic a.a.
57
What does synthetase require to function?
ATP
58
Does synthase require ATP?
Nope
59
How does phosphatase work?
Uses water to remove phosphoryl group
60
How does phosphorylase work?
Phosphate breaks bond and makes phosphorylated products
61
What does dehydrogenase accept?
Electrons
62
Are the oxygen atoms in the substrate for an oxidase?
Nope
63
Where are the oxygen atoms in oxygenase?
One or both in substrate
64
What are ribozymes?
RNAs which act like enzymes to catalyse cleavage and synthesis of phosphodiester bonds
65
What is Kcat?
Turnover number
| Molecules of substrate to product pre enzyme per second
66
If the additional molecule needed for an enzyme to function is present, what name is given to the enzyme?
Holoenzyme
67
If the additional molecule an enzyme needs to function is not present, what name is given to the enzyme?
Apoenzyme
68
What is a cofactors?
Metal ion needed for enzyme function
69
What is a coenzyme?
Small organic molecule
70
What is a co substrate?
Co enzyme that makes a transient association and dissociates from the enzyme in an altered state
71
What is the name given to a coenzyme permanently associated with an enzyme which is returned to its original form?
Prosthetic group
72
Where are coenzymes often derived from?
Vitamins
73
What is the free energy of activation?
Peak energy difference b/w product and high energy intermediate
74
Does an enzyme change the equilibrium of a reaction?
No, just reached it quicker
75
What is transition-state stabilisation in enzyme action?
Enzyme stabilises structure in which the bonds are neither product or substrate and therefore greatly increase conversion to product
76
Can the transition state caused by enzymatic action be isolated?
Nope
77
How can the presence of catalytic groups increase enzyme action?
Enhance probability of transition state formation
78
What happens in visualisation of transition state during enzyme action?
ES formed --> conform into product shape --> product shape formed
79
What is Vmax?
Maximal velocity - when all available active sites are blocked
80
What kind of curve is formed by an enzyme that follows Michaelis-Menten kinetics when you plot V0 versus [S]?
Hyperbolic
81
What kind of curve is created by an allosteric enzyme when V0 is plotted against [S]?
Sigmoid all
82
What is Km?
Affinity of an enzyme for its substrate
| [S] at 1/2 Vmax
83
Does Km vary with [E]?
Nope
84
What do a small and large Km indicate?
```
Small = high affinity
Large = low affinity
```
85
When [S] >> Km, what can be said about the reaction kinetics?
0 order w.r.t. [S]
86
What is used to graphically calculate Km, Vmax and mechanism of action of enzyme inhibitors?
Lineweaver-Burk plot
87
What does the y-intercept of a Lineweaver-Burk plot give?
1/Vmax
88
What does the gradient of a Lineweaver-Burk plot give?
Km-Vmax
89
What are suicide inhibitors?
Conversion of molecule to form which covalently bonds to active site of enzyme by the enzyme itself
90
Is competitive inhibiting reversible?
Yes
91
What kind of bonds are formed in competitive inhibition?
Non-covalent
92
What is observed at high [S] in competitive inhibition?
Vmax
93
What happens to Km in competitive inhibition?
Increases
94
What effect does competitive inhibition have on the Lineweaver-Burk plot?
Rotates anti-clockwise
95
How does non-competitive inhibition affect Vmax and Km?
Decreases Vmax
| Km unaffected
96
What affect does non competitive inhibition have on the Lineweaver-Burk plot?
Rotates clockwise
97
How do you distinguish between competitive and non-competitive inhibition by using a graph?
Plot 1/V0 v.s. 1/[S] and see Vmax decrease and Km remain constant if non-competitive inhibitor
98
How do captopril, enalapril and lisinopril cause vasodilation?
Block conversion of angiotensin I to II
99
What action does aspirin have?
Irreversibly inhibits prostaglandin and thromboxane synthesis
100
What are allosteric enzymes regulated by?
+ve and -ve effectors which bind noncovalently to an allosteric site
101
What can binding of an effector do to an allosteric enzyme?
Affect affinity of enzyme for its substrate
Modify Vmax
Both
102
What do allosteric enzymes often catalyse?
Early committed step early in a pathway
103
What form are amino acids always written in?
Ionised
104
What is the structure of haemoglobin?
Tetramic - 2 alpha and 2 beta subunits
105
Why does haemoglobin have a sigmoidal binding curve?
Has cooperativity
106
What conformational change occurs between the T and R states of haemoglobin?
Twisted through 15 degrees
107
How does binding of an oxygen molecule affect the affinity of haemoglobin for oxygen?
Increases it
108
What does 2-3 bisphosphoglycerate do to a molecule of haemoglobin?
Sits in the middle of the 4 subunits to interact with histidine and lysine residues
109
How does 2-3BPG affect the oxygen binding curve for haemoglobin?
Shifts it to the right
110
When is 2-3BPG released into the tissues?
High altitude
111
What action does 2-3BPG have on the affinity of haemoglobin for oxygen?
Lowers it
112
How can the charge on 2-3BPG be described?
V. negative
113
What change in residues is seen in sickle cell anaemia?
Glutamate is replaced by valine in the beta-global chain
114
What does the 'sticky' hydrophobic pocket created in SCA do?
Polymerises deoxygenated HbS
115
What is beta-thalassaemia?
Decreased or absent beta globin chains
116
Why are beta-thalassaemia patients symptomatic after birth?
Alpha globin chains cannot form stable tetramers
117
What is alpha-thalassaemia?
Lack of alpha globin chains
118
What is the function of the Bohr effect?
Ensure delivery is coupled to demand
119
What causes the Bohr effect?
Local increase in hydrogen ions and carbon dioxide
120
What does the Bohr effect cause?
Reduction in affinity for oxygen therefore release of oxygen into metabolising tissues
121
Why is carbon monoxide toxic?
Binds 250x more readily to haemoglobin than oxygen and upon binding increases the affinity of haemoglobin for oxygen so it is not released
122
What effect does carbon monoxide have on the oxygen binding curve?
Shifts left
123
How can haemoglobin be used to measure diabetes?
Measure HbA1c levels
124
Which type of haemoglobin has the highest affinity for oxygen?
Foetal
125
How many amino acids form a molecule of myoglobin?
153
126
What percentage of a myoglobin molecule is alpha-helical
75
127
How many polypeptide chains make up a myoglobin molecule?
1
128
Where is iron located in deoxymyoglobin?
Slightly below plane of ring
129
How is deoxymyoglobin transformed into its ferric from?
Binding of oxygen moves iron into the plane of the ring
130
What shape is the binding curve of myoglobin?
Hyperbolic
131
What happens to myoglobin in the presence of carbon monoxide?
Combines which blocks oxygen transport
132
What does the saturation of myoglobin depend on?
Partial pressure of oxygen
133
What structural changes to the myoglobin molecule cause it's change into the ferric form?
Movement of His F8
| Small overall conformation change
134
How do allosteric activators and inhibitors affect V v.s. [S] curves for allosterically controlled enzymes?
Activator: shifts to left
Inhibitor: shifts to right
135
Where can phosphate groups be added to enzymes?
-OH of serine, threonine and tyrosine
136
What is addition of a phosphate group catalysed by?
Kinase
137
What is removal of a phosphate group catalysed by?
Phosphatase
138
What are zymogens?
Inactive precursor enzymes
139
How are zymogens activated?
Removal of part of the polypeptide chain
140
What do zymogens allow?
Safe transportation of inactive form without causing premature effects e.g. preventing premature proteolytic cleavage by proteases
141
How is the rate of enzyme synthesis regulated?
Increase or decrease in the rate of mRNA transcription
142
What is the function of ubiquitin?
Added to proteins to tag them for destruction
143
What is feedback inhibition?
End product inhibits enzymes earlier in pathway
144
What is feedforward activation?
Increase in initial substrate increases first pathway step
145
What is counter regulation of opposing metabolic pathways?
Catabolic pathway breaking down A inactivates anabolic pathway making A e.g. glycogenolysis and glycogenesis
146
What are the main mechanisms which regulate the blood clotting cascade?
Inactive zymogens at low conc
Amplification of initial signal
Localisation of clotting factors to site of damage
Feedback activation of thrombin
Termination of clotting by multiple processes
147
What does activated thrombin enhance activation of?
Factors V, VIII and XI
148
How are clotting factors localised to the site of damage?
Gla domains on factors bind to damaged endothelial cell lining and allow rapid activation of downstream effectors
149
What is heterochromatin?
Solenoid 30 nm fibres which are not used in gene expression
150
What is euchromatin?
'Beads on a string' DNA used for gene expression
151
Describe the structure of chromosomes.
Double DNA strand --> nucleosomes (around histones) --> sole lids --> hierarchical loops
152
What is a nucleoside?
Base+sugar
153
What is a nucleotide?
Base + sugar + phosphate
154
What is DNA a polymer of?
Deoxyribonucleotides
155
What is RNA a polymer of?
Ribonucleotides
156
What secondary structure does DNA form?
RH double helix
157
What secondary structure does RNA form?
Stem loops
158
What is at the 5' and 3' ends of a single stranded chain of polynucleotides?
```
5' = phosphate
3' = OH
```
159
What are purines?
2 ring nitrogenous bases
160
What are pyrimidines?
Single ring nitrogenous bases
161
Which bases are purines?
A and G
162
Which bases are pyrimidines?
C, T and U
163
What types of duplex structure can form by complementary antiparallel arrangement?
DNA-DNA
RNA-RNA
DNA-RNA
164
What is the convention for writing polynucleotide sequences?
5' --> 3' left to right (complementary strand underneath 3' --> 5' for duplex structures)
165
Describe mitosis.
Forms 2 genetically identical diploid daughter cells
Somatic
One round of replication and one round of division
Homologous pairs
166
Describe meiosis.
```
4 haploid daughter cells - gametes
One round of replication, 2 rounds of division
Crossing over essential
Homologous pairs form tetrads
Generates genetic diversity
```
167
Where are the checkpoints in the cell cycle located?
End of G1 and G2
168
What is G0?
Resting phase where cell carries out its normal function
169
What method is used for DNA replication?
Semi-conservative
170
What is the function of DNA polymerase?
Control ribose-phosphate bind formation in semi-conservative replication of DNA
171
What happens when two facing DNA replication forks meet in semi-conservative replication?
DNA lipase joins fragments
172
Describe the process of DNA replication in prokaryotes.
Circular 'naked' chromosome --> initiation: strands separate --> elongation --> termination
173
Which enzyme gives DNA polymerase a kick start?
Primate
174
Why are Okazaki fragments formed in DNA replication?
Helical arrangement of DNA
175
What joins Okazaki fragments?
Lipase
176
Which ends of the DNA strand does DNA polymerase extend?
3' only
177
How does the definition of a chromosome differ before and after replication?
Before 1 chromosome = 1 DNA molecule
| After 1 chromosome = 2 DNA molecules = 2 identical sister chromatids
178
What is the function of DNA helicase?
Unwind double helix
179
How are chromosomes classified?
Position of centromeres
180
Describe the passage of neurones in the cell cycle.
Enter G0 and do not undergo mitosis after specialisation
181
What happens in mitotic prophase?
23 pairs of highly condensed chromosomes present
Kinetochore present for spindle connection
Nuclear membrane broken down
182
What happens in mitotic prometaphase?
Spindle fibres attach to chromosomes
| Centrioles move to poles
183
What happens in mitotic metaphase?
Chromosomes randomly align along metaphase plate
184
What happens in mitotic anaphase?
Spindle moves to equator of cells
Sister chromatids pulled to opposite poles
Centromeres divide
185
What happens in mitotic telophase?
Nuclear envelope forms around both sets of separated chromatids
Nucleolus forms in both
Chromosomes decondense
Spindle fibres disappear
186
What happens in mitotic cytokinesis?
Cytoplasm divides
| Parent cell becomes two daughter cells w/identical genetic information
187
What happens during metaphase I in meiosis?
Maternal and paternal chromosomes find each other to arrange in a tetrad
Crossing over incl. sister chromatids
188
Does crossing over of sister chromatids have a consequence?
No as they are identical
189
What happens in anaphase I during meiosis?
Homologous pairs separate
190
What happens in prophase II during meiosis?
Random arrangement of chromosomes
| Retention of swapped over parts of chromatid
191
Why is there random arrangement of chromosomes in prophase II?
No homologous pairs
192
What happens in metaphase II of meiosis?
Chromosomes align along equator at 90 degrees to metaphase plate and spindle attaches
193
What happens in anaphase II of meiosis?
Chromosomes pulled to opposite poles
194
Give an overview of meiosis I and meiosis II.
I: homologous chromosomes of each chromosome pair divided
II: chromatids of each chromosome divided
195
What happens in spermatogenesis?
Spermatogonium (2n) --> primary soermatocyte (2n) --> spermatids (n) --> mature sperm
196
How long does spermatogenesis take?
~48 days
197
What happens in oogenesis?
Oogonium --> primary oocyte --> 3 polar bodies + 1 ovum --> mature ovum
198
How does the immature ovum compare to the three polar bodies formed during its genesis?
It has all of the energy stored within it
199
How long does oogenesis take?
12-50 years
200
Why is crossing over essential?
Ensures correct number of chromosomes in each cell by preventing chromosomes from sticking to each other
201
What does faulty meiosis lead to?
1/3 of all identified miscarriages
Infertility
Mental retardation
202
What is the frequency of faulty meiosis?
30 in 100
203
What gives 2^n possible arrangement of chromosomes where n is the number of chromosomes?
Independent assortment of chromosomes
204
What pattern of inheritance does Cystic Fibrosis show?
Autosomal recessive
205
How does an autosomal recessive inheritance pattern appear on a pedigree chart?
Appears to 'come out of nowhere'
Can skip generations
Makes and females equally affected
206
What pattern of inheritance does Huntingdon's disease show?
Autosomal dominant
207
What is the probability of heterozygotes with an autosomal recessive having affected offspring?
25%
208
What is the probability of heterozygotes with an autosomal dominant disease having affected offspring?
50%
209
Why are autosomal dominant diseases rare in the homozygous state?
Likely to result in termination
210
How do autosomal dominant inheritance patterns appear on a pedigree diagram?
Present in ever generation unless de novo
| Males and females equally affected
211
What pattern of inheritance does Haemophilia A show?
X-linked recessive
212
Who is affected by an X-linked recessive inheritance pattern disease?
Hemizygous males and homozygous females
213
How does an X-linked recessive inheritance pattern appear on pedigree diagram?
More common in males
Every affected female has carrier mother and affected father
Daughters of affected males always at least carriers
214
What is the probability of a female carrier of an X-linked recessive genetic disease having an affected son?
50%
215
What is co-dominance?
New phenotype is formed when neither allele is dominant over another
216
Use blood groups to describe co-dominance.
A and B both dominant over O but neither dominant over the other --> AB blood type
217
What codes for glycoproteins on RBC surface which determine blood group?
Human isoglutamin gene
218
Which antigens are present on the RBCs of blood group O?
None
219
Which blood those can be given to AB blood group patients?
All
220
How can receive blood transfusion of type O?
All blood groups
221
What is a gene?
Stretch of DNA at a specific chromosomal locus
222
What are genes condensed into?
Chromatin
223
What are the types of RNA?
```
Messenger
Ribosomal
Transfer
Micro
Noncoding
```
224
What is microRNA used for?
Control of gene expression in eukaryotes
225
What enzymes are needed for DNA replication, transcription and translation?
Replication: DNA polymerase
Transcription: RNA polymerase
Translation: ribosome
226
Describe the process of initiation in transcription.
Initiation: sequence dependent promoter recognition, transcription initiation factors, RNA polymerase
227
Describe the process of elongation in transcription.
5' to 3' chain growth
228
What does the termination of transcription depend on?
Sequence
229
What happens in the initiation stage of transcription?
TATA box recognised in 5' --> 3' direction
General transcription factors recruit polymerase II
RNA polymerase II phosphorylated
230
How does initiation of transcription vary between eukaryotes and prokaryotes?
Eukaryotes: TATA box at -30, variety of upstream sequences, complex regulation
Prokaryotes: Pribnow box at -10, upstream sequences at -35, simple regulation
231
How is transcription regulated?
Protein-DNA and protein-protein interactions
| Promoters have numerous sequence activators
232
What happens to the DNA molecule during the elongation stage of transcription?
Opens to allow for gene expression the closes when DNA polymerase is finished
233
In which direction does mRNA synthesis take place?
5' --> 3'
234
What is capping?
Methylated guanine creates a 5'-5' triphosphate bridge immediately after transcription to prevent degradation
235
What is polyadenylation?
Addition of large numbers of adenine residues to 3' end of mRNA
236
What is the function of polyadenylation?
Protect against degradation
| Signal export from nucleus
237
What does the length of the polyadenine tail on a mature mRNA molecule indicate?
Half-life
238
What is splicing?
Removal of introns and some exons depending on sequence
239
What is likely to happen to a protein if splicing goes wrong?
Likely to be ineffective
240
Give an example of a condition where there is an error with splicing.
PKU
241
Describe the structure of a mature mRNA molecule.
5' cap --> 5' UTR --> ORF --> 3' UTR --> 3' poly A tail
242
Where in the cell does translation take place?
Cytoplasm
243
How many kinds and copies of rRNA are present in a eukaryotic cell?
6-8 kinds
| Many copies of each
244
Which type of RNA polymerase is associated with rRNA?
I
245
How many kinds and copies of mRNA are there in a cell?
100,000s of kinds
| Few copies of each only present when proteins need to be made
246
Which type of RNA polymerase is associated with mRNA?
II
247
How many kinds and copies of tRNA are there in a cell?
~100 kinds
| Lots of copies of each
248
Which type of RNA polymerase is associated with tRNA?
III
249
How many rRNAs are present in a eukaryotes?
4
250
How many proteins are there in eukaryotes?
82
251
Describe the structure of a eukaryotic ribosome.
40S and 60S subunits
| 80S ribosome
252
Describe a prokaryotic ribosome.
30S and 50S subunits
| 70S ribosome
253
How many rRNAs are there in prokaryotes?
3
254
How many proteins are there in prokaryotes?
56
255
In which direction is the template read during translation?
5' to 3'
256
In what direction does the polypeptide extend during translation?
Amino to carboxyl
257
What initiates translation?
AUG
258
Which codons terminate translation?
UAA
UAG
UGA
259
Why is the genetic code said to be degenerate?
More than one codon codes for the same amino acid
260
What differences in bacterial translation give opportunity for attack?
```
Simple promoter
Different transcription factors
1 RNA polymerase
Coupled transcription and translation
No post transcriptional processing
Short lived mRNAs
Simpler ribosomes
Distinctive translation initiation
Different translation factors
```
261
What is the wobble position on a tRNA molecule?
5' base of anticodon and 3' base of codon which allows single tRNA to recognise more than one codon
262
What is inosine?
Purine derived aspecific nucleotide
263
What is the function of inosine?
Give extra degeneracy
| Less susceptibility to mutation
264
What happens during initiation of translation?
5' cap recognised --> (40S subunit) methionyl recognises AUG --> phosphorylation (60S subunit) --> fully functional subunit
265
What happens during the elongation stage of translation?
tRNA occupies P site --> tRNA w/correct codon binds to A site --> peptidyl transferase forms peptide bond --> ribosome moves --> empty A site
266
What happens during termination in translation?
P site full --> stop codon recognised by uncharged tRNA which physically moves ribosome along --> water, peptide and tRNA formed
267
When do ribosomes attach to the ER membrane?
If protein is destined for membrane or secretory pathway
268
How do ribosomes attach to the ER?
Co-translational insertion
269
When do ribosomes remain in the cytosol during protein synthesise?
If the protein is destined for the cytosol or posttranslational import into organelles
270
How are proteins directed to the correct destinations?
Intrinsic signal
Receptor recognises signal and directs to correct membrane
Translocation machinery transports across membrane
Energy available to transport protein to new place
271
Where can proteins exist in mitochondria?
All areas
272
How are mitochondrial matrix proteins directed?
Chaperone keeps protein folded --> signal binds to receptor --> protein through TOM --> protein through TIM --> targeting signal cleaved
273
Where is the signal sequence on a mitochondrial matrix protein located?
N-terminus
274
What are TOM and TIM?
Channels which allow passage of a mitochondrial matrix protein mRNA across the outer and inner mitochondrial membranes
275
What causes pyruvate dehydrogenase deficiency?
Mutation at codon 10 in precursor protein
276
What does the mutation in pyruvate dehydrogenase deficiency cause in the precursor protein?
Pro replaces Arg
Lose basic residue on hydrophilic face of amphipathic helix
Reduce mitochondrial uptake
277
What supplies the energy for nuclear import of proteins destined for the nucleus?
GTP hydrolysis
278
What happens in the cytosol before nuclear import?
Importin binds cargo containing a nuclear localisation signal
279
After migrating the rough the nuclear pores, what happens to importin?
Ran-GTP binds --> conformational change --> cargo released --> importin w/bound Ran-GTP recycled to cytoplasm
280
What binds with cargo that has a peroxisomal targeting signal?
Peroxisomal import receptor
281
What happens to the peroxisomal protein as the receptor integrated into the translocon?
Remains folded
282
What happens when the receptor integrates with the translocon in peroxisomal protein synthesis?
Translocon opens
PTS dissociated from receptor
Receptor uses ATP to move to cytosol
283
Where can a mutation occur in peroxisomal protein synthesis?
In receptor for subset of peroxisomal proteins
284
How are proteins for the ER or secretory pathway directed?
Co translational transport
285
Describe how proteins destined for the secretory pathway are synthesised.
Produced by ER ribosomes w/ co translational transport in/across ER membrane --> bud off in vesicles --> fuse w/Golgi --> cisternae progression --> trans-Golgi network --> lysosome or secretion
286
What is another name for cisternae progression in the secretory pathway?
Retrograde transport
287
What is constitutive cellular secretion?
Proteins always secreted e.g. extracellular matrix enzymes
288
What kind of cellular secretion do specialist cells carry out?
Regulated
289
What are secretory cells polarised?
So secretory granules at apical side and nucleus basal
290
What prevents damage caused by secretion of enzymes into tissue?
Polarisation of secretory cells
291
Signal sequences at which terminus of secretory proteins are hydrophobic?
N
292
What does the pre- prefix of a protein indicate?
Activator sequence still attached
293
What are hydrophobic signal sequences rich in?
Basic side groups
294
What is signal recognition protein?
Multi domain riboprotein that mediates 3-way association w/SRP-receptor in the ER, ribosome, and signal peptide
295
What is the structure of the SRP receptor in the ER membrane?
Alpha-beta tetradimer
296
What happens after SRP and GTP bind to SRP receptor in synthesis of secretory proteins?
Translocon is opened, sequence enters --> signal peptidase cleaves signal --> protein synthesis --> released into cell
297
Where must proteins destined for plasma membrane or internal membrane of secretory pathway insert?
ER membrane
298
What exists in a membrane protein which anchors it during protein synthesis and prevents further transfer into the ER lumen?
Second hydrophobic sequence
299
What sequence in a membrane protein remains in the cytosol during its synthesis?
Stop transfer anchor sequence
300
What are the functions of ER in protein synthesis?
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Insertion of proteins into membrane
Glycosylation
Proper protein folding
Hydroylation of selected Lys and Pro residues
Specific proteolytic cleavage
Formation of disulphide bonds
Assembly of multi subunit protein
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301
Why is N-linked glycosylation of proteins important?
Correct protein folding
Protein stability
Deficiency --> sever congenital disorder
302
What is the oligosaccharide preassembled on in N-linked glycosylation?
Lipid carrier - dolichol
303
What is the oligosaccharide in N-linked glycosylation transferred to after preassembly?
Asparagine
304
Is the same oligosaccharide always used in N-linked glycosylation?
Yes
305
How is the oligosaccharide in N-linked glycosylation extensively modified in the ER and Golgi?
Trimming and addition of further sugars
306
What is the function of peptidyl-prolyl isomerases?
Accelerate inter conversion of cis/trans isomers of proline residues
307
What is the role of protein disulphide isomerase in the ER lumen?
Form disulphide bonds
308
How does protein disulphide isomerase carry out its role?
It is itself oxidised and can then be reduced by oxidising the substrate protein
309
What prevents secretion of ER lumen proteins from the ER during their synthesis?
Specific signal
310
What recognises Lys-Asp-Glu-Leu sequence in soluble ER resident proteins to return them back to ER from cis-Golgi cisternae?
KDEL receptor
311
What is anterograde transport?
KDEL receptor points to vesicle formation --> pH prevents direct KDEL binding --> secreted protein w/out KDEL
312
What is retrograde transport?
Decrease in Golgi pH causes KDEL binding --> higher ER pH causes dissociation of ER resident protein
313
What folding problems can arise during protein secretion?
Trapped in mis-folded conformation
Protein contains mutation resulting in misfolding
Protein incorrectly assoc. w/other subunits
314
How does the ER respond to misfolded proteins?
Chaperone attempts to correct protein
| Retained unfolded proteins in ER --> downregulates protein synthesis
315
What happens to proteins if misfolding cannot be corrected?
Protein --> cytosol for degradation
| Protein accumulates to toxic levels in ER
316
What diseases arise as a result of protein misfolding?
Parkinson's
| Wilson disease
317
What happens to lysosomal enzymes as they pass through the Golgi?
Phosphate group added to hydroxyl group of C6 mannose sugar
318
Which enzymes are found in the Golgi body that act on lysosomal enzymes?
Glucosamine phosphotransferase
| Phosphodiesterase
319
What mediates lysosomal enzyme delivery by determining whether vesicle buds off from trans-Golgi network?
Mannose-6-phosphate receptor
320
What is O-linked glycosylation?
Attachment of sugar to hydroxyl group of serine (mainly) or threonine
321
What type of molecule is O-linked glycosylation important in?
Proteoglycans
322
Where is O-linked glycosylation prevalent?
Extracellular matrix and mucus secretions
323
Where is O-linked glycosylation prominent?
ER and Golgi
324
Give an example of a protein released by the unregulated constitutive secretory pathway.
Collagen
325
Give an example of a protein released by the regulated secretory pathway.
Insulin
326
Which action in the secretory pathway determines whether a protein is released by regulated or constitutive pathway?
Whether membrane fusion is regulated or not
327
Which protein is the most abundant in the body?
Collagen
328
What secretes collagen in connective tissue?
Fibroblasts
329
What is the basic unit of collagen?
Tropocollagen
330
What is the repeating structure in collagen?
Gly-X-Y
331
How many polypeptide alpha chains are in one molecule of tropocollagen?
3
332
Why are the alpha chains of tropocollagen highly extended?
Presence of proline and hydroxyproline in X and some Y parts of the repeating structure
333
What are the structural features of the RH triple helix which forms collagen?
Non-extensible
Non-compressible
High tensile strength
334
What stabilises the structure of the RH triple helix in collagen?
H binds b/w alpha chains
335
Which type of collagen accounts for 90% of all body collagen?
I
336
Which unites are present in collagen type I?
2 x alpha-1
| 1 x alpha-2
337
Where is type II collagen found?
Cartilage
| Intervertebral discs
338
Which units make up type II collagen?
3 x alpha-1 units
339
Where is type III collagen found?
Foetal skin
| CVS
340
Which units make up collage type III?
3 x alpha-1
341
Where is type IV collagen found?
Basement membrane
342
Where is type V collagen found?
Placenta and skin
343
What is associated with protein disulphide isomerase in the ER and is used for collagen synthesis?
Prolly hydroxylase
344
What dos prolyl hydroxylase require to function?
Vitamin C
| Iron(II) ions
345
How does prolyl hydroxylase increase the stability of collagen?
Creates hydrogen bonds
346
What happens to the tropocollagen triple helices in scurvy?
They are weak
347
Why is collagen not synthesised within the cell?
Molecules too long
348
Give the first four stages of the modification and synthesis of collagen in the ER.
Synthesis and entry of chain into ER lumen
Cleavage of signal peptide
Hydroxylation of selected proline and lysine residues
Addition of N-linked oligosaccharides
349
What causes the transition of prepro-alpha to pro-alpha in collagen synthesis?
Signal peptidase
350
What causes hydroxylation of selected proline and lysine residues in collagen synthesis?
Prolyl hydroxylase
351
Where are N-linked oligosaccharides added in collagen synthesis?
C-terminal propeptide
352
Give an example of a sugar that can be added to collagen when N-linked oligosaccharides are added to the C-terminus.
Galactose
353
What is added to hydroxylysine residues in collagen synthesis?
Galactose
354
What occurs in chain alignment of 3 alpha chains during collagen synthesis?
Formation of disulphide bonds
355
How is the triple helical procollagen assembled in collagen synthesis?
From C to N terminus
356
What is found at both the N and C termini of a collagen molecule?
Extra amino acids that do not form the triple helix
357
How is completion of O-linked oligosaccharide chains achieved?
Addition of glucose
358
What links the N and C terminal extensions in the transport vesicle?
Disulphide
359
What happens to the N and C terminal propeptides extracellularly?
Extensions removed
| Alpha-chain formation stimulated
360
How is a collagen fibre formed once the N and C terminal propeptides have been cleaved?
Lateral association of molecules
| Followed by covalent cross linking
361
How do collagen fibrils form a fibre?
Aggregation
362
What is formed by lateral association of individual collagen units?
Form 50 nm fibrils
363
Why does collagen have a striated appearance?
Formed of 50 nm fibrils
364
What happens when heavy metal staining is used on collagen?
Sit in gaps b/w molecules giving striated appearance
365
How is an aldol cross-link formed?
Lysine residues --> aldehyde derivatives --> potentially spontaneous aldol cross-links
366
Which enzyme converts lysine residues to aldehyde derivatives?
Lysyl oxidase
367
Which enzyme is affected in Ehlers Danlos syndrome?
Lysyl oxidase
368
What is needed for lysyl oxidase function?
Vitamin B6
| Copper(II) ions
369
What is the action of lysyl oxidase?
Form covalent cross-links
370
What are the two steps in insulin processing that take place in the ER?
Hydrophobic sequence cleaved from proinsulin
| Specific folding stabilised by 3 sulphide group bonds
371
What happens post-Golgi to leave a complete two-chain insulin molecule?
Connecting peptide removed
372
Which three enzymes are involved in the ER processing of insulin?
PC3 endoprotease
PC4 endoprotease
Carboxypeptidase
373
Where is the proinsulin antibody found?
Secretory glands waiting to mature
374
What is the third sulphide bond in an insulin molecule important for?
Structure
375
Why is proteolytic processing needed for small secretory products such as enkephalins in the secretory pathway?
They are too short to enter the ER via co-translational mechanism
376
What would happen if hydrolytic enzymes were activated in the cell instead of being proteolytically processed in the secretory pathway?
They would be destructive to the cell
377
How are multiple bio active products produced from the same polypeptide?
Proteolytic processing in the secretory pathway
378
How is activation of the insulin receptor avoided in the secretory pathway?
Proteolytic processing
379
How are bio active growth factor and insulin prevented from acting at the same time?
Proteolytic processing in the secretory pathway
