Biochemistry Flashcards
1
Q
What is the linkage found in cellulose? Can it be broken down by polysaccharides?
A
B(1,4) linkage.
No.
2
Q
What is the linkage found in glycogen for branching?
A
a(1,6) linkage
3
Q
What is the linkage found in glycogen for linear residues?
A
a(1,4) linkage
4
Q
What is the product of pentose phosphate pathway for oxidation of glucose?
A
Ribose-5-phosphate
** For nucleotide synthesis and DNA repair
5
Q
What is the product of anaerobic glycolysis? What is the process called?
A
Lactate.
Fermentation - rapid but inefficient and less ATP
6
Q
What is the product of aerobic glycolysis? What is the process called?
A
Pyruvate.
Oxidation.
7
Q
Does glycolysis use substrate phosphorylation or oxidative phosphorylation?
A
Substrate
8
Q
GLUT 1, 2 and 3. Which are found in the brain and liver? What are their KMs relative to each other?
A
Brain - 1,3 - Low KM (Still transports effeciently at low glucose conc.)
Liver - 2 - High KM
9
Q
What component/ nutrient from our diet gives us NADH?
A
Niacin
10
Q
At which part of the cell does glycolysis take place?
A
Cytosol
11
Q
How many ATP does glycolysis use and yield? How many NADH yielded?
A
2 ATP used
4 ATP and 2 NADH + 2 H+ yielded
12
Q
In the first step of glycolysis, glucose is converted into glucose-6-phosphate via which enzyme?
A
Hexokinase
13
Q
Aldolase acting on Fructose 1,6 biphosphate yields?
A
2 interconvertible 3C molecules
14
Q
What are the 3 enzymes that catalyses the control points in glycolysis?
A
Hexokinase (1st; ATP-dependent)
Phosphofructokinase (3rd; ATP-dependent)
Pyruvate kinase (9th; ATP-yielding)
15
Q
Does ADP or AMP have a stronger influence in promoting phosphofructokinase?
A
AMP.
ADP can still be broken down to give AMP and Pi by adenylate kinase
16
Q
What is the effect of Fructose 2,6-bisphosphate on Phosphofructokinase?
A
Stimulates its action.
Fructose 2,6-biphosphate levels will be high when glucose concentration is high
17
Q
What are the 3 inhibitors of glycolysis?
A
ATP (energy abundant)
Citrate (slows entry into TCA cycle)
H+ (excess lactic acid)
18
Q
What happens when there is lack of oxygen for pyruvate to enter the TCA cycle?
A
NADH will be used to ferment pyruvate into lactic acid
19
Q
What does NADH become when it converts pyruvate to lactic acid?
What are the 2 fates of this product?
A
Becomes NAD+.
- Decarboxylates Pyruvate to Acetyl-CoA
- Used in 5th step of glycolysis to regenerate NADH
20
Q
What is the Warburg effect?
A
Preferential anerobic glycolysis (Lactic acid) over aerobic glycolysis in cancer cells
21
Q
Does hexokinase in cancer cells have a high or low KM?
A
Low
22
Q
What are the 3 advantages and 2 disadvantages of the Warburg effect?
A
Advantages: Rapid energy production, rapid growth, supports other pathways for nucleotide synthesis
Disadvantages: Inefficient ATP synthesis, High glucose consumption (weight loss)
23
Q
Where is glycolysis targeted to treat cancer?
A
At or just after rate-limiting/ control points
24
Q
How is NAD+ regenerated?
A
Oxidative metabolism of pyruvate via Pyruvate Dehydrogenase Complex (PDC) yielding Acetyl-CoA as well
25
Where does the TCA cycle take place?
Mitochondria matrix
26
What is the H+ gradient across the inner mitochondria membrane?
Inwards as the matrix is more negative
27
What kind of reaction does Pyruvate Dehydrogenase Complex (PDC) result in?
An irreversible one; thus it is a rate-limiting step
**Acetyl-CoA cannot go back to becoming pyruvate
28
How many reactions does one TCA cycle have?
8
29
Where are the enzymes of the TCA cycle located at?
All in matrix except succinate dehydrogenase (6th step) (integrated in inner mitochondria membrane)
30
Metabolites of the TCA cycle can exit the cycle to participate in what kind of reactions?
Anabolic
| Making fatty acid from citrate
31
What kinds of products can give rise to Acetyl-CoA to enter the TCA cycle?
Glucose, fatty acids, amino acids
32
What are the positive (5) and negative (2) controls of the TCA cycle?
Positive: ATP, NADH, Acetyl-CoA, Succinyl-CoA, Citrate
Negative: ADP, NAD+
33
What are the 4 control points of the TCA cycle?
Formation of acetyl CoA, Citrate, a-ketoglutarate, succinyl-coA
34
What is the net yield from glycolysis and TCA cycle from 1 glucose molecule?
Glycolysis: 2 ATP (4-2), 2 NADH, 2H+
| TCA (2 cycles): 2 GTP, 8 NADH, 8 H+, 2 FADH2, 6 CO2
35
What is the inheritance pattern of a PDC deficiency?
| Which gender results in carrier and which results in a stillborn?
X-linked.
Daughter - carrier
Son - stillborn
36
Where will the more severe phenotype manifest in in PDC deficiency?
Energy-demanding tissues (E.g. Brain - neurological and developmental symptoms)
37
What is the inheritance pattern for Fumurate Hydratase (TCA cycle enzyme)? Which disease is it associated it?
Autosomal dominant
| Associated with Hereditary Leiomyomatosis (smooth muscle tumours) and Renal Cell Cancer (HLRCC)
38
What are the 4 stages of intracellular metabolism?
1. Ingestion/ Absorption
2. Acetyl-CoA formation
3. Acetyl-CoA oxidation (TCA)
4. Electron transport and oxidative phosphorylation
39
Where does oxidative phosphorylation take place?
Inner mitochondria membrane
40
What are electrons from NADH and FADH2 used reduced? What is the energy from this reduction used for?
O2 to H20.
| Energy used for pumping H+ to intermembrane space against gradient
41
What are 2 ways in which the 2 NADH from glycolysis can cross the inner mitochondria membrane?
1. Malate-Aspartate shuttle (NADH generated again)
| 2. Glycerol-3-phosphate shuttle (NADH oxidized to reduce FAD to FADH2)
42
Reduced form of molecules have a lower or higher affinity for electrons?
Does O2 accept or donate electrons?
Lower - thus they tend to donate; thus eventually oxidised
| O2 accepts electrons thus eventually reduced to H2O
43
What is electron transfer potential and phosphoryl transfer potential?
What is converted to what?
ETP: Redox potential of compound/ how readily they donate electrons
PTP: Free energy change to hydrolyse ATP
ETP of co-factors are converted to PTP of ATP
44
Are the proton pumps used in the ETC and phosphorylation the same?
No
45
How many complexes does the ETC have and where are they located?
4.
| Inner mitochondrial membrane
46
Which ETC complex does electrons from NADH and FADH2 enter?
e- from NADH enters at complex I
| e- from FADH2 enters at complex II (part of TCA cycle)
47
What is the trend of the ETC as electrons are being passed down?
Complexes become more oxidizing/ positive redox potentia/ accepts e- more readily
48
Cytochromes in the ETC possesses what groups to take and release electrons?
Haem groups containing Fe2+
49
Which ETC complex does not pump H+ out?
Complex II
50
What happens to the H+ that are pumped to the intermembrane space?
Flows back down electrochemical gradient via ATP synthase
*Electro because matrix is more negative from pumping protons out
51
What are the 3 components of ATP synthase and what 2 substrates are needed to synthesize ATP?
Proton channel, Stator (does not rotate, ATP forms here), Rotor (changes conformation of stator as proton flows)
Substrates: ADP, Pi
52
What are 3 substances that can inhibit electron transfer from complex IV to O2?
What is the consequence?
Cyanide, Azide, Carbon monoxide
| No energy to pump protons out -> no gradient -> no ATP synthesis
53
What do brown adipose tissue contain more than white fat?
Uncoupling protein (UCP)/ Thermogenin and mitochondria
54
What is non-shivering thermogenesis?
Heat generation via flowing of protons down UCP-1 (Proton leak) instead of ATP synthase
55
What is UCP-1 activated and inhibited by?
Activated by fatty acids (Cold -> NA -> B-adrenoceptors -> lipolysis)
Inhibited by nucleotides
56
How does artificial uncoupler 2,4-DNP (Proton leak) cause weight loss?
By increasing metabolic rate via thermogenesis but can cause overheating
57
What does ecstasy (MDMA) target? Where is this found at?
Targets UCP-3 at skeletal muscle.
| Can result in sustained hyperthermia and rhabdomyolysis
58
What is the P/O ratio of NADH and FADH2?
*# of Pi incorporated into ADP per atom of oxygen used
NADH: 2.5
FADH2: 1.5 (less yield as electrons only enters from complex II)
59
What strongly influences P/O ratio?
Uncoupling protein activity
60
What are the 2 factors that influences the final ATP yield per complete oxidation of 1 glucose molecule?
What is the final ATP yield?
P/O ratio and shuttle used to transport cytoplasmic NADH into mitochondria matrix.
32 ATP if malate-aspartate shuttle used (no change in # of NADH)
30 ATP if glycerol-3-phosphate shuttle used (2 glycolytic NADH to 2 FADH2)
61
What is the configuration of a heme group?
Planar
62
What is electronegativity?
Attractive force that atomic nucleus exerts on electrons within bond
63
What are the 3 characteristics of a receptor to hormones/ enzymes?
Recognition, communication & specificity
64
How many carbons does glucose have?
6Cs (Ringed hexose)
65
What is the relation between energy of reactant and products in an exergonic reaction?
Is Gibb's free energy + or -?
Reactant less energy than product
| Gibbs: negative
66
What is the relation between energy of reactant and products in an endergonic reaction?
Is Gibb's free energy + or -?
Reactant more energy than product
| Gibbs: positive
67
When does a reaction occur spontaneously (does not need energy)?
When Gibb's free energy is negative
| Tend to go towards 0 (equilibrium)
68
What determines if Gibb's is + or -?
Initial concentration of reactant
69
What is the universal gas constant?
8.3J/Kmol
70
If Gibb's energy is close to 0, what does it say about the reaction?
It is readily reversible
71
How do cells carry out unfavorable processes such as active transport and anabolism (Gibbs: +)?
By coupling with favourable processes (Gibbs: very negative) such as ATP hydrolysis
72
How many carbons does the sugar group have in ATP?
5Cs (Ribose)
73
What is the name of the high energy bond that links phosphates together in ATP?
Phospho-anhyride linkage (-P-O-P)
74
Why is ATP less stable than ADP?
Due to electrostatic repulsive strain from close proximity of negative charges between phosphate groups
**Thus usually there is a higher concentration of ADP
75
How is ATP regenerated in muscle cells?
By reacting ADP with creatine phosphate to yield creatine and ATP
76
ATP concentration is kept under?
<10mM
| Excess broken down --> energy release
77
Can reactions with negative Gibb's energy be used as control points?
No, it'll cause the reaction to occur more spontaneously
78
How many pyruvates are produced per glycolysis?
2 pyruvates thus 2 acetyl-CoA will be formed
| 1 glucose = 2 TCA cycles
79
What is the configuration of H-bonds?
Linear
80
What are 3 H-bond acceptors?
F, N, O
81
What are the 2 stereoisomer forms of amino acids?
| *Non-superimposable mirror image
D and L
| *L found in humans
82
What structure does amino acids have?
Tetrahedral
83
What is the carbon at the centre of the amino acid known as?
Alpha carbon
84
What catalyses the condensation of 2 amino acids?
Peptidyl transferase
85
How are peptide chains read?
From N to C terminus
86
What are the characteristics of a peptide bond (5)?
Planar
Strong
Rigid
Rotatable between alpha carbon and C and alpha carbon and N
Resonant (partial double bond from electrons from N and C)
87
What determines the characteristic of an amino acid?
The R group
88
What is the Ka and pKa of a strong acid?
```
High Ka (Higher ratio of ionized form)
Low pKa
```
89
What is the formula for pH?
-log10 [H+]
90
What is the formula for the Henderson-Hasselbach equation?
pKa - pH = log ([HA]/[A-])
91
When [HA] = [A-], what is pKa - pH?
0 as pKa = pH.
| Shows that unionised:ionised ratio is 1
92
When pH = pKA, what can the solution act as?
A buffer to resist change of pH when moderate amounts of acid or base is added
93
What is the isoelectric point/ zwitterion?
0 net charge, charges on side groups cancel out
94
How many pKa values does uncharged amino acids have?
2 due to having 2 groups (N and C)
| **with isoelectric point in between
95
What is the primary structure of proteins?
Amino acid residue sequence
96
What is the secondary structure of proteins?
H-bonded 3D arrangement of polypeptide chains and only considers backbone of polypeptide
97
How often does H-bond occur between C=O and N-H in an alpha helix?
Every 4 residues
98
Which amino acid residue breaks alpha helices?
Proline - introduces a destabilising kink which can allow another secondary structure to start
99
What happens to the polypeptide backbone in Beta sheets? And what are the 3 ways that the sheets can be arranged in?
Almost completely extended.
Parallel, anti-parallel, zig-zag (pleated sheet; alpha-carbon comes in and out of plane)
100
Which 2 amino acids introduces turns between strands?
Glycine and Proline
101
Where are Collagen triple helix found in?
Bone and connective tissue (Very strong)
102
What is the structure of a collagen triple helix?
What is the bond found between chains?
What is the sequence of amino acid in a collagen triple helix?
3 left handed helical chains twisted around each other forming a right handed superhelix (Tropo-collagen)
- Stabilised by H-bonds between chains by hydroxylysine and hydroxyproline
Repeating sequence of X-Y(Proline or hydroxyproline)-Gly in all strands
103
What is needed to make hydroxyproline? What is the consequence if there is a deficiency?
Vitamin C is needed to hydroxylate proline to form inter-chain H-bonds
Scurvy due to weakened collagen --> bleeding gums, discolouration
104
What is the tertiary structure of proteins?
Arrangement of all atoms of a polypeptide in space with local regions of distinct secondary structure
105
Which amino acid oxidises SH-SH to form covalent disulfide bonds?
Cysteine
106
What are the 2 types of protein seen in tertiary structures of protein?
Fibrous and Globular
107
What are fibrous proteins?
| Give 2 examples
Polypeptide chain organised parallel along a single axis either as long fibers or large sheets
E.g. Keratin, Collagen
108
What are 2 characteristics of fibrous proteins?
Mechanically strong, insoluble in water and slightly in salt solution
109
Are Collagen triple helix water-soluble?
Yes
110
What are globular proteins?
| Give 2 examples
Folded into a spherical shape with polar side chains facing out and non-polar side chains facing in
E.g. Hb and Myoglobin
111
What is the solubility of globular proteins?
Soluble in water and salt solution
112
What is the SNP involved in sickle-cell anaemia?
E6V
| Hydrophilic glutamic acid substituted with hydrophobic valine
113
What happens at low oxygen condition in sickle-cell anaemia?
Haemoglobin polymerises resulting in a rigid, sickle-shaped RBC which can occlude flow in capillaries
114
How are polypeptide chains folded?
Spontaneously (slow and erroneous)
| Aided by chaperones
115
What are prions?
| 1 example of a disease that it can cause.
Misfolded proteins that can misinform the folding of normal variant proteins - can aggregate to form amyloids
E.g. Creutzfeldt–Jakob disease (CJD)
116
What are quarternary structures of a protein?
| Give an example and how many subunits it has.
Has >1 polypeptide chain (and many subunits)
| E.g. Hb has 4 subunits (2a and 2B) each with own haem group to bind to 1 O2
117
What can heat, extreme pH, detergents, reducing/ thiol agents cause?
Protein denaturation
**Reducing agents disrupts disulfide bonds
118
What happens when 1 O2 binds to Hb?
Affinity of other subunits to O2 increases as conformation changes (Allosteric regulation & cooperative binding)
119
DNA replication is required before transcription.
T/F?
What is the product of transcription?
False.
| mRNA
120
What are the 2 differences between DNA and RNA?
RNA vs DNA
1. Ribose and Deoxyribose
2. Uridine and Thymine
121
What are purines and pyrimidines?
Purine: A, G
Pyrimidine: U, T, C
122
What is the bond linking free 3'OH group of the ribose to 5' triphosphate called?
Does this take energy?
Phosphodiester bond
| Yes.
123
Which direction to read DNA in?
5' to 3'!!!
124
How are viral DNA targeted to terminate elongation?
Via thymidine analogues (lack free 3'OH group) where viral reverse transcriptase has a higher affinity for.
125
How are the strands of a DNA double helix arranged?
| What faces inside and outside?
Anti-parallel.
| Sugar phosphate backbone outside and base pairs inside
126
What force holds nucleotide base pairs together?
| What is the combination of base pairing?
H-bond.
A to T/ U
C to G
127
When is DNA replication needed?
| What model does it operate on?
Before cell division to have complete complement genome for daughter cells.
Semi-conservative model (Each parental strand synthesizes a complementary strand and forms the double helix together)
128
What enzyme is needed for DNA replication?
| What is required before that to start?
DNA Polymerase.
| Needs RNA Primer does DNA Pol only adds to existing nucleic acids
129
How many origins of replication does eukaryotes have?
| What direction does it go in?
Many thus replication can start simultaneously
| Bidirectional to over more area
130
What direction does replication occur in?
3' to 5'!!
| Opposite from how DNA is read!!
131
What happens at the start of replication? (4)
Formation of replication bubble and bidirectional fork
DNA helicase unwinds double helix and stop it from rewinding
Single strand binding protein keep template strand separated
DNA primase to synthesize RNA primer
132
What are the 2 template strands in DNA replication called?
Leading and lagging strands
133
What direction does leading strand go in in DNA replication?
Follows fork movement.
| Has free 3' end thus elongates complementary DNA smoothly
134
What are the strands replicated in short segments in the lagging strand called?
What direction does it occur in?
Okazaki segments
| Done backwards in bits with short RNA primers (degraded after and gaps filled in by DNA polymerase)
135
What other activity does DNA polymerase have other than replication?
3' to 5' exonuclease activity (backwards) for proofreading by remove incorrect nucleotides
136
Which nucleic acids can have stem loops in them?
RNA, from intramolecular base pairing
137
What are the 3 types of RNA in order of abundance?
rRNA > tRNA (carries amino acid) > mRNA
138
What structure does tRNA have?
| What is the 3 nucleotide segment in the tRNA called?
Seen as cloverleaf when 2D.
| Anticodon base-pairs with specific codon on mRNA.
139
How many types of RNA Polymerase does eukaroytes and prokaryotes have?
Which type synthesizes all mRNA in eukaroytes?
Eukaryotes: 3 types, RNA Pol II synthesizes all mRNA
Prokaryotes: 1 type
140
How many DNA strands are used as template in replication and transcription?
Replication both strands (Leading and lagging).
| Transcription only 1 strand.
141
What does RNA polymerase bind to?
Is RNA primer needed?
What direction does it move?
Promoter/initiation site along with other transcription factors.
No.
3' to 5'
142
Relation of transcript to template and coding strand?
Template: Complementary and anti-parallal
Coding: Almost identical except U and T bases
143
Does the coding or template strand take part in transcription?
Only template strand
144
What is the TATAbox and which protein binds to it first?
RNA Pol II specific promoter region 25 nucleotide upstream of initiation site.
TATA-binding protein which is part of TFIID as a platform to allow for RNA Pol II and other transcription factors to bind.
145
Why does TFIID remain at promoter when transcription is occuring?
Allow for new initiation complex to assemble thus transcription takes place at low, basal rates (constitutive).
No effect on RATE of transcription.
146
What kind of transcription factors does the initiation stage of transcription require?
Does the order of assembly matter?
General transcription factors.
| Yes.
147
In what direction does the replication and transcription bubble move in?
Replication bubble: Bidirectional
| Transcription bubble: 1 direction
148
As the transcription bubble moves what happens to the DNA?
DNA unwinds in front and rewinds behind
149
What happens during the termination stage of transcription? (3)
RNA makes stem-loop structure with a stretch of Us behind
Specific enzymes recruited to cleave RNA
RNA Pol dissociates
150
What are the 3 stages of transcription?
Initiation
Elongation
Termination
151
What kind of transcription factors are needed for regulation?
Specific transcription factors binding to specific DNA seq near promoter
*General TFs for initiation
152
What are 3 types of specific transcription regulators?
1. Enhancers
2. Repressors
* Both can be far away from promoter; E.g. DNA bending brings activator protein bound to enhancer to the transcription complex
3. Stimuli-specific TF
* Regulatory protein binds to stress response element to transcribe specific genes involved in stress response
153
Homodimers of steroid receptors bind to what in the DNA?
Steroid response element
154
What happens to the mRNA before it proceeds to translation? (3)
Processing to become mature.
1. Spliceosomes splice out introns
2. Polyadenylation - add Poly(A) tail after cleaving 3' sequence away (Stretch of Us)
3. 5' capping with modified 5' GTP cap to prevent degradation by exonuclease
155
Where does translation and transcription occur?
| In what order does in order in eukaryotes and prokaroytes?
Transcription in nucleus, translation in cytosol
In eukaroytes, sequential
In prokaryotes, simultaneous
156
What are the 3 characteristics of the genetic code?
1. Degenerate - many amino acids have >1 codon
2. Unambiguous - but each codon only codes for 1 amino acid/ stop
3. Nearly universal
157
What is the start and stop (3) codon?
Start: Methionine (AUG)
Stop: UGA, UAG, UAA
158
How many reading frames does translation have?
3
159
What happens during the initiation stage of translation? (6)
40S (small) subunit with initiation factors bind to 5' mRNA
Scans until AUG found (ATP dependent)
Initiator tRNA base pairs with start codon
60S (large) subunit joins (ATP dependent)
Initiation factors released
tRNA on P site
160
Where are the tRNA binding sites located at? Where are they called?
60S subunit
| A, P, E
161
What are the ribosomal subunits for prokaryotes and eukaryotes?
Prokaryotes: 50S, 30S
Eukaryotes: 60S, 40S
162
What happens during elongation stage of translation (6)?
EF-1a brings aminoacyl-tRNA to A site
EF released from tRNA (GTP-dependent)
Peptidyl transferase catalyses peptide bond formation between amino acid of A and P site
Peptide chain then shifted to A site
EF-2 moves ribosome along mRNA by 1 triplet (GTP-dependent)
Empty tRNA moves from P to E site and exits while tRNA with peptide chain moves from A to P site
163
What is the role of aminoacyl-tRNA synthetase?
Highly specifically binds activated amino acid to correct tRNA
164
When is EF-1a available to pick up aminoacyl-tRNA?
When it is GTP bound
165
When and where does translation terminate?
At A site.
| When stop codon is encountered.
166
What happens when a stop codon is encountered?
Release factor binds to it (GTP-dependent) as there is tRNA for stop codons
Polypeptide cleaved off tRNA
Complex dissociates
167
What are polysomes?
Multiple ribosomes bound at different sites of mRNA producing multiple growing peptide chains
168
What kind of mutation have changes to amino acid sequence?
Missense
169
What kind of mutation results in a truncated polypeptide?
Nonsense - premature stop codon
170
What are the 5 DNA/ amino acid mutations?
1. Point (single base change)
2. Missense
3. Nonsense
4. Silent (no change in amino acid sequence due to degenerate genetic code where a few codons can code for 1 amino acid)
5. Frameshift (Add/ Del of bases)
171
What are the 5 chromosomal mutations?
```
Deletion
Duplication
Inversion
Insertion
Translocation
```
172
What happens to the polypeptide after translation? (3)
1. Targeting/ transport
2. Post-translation modification
3. Degradation if damaged/ unwanted
173
What are the 2 types of ribosomes in the cytosol?
What kinds of proteins do each translate?
When are they translocated?
1. Free - proteins for cytosol, nucleus, mitochondria
- translocated post-translation
2. Bound on RER - proteins for plasma membrane, ER. Golgi apparatus, secretion
- translocated co-translation
174
What is hereditary emphysema due to?
Misfolding of a1-antitrypsin in ER
175
What is the inheritance pattern of inclusion cell disease (mucolipidosis)? What is the pathology?
Autosomal Recessive.
Proteins destined for degradation at lysosome not sorted properly at golgi apparatus -> ends up being secreted.
Death before 8.
176
What do enzymes do?
SPEEDS UP RATE of reaction by stabilizing transition/ intermediate state of a reaction via an alternate pathway with lower activation energy
***No effect on equilibrium position, start and end point does not change
177
Are all enzymes proteins?
No, some are ribozymes (RNA)
178
What kind of environment do enzymes work in?
Body temp
Neutral pH
Aqueous solution
179
Does enzyme affect the start and end point of a reaction?
No
180
How much enzyme is used up in a reaction?
Enzymes are not consumed
181
What is the activation energy?
Energy of reactant to peak.
182
How can substrates be forced closer to react?
Heat (Kinetic energy) or pressure (compact space)
183
What does non-functional Glucose-6-phosphatase result in?
Glycogen storage disease. (Von Gierke's disease)
| Hinders glycogenolysis - cannot produce glucose
184
What are co-factors?
Inorganic metal ions
185
What are co-enzymes?
Organic carriers that transiently associate with enzymes; able to regenerate/ recycle
E.g. Vitamins (Redox reactions, group transfers)
186
What are cofactors tightly bound to enzymes called?
| 1 example.
Prosthetic group.
| E.g. Haem (Metallo-protein)
187
What is the term for an enzyme with and without a cofactor?
With - holoenzyme
| Without - Apoenzyme
188
What are the 2 models for specific binding of substrate to enzyme?
```
Lock and key (Complementary shape)
Induced fit (enzyme changes conformation to match substrate)
```
189
How are the active sites of the 3 pancreatic serine proteases like?
Chymotrypsin, Trypsin, Elastase
Chymotrypsin - hydrophobic pocket
Trypsin - lined with negatively charged aspartic acid
Elastase - small hydrophobic pocket
190
What are physical factors that influences rate of reaction?
Temp
pH
*To optimal levels
191
What are isozymes?
| 1 example?
Isoforms of enzymes with differenr properties and structure but catalyses same reaction (at slightly different condition)
E.g. LDH 1-5
192
Is pyruvate reduced or oxidised to lactate?
| What are the 2 substances needed to catalyse the reaction?
Reduced
By NADH and LDH-5
**Same enzyme used to oxidise lactate back to pyrvuate but LDH-1
193
What can be used to stabilise charge?
Metal ions
194
What transcriptive mechanism does hypoxia result in?
Activation of hypoxia sensitive TF binding to hypoxia response element which encodes for LDH-5 (Promotes pyruvate reduction to lactate)
195
What are the 3 isotypes of CK and where are they found at?
M - Skeletal muscle
B - Brain
MB - Heart (heterodimer)
196
What does phosphorylation (covalent modification) of enzyme result in? What helps to carry it out?
Is it reversible?
Activation and inactivation of enzyme.
Carried out by protein kinase (transfers phosphate from ATP - uses energy)
Reversible
197
What does irreversible covalent modification of enzyme result in?
1 example.
Activation of enzyme.
E.g. Zymogens irreversibly activated by proteolytic enzymes to active enzymes via covalent bond cleavage (GI enzymes, coagulation cascade, fibrinolysis)
198
What is [KM]
Substrate concentration at 50% Vmax
199
What is the Michaelis Menten equation?
Initial reaction rate, Vo
| Vo = Vmax [s] / (KM + [s])
200
Does Vo ever reach Vmax?
No, kinetics is not linear (asymptote)
201
What is the double reciprocal plot of Vmax vs [s] called?
| What does it help to determine? (2)
Lineweaver Burk Plot
| Helps to accurately determine KM and Vmax by becoming linear
202
Relation between low KM and 50%Vmax?
low KM: low [s] needed for enzyme to work at 50% Vmax
203
2 enzymes that plateau off at the same Vmax but with different speed will have?
Different KMs
204
In the Lineweaver Burk Plot, smaller values will be ___ to/from the origin (0,0)?
further
205
Isoenzyme Hexokinase in RBCs have a significantly lower KM than glucokinase in liver/pancreas.
Both converts glucose to G6P by hydrolysing ATP.
What does the KM difference help each enzyme to do?
Hexokinase - energy production maintained even at low [glucose]
Glucokinase - more sensitive to rise and fall of glucose thus activating insulin if [glucose] >5mM
206
Is the KM high/low for Prolyl hydroxylases (PHD)?
| What happens in hypoxia?
High KM - allows for O2 sensing
| Hypoxia initiation factor activatd --> dimerizes and transcribe genes to survive hypoxia (angiogenesis, RBC synthesis)
207
Where/Who does Monge's disease occur?
| What happens to haematocrit levels and O2 regulation?
Native population at high altitudes.
| High haematocrit and loss of O2 regulation of Epo production (for RBC synthesis)
208
What is Von Hippel Lindau (VHL) syndrome?
| What is 1 consequence?
Loss of PHD activity and excessive angiogenesis as VHL cannot bind to H-IFa, thus HIF not degenerated.
Brain haemangiomas.
209
In reversible competitive enzyme inhibition, what happens to Vmax and KM?
Vmax does not change
| KM increases as more substrate needed to fight for site (right shift in LB plot)
210
40% ethanol with dialysis and ventilation is used to treat methanol poisoning - an example of competitive binding/ inhibition.
What is the KM difference in ethanol and methanol?
What does methanol poisoning result in? (2)
Alcohol dehydrogenase KM for ethanol is higher than methanol.
Results in blindness from formaldehyde and metabolic acidosis.
211
What is the difference between orthostatic and allosteric site?
Orthostatic site - same site
| Allosteric site - different site
212
Treatment for methanol poisoning (3)
40% ethanol with dialysis and ventilation
213
In reversible non-competitive enzyme inhibition, what happens to Vmax and KM?
```
Vmax reduced (Upward shift in LB plot)
KM unchanged
```
214
What does irreversibly non-competitive enzyme inhibition involve?
Formation/ breakage of covalent bond in enzyme complex
215
What are rate-limiting enzymes inhibited by?
| Is this orthostatic or allosteric?
End product via negative feedback
| Allosteric control
216
Do allosteric enzymes follow Michaelis-Menten?
| What do they exhibit?
No, it is a SIGMOIDAL curve instead of a hyperbola.
| Exhibits cooperative binding.
217
What are allosteric enzymes controlled by?
| What behaviour do allosteric enzymes exhibit?
Activator (upward shift) and Inhibitor (downward shift)
| Co-operative behaviour
218
What is cooperativity?
1 Example of positive co-operativity?
Effects seen only AFTER substrate has bound where affinity increases
*Enzyme must be able to bind to >1 substrate sequentially
E.g. Hb: Hb(O2)4
219
What are the negative allosteric controls of Hb?
```
CO2
Acidosis
DPG (or 2,3-BPG)
Exercise
Temperature
```
**CADET shifts graph to the right (for the same PO2 there is lower O2 sat%)
220
1 example of an enzyme exhibiting non-cooperative binding?
Myoglobin - binds to O2 tightly (MbO2)
| *Follows Michaelis menten equation (hyperbolic)
