Biochemistry Monica Flashcards
(432 cards)
1
Q
What type of bond can carbon form with itself?
A
Covalent
2
Q
How many covalent bonds can carbon form?
A
4
3
Q
What does the bonding of carbon lead to?
A
A tetrahedral form
4
Q
What can carbon also form bonds with/
A
hydrogen, nitrogen and oxygen
5
Q
What is phosphorylation?
A
Addition/ removal of PO4
6
Q
What is acylation?
A
Addition of C+)
7
Q
What is carboxylation?
A
Addition of C=O, O-H
8
Q
In condensation is water added or removed?
A
Removed
9
Q
In hydrolysis water is added?
A
True
10
Q
What happens in redox equations?
A
Electrons are transferred. As 1 molecule is oxidised the other molecule is reduced.
11
Q
Oxidation is…
A
Loss of electrons
12
Q
Reduction is…
A
Gain of electrons
13
Q
Redox pairs are?
A
Biologically important
14
Q
The oxidation states of carbon are?
A
alkane (in fats) > alcohol (in carbohydrates) > aldehyde > carboxylic acid > carbon dioxide (final product of catabolism)
15
Q
Information storage location
A
DNA
16
Q
Biomolecules structures?
A
Teeth, bones, cartilage
17
Q
Where does energy generation occur?
A
Glycolysis, citric acid cycle, electron transport chai
18
Q
What is the energy currency/storage location?
A
ATP
19
Q
Where is biomolecule recognition?
A
Receptors
20
Q
Where is biomolecule communication?
A
Hormones
21
Q
What is biomolecule specificity?
A
Enzymes
22
Q
What do peptides and proteins consist of?
A
Amino Acids
23
Q
What are lipids?
A
Triglycerides, phospholipids, steroids
24
Q
What are nucleic acids?
A
DNA, RNA
25
What are carbohydrates?
Mono, di, polysaccharides
26
An example of monosaccharides?
Glucose
27
Examples of disaccharides?
Lactose, maltose, sucrose, cellobiose
28
Example of polysaccharides?
Cellulose, glycogen
29
First law of thermodynamics?
Energy is neither created nor destroyed
30
Second law of thermodynamics?
When energy is converted from 1 form to another, some of that energy becomes unavailable to do work
31
Enthalpy?
Het content of a system
32
Entropy?
Degree of disorder of a system
33
The most important change in free energy is?
ΔG = ΔH – TΔS
| T is the temperature in K
34
Free energy change?
ΔG = (energy of the products) – (energy of the reactants)
35
An exergonic reaction is defined as one in which?
The total free energy of the products is less than the total free energy of the reactants
36
The free energy change of an exergonic reaction is?
Negative
37
Exergonic reactions can occur spontaneously?
True
38
In an endergonic reaction?
The total free energy of the product is more than the total free energy of reactants
39
The free energy change of an endergonic reaction is?
Positive
40
Can endergonic reactions occur spontaneously?
Usually no, however there are exceptions to the rule
41
Endergonic reactions require an input of energy to proceed?
True
42
What equation is used to determine deltaG for a given reaction?
ΔG = ΔGo’ + RTln([C][D]/[A][B])
43
What does R stand for in the deltaG equation?
Universal gas constant (8.3 JK-1mol-1)
44
What does T stand for in the deltaG equation?
The absolute temperature (degrees Kelvin used)
45
What are the units for deltaG?
kJ/mol
46
What does deltaGo' represent?
Change in free energy under standard conditions
47
Conditions for physical chemists?
T=298K
1 atmospheric pressure
1 < (1mol/l) concentration
deltaGo
48
For biochemists conditions are?
```
T=298K
1 atmosphere pressure
1M(1 mol/l) concentration
pH=7
deltaGo'
```
49
DeltaG is related to the point of equilibrium?
True
50
The further towards completion the point of equilibrium is, the ___________ free energy is released?
More
51
Readily reversible reactions have deltaG values
Closer to zero
52
Forward and backwards reactions are balanced when?
The system is in equilibrium ΔG = 0 and therefore
| ΔGo’ = -RTlnKeq
53
Keq =
[C][D]/[A][B]
54
What does increasing (A)(B) relative to (C)(D) do to deltaG?
(C)(D)?(A)(B) becomes smaller than 1. the ln of a smaller number smaller than 1 = negative
55
What is the effect of cellular processes that are unfavourable?
1. Have to proceed in the direction of a positive deltaG
2. Transport against a gradient
3. Synthesis of large molecules
56
What is ATP used as?
A universal energy currency for driving many different cellular processes
57
How do many reactions occur within the body?
By coupling up an unfavourable reaction with a very favourable reaction
58
What makes the ATP molecule less stable than ADP?
The negative charges close together
59
How is strain relieved in ADP?
By removing 1 or more phosphate groups
60
What type of bonds are high energy?
Anhydride bonds
61
Cells store large amounts of energy
False - it is constantly regenerated
62
Do active muscle cells for example use ATP at higher or lower rates?
Higher
63
Examples of ways ATP is regenerated
Using creatine phosphate (standard free energy of hydrolysis = -43kJ/mol
Using 2ADP ATP + AMP
64
Define metabolism
All reactions taking place in the body
65
Define Catabolism
Breaking down complex molecules into smaller ones
66
In catabolism energy is used
False
67
Define anabolism
Synthesising complex molecules out of smaller ones
68
Is energy released or required for anabolism?
Required
69
There are energy consuming steps in some catabolic reactions
True
70
What type of pathway is glycolysis an example of?
A catabolic pathway
71
What type of pathway os glucogenesis an example of?
An anabolic pathway
72
What is the purpose of glucogenesis?
To make new glucose from non-carbohydrate precursors
73
Reactions close to equilibrium are used as control points?
False
74
What kind of reactions are useful for control points?
Reactions with large deltaG values
75
How is flux controlled through these points?
By altering the activity of the enzyme involved
76
water is polar what does this mean?
Electrons are shared unequally
77
What does a water molecule form?
A dipole, tetrahedral shape
78
What are hydrophilic molecules?
Ionic and polar substances that dissolve in water
79
What are hydrophilic substances based on?
Electrostatic interactions
80
Hydrogen bonds are much weaker than covalent bonds?
True individually however can be strong collectively
81
Hydrogen bonding is not very important in water and biological structures?
False
82
What are hydrogen bonds shared between?
2 electronegative atoms
83
Hydrogen bonds tend to be...
Linear
84
Non polar substances are insoluble in water
True - hydrophobic
85
Attractions between water molecules are?
Powerful
86
Do water molecules prefer to interact with themselves or other non-polar molecules?
Themselves
87
Hydrocarbons are?
Very non-polar and hydrophobic
88
What are hydrocarbons?
Compounds consisting of only hydrogen and carbon
89
'Oil and water don't mix' what is this often referred to as
Hydrophobic effect
90
Amphiphilic molecules are
Both hydrophilic and hydrophobic
91
Polar 'head' groups
Interact well with water
92
Non polar tails...
Do not interact well with water
93
Amphipathic molecules form what in water
Micelles
94
Examples of amphipathic molecules are?
Sodium palmitate
95
What is the importance of the cell membrane?
Aid compartmentalisation by isolating organelles
96
What are the components of the cell membrane?
lipids of various types
structural (lipid bilayer)
precursors of signalling
molecules (DAG, IP3)
proteins of various types
confer selectivity
involved in recognition
and more
97
All alpha carbon are bonded to?
An amino group (NH2)
A Carboxyl group (COOH)
A hydrogen (H)
A side chain (R)
98
D and L forms are?
Stereoisomers
99
Stereoisomers are?
Non-superimposable mirror images
100
What kind of bonds have partial double bond character?
Peptide bonds
101
What are characteristics of peptide bonds?
They are planar
| They are strong and rigid - important for folding of proteins
102
Do acids donate or accept protons?
Donate
103
Bases are proton donators
False
104
How is the strength of an acid determined?
By how quickly it donates a proton
105
How is the strength of an acid measured?
Using dissociation constant Ka
106
How is Ka calculated?
Ka =(H+)(A-)/(HA)
107
pH=
pH = -log10[H+]
108
pH=
amount of protons in a solution
109
What does a change of one pH unit imply?
A tenfold change on proton concentration
110
An equivalent measure for acid strength other then pH is?
pKa = -log10[Ka]
111
A solution with pH=7 is?
Neutral
112
A solution with pH<7 is?
Acidic
113
A solution pH>7 is?
Basic
114
What is the purpose of the Henderson - Hasselbalch equation?
Connects the Ka of a weak acid with the pH of a solution containing this acid
115
Henderson Hasselbach equation is
pH=pKa + log (A-)/(HA)
116
What does the henderson hasselbalch equation allow us to calculate?
The properties of buffer solutions - dependent on the concentrations of acid and conjugate base
117
What is a buffer?
A solution used to control the pH of a reaction mixture
118
what equations exhibit when the concentration of an acid equal the concentration of a base?
[HA] = [A-]
[A-]/[HA] = 1
log [A-]/[HA] = 0
pH = pKa
119
what happens at buffers pKa values?
They tend to resist a change of pH on moderate addition of acid or base
120
What do titration curves do?
Plot pH as a function of a base added to an acid
121
What happens close to the pKa on a titration curve?
The pH remains relatively unchanged in response to addition of a base
122
What do AA without charged side groups exist as _______ in neutral solution?
Zwitterions - n net charge
123
What do zwitterions contain?
2 titratable groups
124
What is the pH called when the molecule has no net charge?
The isoelectric pH
125
What is special about AA that have 2 titratable groups?
They have 2 pKa values
126
The ends of proteins can be ionised
True
127
Can proteins act as buffers?
Yes - e.g. haemoglobin in blood
128
A change in pH can change ionisation of a protein. What can this lead to?
A change in structure, thereby function
129
Primary structure of proteins
The sequence of amino acid residues
130
Secondary sequence of proteins
The localised conformation of the polypeptide backbone
131
Tertiary structure of proteins
3D structure
Entire polypeptide
Includes all side reactions
132
Quaternary structure of proteins
Spatial arrangement
Polypeptide chains
Multiple subunits
133
Polypeptides can rotate around angles between...
the α carbon and the amino group
| the α carbon and the carboxyl group
134
what are the three types of secondary structures?
alpha (α) helix
beta (β) strands and sheets
triple helix
135
Give points about hydrogen bonded 3D arrangements of a polypeptide chain?
Localised
| Only considers backbone of polypeptide
136
Alpha helix is rod like
True
137
Alpha helix has how many polypeptide chains
1
138
Are alpha helixes normally right or left handed
Right
139
How do alpha helixes arrise
C-O group of one amino acid forms a hydrogen bond with the -N-H group of an amino acid four residues away
140
Polypeptide backbone almost completely extended
True
141
How many chains can B sheets involve
1 or more
142
What directions are possible in B sheets
Parallel and anti-parallel
143
B sheets do not contain turns
False
144
What is the most abundant protein in vertebrates?
Collagen triple helix
145
The collagen triple helix is a component of what?
Bone and connective tissue
146
Collagen triple helix contains water soluble fibres
False water insoluble fibres
147
What kind of bonds does collagen triple helix exhibit?
Covalent inter and intra molecules
148
What are twisted round each other in a collagen triple helix?
Three left-handed helical chains to form a right-handed superhelix
149
Inter chain hydrogen bonds of a collagen triple helix involve
hydroxylysine and hydroxyproline
150
Collagen triple helix is repeating sequences of
X-Y-Gly in all strands
X = any amino acid
Y = proline or hydroxyproline
also contains hydroxylysine
151
Why is collagen relevant?
influences strength of connective tissue
| weakened collagen results in bleeding gums
152
Covalent crosslinking increases with age what does this explain?
meat from older animals is tougher
153
What is skurvy?
Bleeding gums, skin discolourisation
154
What is the term used to describe the arrangement of all atoms of a polypeptide chain in space?
Tertiary structures
155
What do tertiary structures consist of?
Local regions with distinct secondary structures
156
What are examples of tertiary structures?
Fibrous proteins
| Globular proteins
157
Fibrous molecules contain
Polypeptide chains organised approximately parallel along a single axis.
158
What are 4 characteristics of fibrous molecules?
consist of long fibers or large sheets
tend to be mechanically strong
are insoluble in water and dilute salt solutions
play important structural roles in nature
159
Give examples of fibrous proteins
wool + hair keratin
| collagen of connective tissue of animals including cartilage, bones, teeth, skin, and blood vessels
160
Give 4 characteristics of globular proteins?
they tend to be soluble in water and salt solutions
most of their polar side chains are on the outside and interact with the aqueous environment by hydrogen bonding and ion-dipole interactions
most of their nonpolar side chains are buried inside
nearly all have substantial sections of alpha-helix and beta-sheet
161
Examples of globular proteins include
Myoglobin
| Haemoglobin
162
List forces stabilising tertiary structures?
```
Covalent disulphide bonds
Electrostatic interactions = salt bridges
Hydrophobic interactions
Hydrogen bonds
backbone
side chain
Complex formation with metal ions
```
163
Repulsion occurs
Between similar charges
164
Where are charged molecules normally located?
On the outside of the protein
165
Charged molecules interact with water
True
166
What kind of bonds does water form with other molecules?
Hydrogen
167
Are attractions between water and hydrocarbon stronger or weaker?
Weaker
168
Attractions between hydrocarbon and hydrocarbon are weakest
True
169
Explain the hydrophobic effect
Strong organising influence
170
Where do amino acids with hydrophobic side chains tend to cluster?
In the centre of globular proteins
171
What can a change from glutamic acid to valine potentially lead to?
Significant functional changes
172
What would you expect if a mutation in a given protein changes a glutamic acid into a valine?
glutamic acid is negatively charged at physiological pH
can form ionic bonds or hydrogen bonds with water or other amino acid side chains
valine is hydrophobic
interacts with other hydrophobic amino acids
173
Primary structure of a protein does not contain all the information needed for its 3D shape
False it does contain all information required
174
How may proteins fold into their correct shape?
Spontaneously
175
Why may protein folding be a slow and erroneous process?
protein may begin to fold incorrectly before it is completely synthesised
it may associate with other proteins before it is folded properly
176
Give examples of processes that are slow and erroneous?
Alzheimer’s, Parkinson’s, CJD
177
What are the other specialised proteins that aid in the folding of proteins?
Chaperones
178
What term the process when types of physical conditions or chemical agents disrupt the various protein structures?
Denaturation
179
What does heat increase?
Vibration in proteins
180
What is the result of pH extremes?
Electrostatic interactions interrupted
181
What is the result of detergents, urea, guanidine hydrochloride?
Disrupt hydrophobic interactions
182
Thiol agents and reducing agents disrupt protein structures in what way?
Reduce and thereby disrupt disulphide bonds
183
Give examples of tertiary structures?
Lysozyme
| Myoglobin
184
Give characteristics of myoglobin as a globular protein?
Contains a haem group
Haem group contains an iron ion Fe (2)
Prosthetic group
185
Myoglobin stores oxygen in muscle
True
186
Heam groups bind to what?
Oxygen
187
How many oxygen molecules bind per myoglobin protein?
1
188
Outline the main characteristic of quaternary structures
Contain more than one polypeptide chain
189
Are subunits identical or different?
Can be either
190
Give an example of a quaternary structure?
Haemoglobin
191
What can haemoglobin transport?
Oxygen in blood
192
Outline 4 main characteristics of haemoglobin
4 subunits
2 alpha and 2 beta chains
Each contain a haem group
Each subunit can bind 1 oxygen molecule
193
How many subunits are present in polypeptide chains?
Between 2 and more than a dozen subunits
194
Binding of 1 oxygen changes what?
The affinity of the other subunits - refer to allosteric regulation
195
What is 'The central dogma'?
Total DNA in each cell which constitutes the DNA
196
What does the central dogma carry?
The genetic info required for making the whole organism
197
Where is the information of the central dogma stored?
Nucleotide sequence of the genome
198
What does the DNA nucleotide sequence determine?
AA sequences of polypeptide chains
199
How is information transmitted?
Via an intermediate, RNA
200
Nucleotide----> Nucleotode
DNA------>RNA = transcription
201
Nucleotide ------> AA
RNA-------> Protein = Translation
202
What kind of sugar is in RNA?
Ribose
203
What kind of sugar is in DNA?
Deoxyribose
204
What is a nucleoside?
A base + sugar
205
What is a nucleotide?
Nucleoside + phosphate group
206
What are the 4 bases of DNA?
A, C, G, T
207
What are the 4 bases in RNA?
A, C, G, U
208
List the building blocks of nomenclature
```
base nucleoside
adenine adenosine
cytosine cytidine
guanine guanosine
thymine thymidine
uracil uridine
```
209
List the building blocks of DNA
dATP, dCTP, dGTP, dTTP
| deoxy-adenosine-triphosphate etc.
210
List the building blocks of RNA
ATP, CTP, GTP, UTP
| adenosine-triphosphate etc.
211
What is a phosphodiester bond formed between?
A free 3' OH group and 5' triphosphate
212
Polymerisation consumes 2 high energy bonds
True
213
Where are new nucleotides added?
Only to a free 3'end
214
Nucleotide strands are parallel
False - ant-parallel - one 5' t 3' other 3' to 5'
215
Where is the sugar phosphate backbone?
On the outside
216
What bond exists between base pairs?
Hydrogen bonds
217
What are the DNA base pairs?
A=T
| C=-G (triple bond)
218
What must DNA undergo before cell division?
Must be replicated
219
Why must DNA be replicated before cell division?
So the daughter cells have a complete complement of the genome
220
Replication is semi-conservative?
True
221
What catalyst is used for DNA replication?
DNA polymerase
222
Outline the requirements of DNA polymerase
Can only add to existing nucleic acids
Inability to start DNA synthesis on their own
Requires an RNA primer to start replication
223
Eukaryotic genomes have many origins of what?
Replication
224
Replication does not start simultaneously at several points in the genome
False - it does start simmultaneously
225
Replication is in one direction?
False - bidirectional
226
What is the importance of replication starting simultaneously at several points in the genome?
Ensures replication completed in reasonable time
227
Explain why replication is discontinuous?
Nucleotides can only be added to feee 3' end
228
What does a leading strand always exhibit?
A free 3' end
229
Lagging strand must be replicated in what?
Short segments - Okazaki fragments
230
Outline the steps of DNA replication
Helicase unwinds DNA
Primase synthesises an RNA primer
DNA polymerase synthesises a complementary DNA strand
The lagging strand is replicated as Okazaki fragments
The second Okazaki fragments is synthesised
A third okazaki fragment is synthesised
The tail end of another okazaki fragment
RNA primers are degraded
Gaps are filled in by DNA polymerase
231
What can incorporating the wrong nucleotide create?
Mutations
232
Mutations can...
Be deleterious
| Lead to errors occurring once every 10^4 to 10^5 base pairs
233
What kind of exonuclease activity does DNA polymerase exhibit?
3' ------->5'
234
What does 3' to 5' exonuclease activity remove and improve?
Remove incorrect nucleotide
| Improve error rate to one in 10^9 to 10^10 base pairs
235
Further repair systems do not exist
False
236
RNA is usually single stranded
True
237
What are stem loops?
Local stretches of intramolecular base-pairing
238
Name the 3 main classes of RNA
```
Ribosomal RNA (rRNA)
Transfer RNA (tRNA)
Messenger RNA (mRNA)
```
239
What RNAs are considered stable RNAs?
rRNA and tRNA
240
What is the purpose of rRNA?
Combines with proteins to form ribosomes where protein synthesis take space (80%)
241
What is the purpose of tRNA?
Carries AA to be incorporated into the protein(15%)
242
What is the purpose of mRNA?
Carriers the genetic info for protein synthesis(5%)
243
What does RNA contain instead of thymine?
Uracil
244
Adapters are between...
Nucleic acid code and AA code
245
Anticodons consist of how many nucleotides?
3
246
What is attached to 3' end?
Specific AA (dependent on AA sequence)
247
What kind of RNA have a distinct 3D structure?
tRNA molecules
248
What structure arrises when tRNA is flattened into 2D?
Cloverleaf structure
249
RNA is made by...
RNA polymersaes
250
How many types of RNA polymerases are exhibited by prokaryotic cells?
1 type
251
Eukaryotic cells have 5 types of RNA polymerase
False - 3 types
252
What polymerase synthesises all mRNA
Poll (II)
253
How can polymerases be distinguished?
By their sensitivity to toxins like alpha-amanitin (derived from fungus)
254
List the steps of transcription
```
RNA polymerase binding
DNA chain separation
Transcription initiation
Elongation
Termination
```
255
Explain RNA polymerase binding
Initiation sites detected on DNA
256
Explain DNA chain separation
Local unwinding of DNA
| Gain access to nucleotide sequence
257
Explain transcription initiation
Selection of the first nucleotide of the growing RNA
258
Explain elongation
Adding further nucleotides to the RNA chain
259
Explain termination
Release of finished RNA
260
TBP=
TATA box Binding Protein
261
What is TFIID?
A general transcription factor
262
What is TFIID required for?
All Pol II transcribed genes
263
TBP introduces a kink into DNA what does this determine?
Transcriptional start and direction
264
Initiation of transcription requires additional general transcription factors
True
265
Initiation of transcription requires a _______ order of assembly
Precise
266
What extends transcription on their own?
Pol II and TFIIF
267
TFIID remains at promoter, a new initiation complex can assemble. What does this allow?
Transcription at low, basal rates
268
New RNA sequences are complementary to the template strand
True
269
Is RNA sequence complementary to the template strand
YES
270
What is identical to the coding strand?
New RNA sequences (U instead of T)
271
In Transcription termination what does newly synthesised RNA make?
A stem loop structure
272
What follows the creation of a stem-loop structure?
A stretch of Us
273
What happens when a specific enzyme cleaves RNA?
RNA = release
| Polymerase dissociates
274
Specific regulation of transcription
Go back to slide 45
275
What does coordinated gene expression act in response to?
Specific stimuli e.g. hormones, cellualr stress
276
What are coding regions interrupted by?
Non coding regions (between 1 and more than 50 introns per gene)
277
What must be removed before translation into protein and by what process?
Introns by splicing
278
How are the ends of mRNAS processed?
Addition of poly(A) tail
| Addition of 5' cap
279
What do all anticodons of tRNA molecules form during translation?
Base pairs with codons on mRNA
280
The genetic code is based on pairs
False - based on triplets
281
How many different nucleotides are available?
4
282
How many possible combinations are there?
64
283
How many amino acids do they code for?
20
284
Define degenerate
Many AA have more than 1 codon
285
Define unambiguous
Each codon codes for only 1 AA (or a top)
286
ATP and GTP act as
Sources of energy
287
How many rRNA molecules do ribosomes contain?
4
288
What are the3 tRNA binding sites?
```
E = exit
P = peptidyl
A = aminoacyl
```
289
What does initiation require?
Initiation factors
290
What molecule is hydrolysed to provide energy for initiatuin?
GTP
291
What binds to the 5' end of mRNA?
Small ribosomal subunits
292
What is AUG?
Start codon
293
Moves along mRNA until AUG is found. What is this process is dependent on?
ATP
294
What base pairs with the start codon? And what does this carry?
Special initiator tRNA with UAC anticodons - Carriers methionine
295
What does the large subunit join?
Assembly and initiator tRNA
296
Where is tRNA located?
In P site
297
What does an elongation factor bring?
The next aminoacyl-tRNA to the A site
298
Name the anticodon which pairs with codon during elongation
```
Anticodon = CGU
Codon = GCA
```
299
What is hydrolysed during elongation?
GTp
300
What is released from tRNA during elongation?
tRNA
301
What does a second elongation factor regenerate?
EF1α to pick up the next aminoacyl-tRNA
302
What is the role of peptidyl transferase?
Catalyses peptide bond formation between AA in P and A sites
303
Where is the peptide bond located after peptide bond formation?
Now located in A site
304
Where and what does does the elongation factor move?
Ribosome along the RNA - by 1 triplet
305
Where does empty tRNA move?
To the E site
306
'Empty' tRNA can move to E site and...
Exit and become reloaded with AA
307
Where foes tRNA with the growing peptide move?
From the A to the P site
308
When does termination occur?
When the A site of the ribosome encounters a stop codon
309
Name 3 stop codons
UAA, UAG, UGA
310
Aminoacyl-tRNA base pairs with stop codons
False
311
What does a release factor bind to?
Stop codon - GTP hydrolysis
312
What happens to the finished protein?
It's cleaved off tRNA
313
What components dissociate from each other?
rRNA, mRNA and tRNA
314
Explain termination starting over again?
Small subunit being bound by IF = ready for translation of a new protein
315
What is a point mutation?
A change in single base in DNA
316
What is a missense mutation?
Results in a change of AA sequence
| Can change protein function
317
What does a nonsense mutation create?
A new termination codon
318
What does a nonsense mutation change and how does it do this?
Length of a protein due to premature stop of translation
319
A silent mutation causes a change of AA sequence
False - no change
320
What are silent mutations due to?
Degeneracy of the genetic code
321
What is the effect of a silent mutation on the proteins function?
No effect
322
Define frameshift mutation?
Deletion or addition of a single base (or 2)
323
List 4 chromosomal mutations
Deletions
Duplications
Inversions
Translocations
324
Chromosomal mutations affect smaller portions of the genome
False - affect larger portions of the genome
325
What does a targeting move?
A protein to its final cellular destination
326
Where can targeting take place?
Many possible locations within a cell
327
What is targeting dependennt on?
The presence of specific AA sequences within the translate protein
328
What term is used to describe addition of further functional chemical groups?
Modification
329
What happens during degradation?
Unwanted or damaged proteins have to be removed
330
What do free ribosomes in the cytosol make proteins destined for?
Cytosol
Nucleus
Mitochondria
Translocated post-translationally
331
What do bound ribosomes on the rough ER make proteins destined for?
```
Plasma membrane
ER
Golgi apparatus
Secretion
Translocated co-translationally
```
332
Define glycosylation
Addition and processing of carbohydrates in the ER and Golgi
333
What forms in the ER?
Disulfide bonds
334
Where does folding and assembly of multi-subunit proteins take place?
In the ER
335
What is contained in the ER, golgi and secretory vesicles?
Specific proteolytic cleavage
336
What is the cause of hereditary forms of emphysema?
Misfolding of the protein α1-antitrypsin in the ER
337
Small changes in the abundance, efficiency or distribution in tissue of enzymes can have what effect?
Major complications for disease
338
Enzymes are non-specific
False
339
What characteristic of enzymes makes them useful in diagnosing diseases?
Their catalytic behaviour
340
What type of reaction do enzymes control?
Well defined chemical reactions
341
Enzymes can be used to investigate and develop a wide range of diagnaostic kits and therapeutic drugs
True
342
What must we know to understand how an enzyme works?
The concentration of substrate (S)
| The rate of the catalysed reaction (V)
343
What 2 parameters are used to describe the relationship of enzyme behaviour?
Vmax and Km
344
What model is used to explain the relationship between Vmax and Km
The Michaelis Menten model
345
What makes the enzyme-substrate complex inherently unstable?
The activation energy barrier
346
The enzyme substrate complex is only in 1 direction
false - can go forwards or backwards
347
Write the relationship described by the Michaelis constant Km
Km=(k-1 + k2)/k1
348
What is K1?
The forward rate constant for enzyme associate with the substrate
349
What is K-1?
The backwards rate constant for enzyme dissociation from the substrate
350
What is K2?
The forward rate constant of an enzyme conversion of substrate to product
351
How are Vmax and Km measured?
Measure initial reaction velocity, Vo at a known sunstrate conc.
Repeat at inccreasing substrate conc.
352
How are initial reaction rates Vo plotted?
As a function of the substrate concn.
353
What does the initial reaction rate at infinite substrate concn approach?
A maximal rate (Vmax)
354
What is . Michaelis constant Km equivalent to?
Substrate concn. where initial rate = 1/2 maximal
355
Why is is not straight forward to determine Vmax and Km from certain graphs?
Because the kinetics = not linear. Hence reaction velocity never quite reaches true Vmax
356
What does the michaelis menten equation describe?
The rate of catalysis as a function of substrate concn.
357
Instead of V against S how is the graph plotted?
As 1/V against 1/S
358
What term describes the plotting of linweaver burk plot?
A double reciprocal plot
359
What does a lineweaver burk plot enable?
Accurate determination of Vmax and Km
360
What is the intersection of the straight line with the Y axis?
Vmax
361
What is intersection with the X axis?
Km
362
What does Vmax equal?
The maximum velociety of a reaction
363
What does Km equal?
Concentration in moles of S which gives 1/2 Vmax
| Km=(S) at 0.5 Vmax
364
What is the effect of a low Km?
The enzyme only needs a little substrate to work at 1/2 maximal velocity
365
what is the effect of a high Km?
An enzyme needs a lot of substrate to work at 1/2 maximal velocity
366
Enzymes with the same Vmax can have different?
Km values
367
What type of inhibition is reversible?
Competitive
| Non-competitive
368
What type of inhibition is irreversible?
Non-competitive
369
How do competitive inhibitors act?
Inhibitor binds to active site + blocks substrate access
370
Define orthosteric inhibition
At the same site
371
How do non competitive inhibitors act?
Bind to a site other than the catalytic centre; inhibits enzyme by changibng its conformation
372
Define allosteric inhibition?
At a different site
373
What does non-competitive inhibition usually involve?
Formation of breakage of covalent bonds in the enzyme complex
374
In competitive inhibition what remains the same and what varies?
```
Vmax = does not change
Km = varies
```
375
In non-competitive inhibition what remains the same and what varies?
```
Vmax = varies
Km = no change
```
376
Define feedback inhibition
Inhibition of rate limiting enzymes by end product is a common mechanism of allosteric control
377
Allosteric enzymes follow Michaelis-Menten kinetics?
false - do not follow
378
What does increasing substrate concn. result in?
SIgmoidal curve, instead of a hyperbola
379
How can allosteric enzymes be controlled?
By allosteric inhibitors and allosteric activators
380
What type of behaviour do allosteric enzymes exhibit?
Co-operative behaviour
381
What modulates enzyme kinetic behaviour?
Allosteric factors
382
Outline and describe an important example for allosteric regulation
Binding of O2 to haemoglobin
Positive co-operativity
Controlled by - H+, CO2, 2,3 bisphosphoglycerate (side product of glycolysis)
383
What process do enzymes make up?
Metabolism
384
What is the main purpose of enzymes?
To speed up the rate at which a reaction reaches equilibrium
385
Enzymes affect the position of equilibrium
False
386
What are enzymes?
Biological catalysts
387
What are enzymes most made of?
Protein - exception (some types of RNA - ribozymes - are catalysts)
388
When are enzymes efficient?
At body temperature, in aqueous solution, near neutral pH
389
Efficient enzymes can increase the rate of a reaction by a. factor of up to what?
10^20
390
What is meant by enzymes being specific?
Each enzyme == limited rage of substrates
391
What does the specific nature of enzymes allow?
Some can distinguish stereoisomers
392
What does the potent nature of enzymes allow?
Each molecule can convert many substrate molecules into product per second
393
What do enzymes bind and stabilise?
The transition state
394
What is the transition state?
Reaction intermediate species which has greatest free energy
395
How do enzymes reduce activation energy?
Provide alternative reaction pathways
396
Explain glycogen storage disease
Enzyme deficiency
| Glycogen fails to enter transition "phosporylated" state
397
What is the cause of glycogen storage disease?
Defective glycogen synthesis/breakdown in muscle, liver and kidney
398
What are the symptoms of glycogen storage disease
```
Hypoglycaemia
Hepatomegaly
Skin and mouth ulcers
Bacterial and fungal infections
Bowel inflammation + irritability
```
399
What is the treatment of glycogen storage disease?
Slow release glucose meal
| Feed little and often
400
What does the catalytic activity of many enzymes depend on?
The presence of small molecules called cofactors or coenzymes
401
Metal ions are inorganic and termed
Cofactors
402
Organic molecules are termed
Co-enzymes
403
What do metal cofactors form?
A metal co-ordination centre in the enzyme (AKA metalloprotein)
404
How do coenzymes mostly associate with the enzyme?
Transiently
405
Are coenzymes regenerated
Yes
406
What do coenzymes change during the course of a reaction?
Charge or structure
407
Define a prosthetic group
Tightly bound coenzyme
408
Give an example of a prosthetic group
Haem in haemoglobin
409
What are enzymes without a cofactor called?
Apoenzymes
410
What are enzymes with a cofactor called?
Haloenzymes
411
Holoenzymes are the result of
Apoenzyme + cofactor
412
Examples of metal ions
Zinc, iron, copper
Involved in redox reactions
Stabilise transition state
413
Give exmapes of coenzymes
Many derived from vitamins
Many involved in redox reactions (NAD+, FAD)
Others involved in group transfer processes (ATP transfers phosphate group)
414
WHat do substrates binf to?
An active site
415
Why do substrates contain AA's?
Essential for catalytic activity
| Highly specidc interactions
416
Discuss the lock and key model
Active site of unbound enzyme = complementary to substrate shape
417
Discuss the induced fit model
Binding = induced conformational change in enzyme = complementary fit
418
What are isozymes?
Isoforms of enzymes
419
What do isozymes catalyse
Same reaction but have diff properties and structure
420
When can different isozymes be sunthesised?
During different stages of foetal and embryonic development
421
Where are differennt isozymes present?
In different tissues
| In different cellular locations
422
What are relative amount of isozymes useful for?
Diagnostic purposes
423
How many enzymes are typically used in the clinical lab to diagnose disease?
More than 20
424
What can side groups of serine, theronine and tyrosine form?
Phosphate esters
425
What can phosphorylation convert?
Enzymes to active or inactive form
426
What kind of reactions do protein kinases carry out?
Phosphorylation reactions
427
Give characteristics of phosphorylation reactions
Very fast
Reversible
Found in all cells - especiallu energy generating processes
428
What does the Regulation of enzyme activity by irreversible covalent modification result in?
Activation of enzymes
429
Define zymogens
inactive precursors of an enzyme
430
Zymogens are irreversibly transformed into active enzymes. How is this achieved?
By cleavage of a covalent bond
431
Give examples of zymogens
Digestive enzymes
Blood clotting enzymes
Clot-dissolving enzymes
Pancreas = trypsinogen and chymotrypsinogen, inactive precursors, are formed
Small intestine = enteropeptidase cleaves trypsinogen to form active trypsin which cleaves chymotrypsinogen to form active chymotrypsin
432
List irreversible proteolytoc enzymes
Digestive enzymes
Blood coagulation enzyme
Enzymes involved in dissolving blood clots
Enzymes involved in programmed development
