Cellular Biochemistry Flashcards
2-5
1
Q
Define Anabolism
A
Synthetics reactions the pathways end in ‘genesis’
2
Q
Define Catabolism
A
Breakdown reactions, pathways end in ‘lysis’
3
Q
What is the purpose of ‘free energy’?
A
- provides cells energy to function where heat flow cannot
- this is because cells have to remain in an isothermal state
4
Q
Gibbs Free Energy
A
G= ∆H- T∆S
when G= 0 : reaction is just feasible
when G < 0 : reaction is feasible, catabolism, exo
when G > 0 : reaction isn’t feasible, Anabolism, endo
5
Q
Explain coupling reactions and their use,
A
- coupling an endergonic reaction with an exergonic reaction to make it spontaneously feasible where total ∆G < 0
- this is done through a common intermediate
6
Q
Give an example of a coupling reaction?
A
Glucose + Pi → glucose-6-phosphate + H2O
ATP + H2O → ADP + Pi
Glucose+ ATP → ADP + glucose-6-phosphate
7
Q
Describe and explain Phosphate Group Transfer
A
- the manner in which ATP provides most of the free energy that is required of it
- during reactions, phosphate group forms a covalent bond with a species on the molecule
- this bond is then displaced by another more reactive species forming the new molecule and as lose in a Pi molecule
8
Q
What is the role of Mg2+ with ATP/ADP?
A
- forms a complex with ATP in the cytosol
- interacts with oxygen on triphosphate chain making it susceptible to nucleophilic attack, ( species that are rich in é will attack it)
- Mg2+ deficiency impairs metablosim
9
Q
What is substrate-level phosphorylation and how is it different from respiration-linked phosphorylation?
A
- formation of ATP by phosphate group transfer from a substrate to ADP
- requires a soluble enzyme and a chemical intermediate
whereas
RLP involves membrane-bound enzymes and transmembrane gradients of protons and requires oxygen (Krebs Cycle)
10
Q
What are the 6 main classes of enzymes?
A
- Oxidoreductases ( transfer Oil Rig)
- Transferases (of functional groups)
- Hydrolases ( just add)
- Lyases (syntheses) ( cleavage or formation of bonds)
- Isomerases (transfer of groups within a molecule)
- Ligases (synthetases) (Bond formation coupled to ATP hydrolysis)
11
Q
What are co-factors?
A
- non-protein parts that are essential for the function of an enzyme
split into
- metal ions
- coenzymes
12
Q
What are coenzymes?
A
- participate in the enzymatic reaction
- diffuse between enzymes carrying enzymes é
- cycle between oxidised and reduced forms
- usually derived from vitamins
- divided into cosubstrates and prosthetic groups
13
Q
What is the difference between a prosthetic group and a co-substrate?
A
Co-substrate: loosely associated with the enzyme
Prosthetic group: always covalently bound to the enzyme, not released as part of the reaction
14
Q
What is a vitamin precursor for a prosthetic group?
A
Vitamin B2 (Riboflavin) → FAD or FMN
Flavin Adenine Dinucleotide
Flavin Mononucleotide
15
Q
What is a vitamin precursor for a cosubstrate?
A
Niacin → NAD+
Nicotinamide Adenine Dinucleotide
16
Q
What is the role of coenzymes in Redox?
A
- act as oxidizing agents during respiration
- NAD+ → NADH : gains 2é and one H+ ion
- FAD → FADH : gains 2é and 2H+ ions
17
Q
What is the role of NADH and NADPH?
A
- NADH → ATP synthesis
- NADPH → reductive biosynthesis (anabolic biosynthetic reactions)
18
Q
What are the enzymes involved in the priming stages of glycolysis? Fill in the blanks of the diagram.
A
Hk: Hexokinase
Isomerase
PFK-1: phospho-fructose kinase
ALdolase
Isomerasew
19
Q
What are the enzymes involved in the glycolysis payoff reactions? Fill in the gaps
A
GAPDH: G3P dehydrogenase
PGK: Phosphoglycerate kinase
Mutase: PG mutase
Enolase
PK: Pyruvate kinase
20
Q
How pyruvate transported into the mitochondrion?
A
- travels through a carrier protein embedded in the MM
- Irreversible Link Reaction* between glycolysis and the TCA
- oxidative decarboxylation by the pyruvate dehydrogenase complex → Acetyl CoA
Pyruvate + CoA + NAD+ → Acetyl CoA + CO2 +NADH + H+
21
Q
What constitutes the pyruvate dehydrogenase complex? And which vitamins are vital to four of these complexes?
A
3 enzymes
5 coenzymes
- Thiamine pyrophosphate (TPP): Thiamine
- NAD+: Niacin
- CoA: Pantothenate
- FAD: Riboflavin
- Lipoic acid
22
Q
A Class In Kama Sutra Should Further My Orgasm
What are the 8 intermediates in the TCA cycle? Fill in the blanks
A
Acetyl CoA: 2C
Citric Acid: 6C
Isocitrate: 6C
alpha Ketoglutarate: 5C
Succinyl CoA: 4C
Succinate: 4C
Fumarate: 4C
Malate: 4C
Oxaloacetate: 4C
23
Q
How is the floc of Carbon atoms regulated in the TCA cycle?
A
- conversion of pyruvate to acetly-CoA (PDH reaction)
- entry of acetyl-CoA into the TCA cycle ( citrate synthase reaction)
Also regulated at isocitrate dehydrogenase and apha ketoglutarate dehydrogenase reactions
- these reactions are irreversible
24
Q
Give two important biosynthetic intermediates of the TCA cycle and explain how they are replenished
A
- Oxaloacetate: 4C that combines with Acetyl-CoA to form Citrate also converts to PEP to make amino acids
- Malate the precursor to Oxaloacetate
Oxaloacetate is replenished by
- Pyruvate using pyruvate carboxylase
- Phosphoenolpyruvate (PEP) using PEP carboxykinase and PEP carboxylase
Malate is replenished by
Pyruvate using malic enzyme
25
How do the electrons in NADH enter the inner mitochondrial membrane?
Via electron shuttles
- Glycerol-3-phosphate shuttle largely prevalent in the brain and muscle
- the Malate-aspartate shuttle in the liver and heart
- regenerate NAD+
26
Explain the glycerol-3-phosphate shuttle.
Fill in the diagram
27
Explain the Malate-aspartate shuttle.
Fill in the diagram
28
What happens in the link reaction in the Krebs Cycle?
* Pyruvate loses a CO2 molecule: oxidative decarboxylation
* the pyruvate dehydrogenase complex catalysts this reaction
* this forms Acetyl CoA
* releases CO2 and NADH + H+
This is an irreversible reaction, takes place in the matrix of the mitochondria after pyruvate has crossed the inner mito. membrane
29
What makes up the pyruvate dehydrogenase complex?
* Three difference enzymes
* Five different coenzymes
* Thiamine pyrophosphate: TPP
* vitamin Thiamine
* NAD+
* vitamin Niacin
* CoA
* vitamin Pantothenate
* Flavine Adenine Dinucleotide: FAD
* vitamin Riboflavin
* Lipoic acid
30
How does pyruvate enter the mitochondrion from the cytosol?
- enters via MPC: Mitochondrial Pyruvate carrier
- this is embedded into the inner mitochondrial membrane
31
What are the products of the TCA cycle?
- 3x NADred
- 1x FADred
- 2x CO2
- 1x GTP: guanosine-5-triphosphate, later converted to ATP
32
# A Class In Kama Sutra Should Further My Orgasm
What are the intermediates of the TCA cycle?
- oxaloacetate is regenerated and binds to acetyl CoA to form citrate which is the "start" of the cycle
* Acetyl CoA
* Citrate
* Isocitrate
* alpha-Ketoglutarate
* Succinly CoA
* Succinate
* Fumarate
* L-Malate
* Oxaloacetate
33
What are the rate-controlling enzymatic steps in the TCA cycle?
- oxaloacetate is regenerated and binds to acetyl CoA to form citrate which is the "start" of the cycle
* the condensation reaction between Acetyl CoA and Oxaloactetate
* this forms Citrate: reaction catalysed by citrate synthase
* Oxidative decarboxylation of Isocitrate
* this forms alpha-Ketoglutarate: reaction catalysed by isocitrate dehydrogenase
* Oxidative decarboxylation of alpha-Ketoglutarate
* this forms Succinyl CoA: reaction catalysed by alpha dehydrogenase
34
What are the two main ways the TCA cycle is regulated?
- conversion of pyruvate into acetyl-CoA: Pyruvate dehydrogenase reaction
- the entry of acetyl-CoA into the TCA cycle: the citrate synthase reaction
^ acetyl-CoA could be used to build lipids instead
( isocitrate and alpha-Ketoglutarate reactions are also a way of controlling the rate of reaction)
35
What are the two shuttles that transport the electrons of NADH into the mitochondrion?
* The Glycerol-3-phosphate shuttle: largely prevalent in brain and muscle
* G-3-P dehydrogenase oxidises NADred to NAD+ and reduces DHAP into G-3-P
* G-3-P can enter mitochondria and the electron is used to reduce FAD to FADH2
* The malate-aspartate shuttle: in the liver and heart
* aspartate leaves the mitochondria converted to oxaloacetate by alpha-KG
* oxaloacetate is reduced to malate which enters mitochondria exchanged with alpha-KG
* malate oxidizes back to oxaloacetate
* oxaloacetate to separate using glutamate from outside the mitochondria converted to alpha-KG again
* aspartate leaves to restart the shuttle
36
What are the components that make up the ETC?
* Complex I to IV
* Complex I: NADH dehydrogenase
* Complex II: Succinate dehydrogenase
* Complex III: Ubiquinonep cytochrome c oxidoreductase
* Complex IV: Cytochrome oxidase
* Complexes linked by 2 soluble proteins
* Ubiquinone (coenzyme Q): can move within the IMM
* Cytochrome c
Complex I, III, IV are proton pumps from the matric into the intramembrane space. these are used for further red. of NAD+ and FAD
37
What is the action of Complex I?
* Reaction: NADH +H+ + Q = NAD+ + QH2
* the H+ is lost to FMN to form FMNH2
* eventually is transferred to coenzyme Q- ubiquinone
* overall acts as a proton pump from the matrix into the intramitochondrial space
38
What is the action of Complex II?
* aka Succinate dehydrogenase
* electrons of FADH2 transfer their electrons to complex to
* this is then passed on to ubiquinone (Q) to form QH2
* Succinate --\> Fumarate
39
What are other sources of electrons for the ETC?
* through Beta-oxidation of lipids
* cytosolic Glycerol 3-phosphate
40
What is the action of Complex III and IV?
* Complex III: Ubiquinone: cytochrome c oxidoreductase
* 2nd of 3 proton pumps in ETC
* Complex IV: Cytochrome oxidase
* final proton pump
* terminal electron accepter
* produced water
41
What is the impact of the Complexes in the ETC?
* Complex I and III transfer 4 protons into he intramembrane space
* Complex IV transfers 2
* the combined effect creates a very positive electrochemical gradient in the intramembrane space
* this allows ADP**_3-_** from the matrix to be exchanged for ATP4- from the intramembrane space
* this is carried out by the antiporter _Adenine nucleotide translocase_
42
What is the Adenine nucleotide translocase?
What is it's action?
* antiporter
* facilitates the exchange of ADP from the matrix and ATP from the intramitochondrial space
* the antiporter can be inhibited by **Atractyloside**, can be isolated from a thistle
43
What membrane transporters are involved in the synthesis of ATP?
* Phosphate translocase
* symporter of H+ and H2PO4-
* this provides the phosphate needed for oxidative phosphorylation of ADP
* ATP Synthase
* an F-type ATPase formed of two functional domains- F0 and F1
* F0 is a proton channel
* it is oligomycin sensitive
* F1 is an ATP synthase
44
Summarise how ATP is synthesised by ATP synthase
* F1 made of 5 subunits; the beta subunits have catalytic sites for ATP
* the beta sites change their conformation
* for ADP and Pi binding then
* for binding to ATP tightly then
* change to give active site low affinity for ATP (allows ATP to be released)
* this is facilitated by the rotation of the gamma unit
45
How does Brown adipose tissue generate heat?
* has a high no. of mitochondria
* mitochondria contain thermogenin- **UCP-1**
* acts as an uncoupler
* H+ is transported back into the matrix without synthesizing ATP
* **DNP** is an exogenous example
* important in newborns
46
What is DNP- 2,4-dinitrophenol?
* weak acid that crosses mitochondrial membrane with H+ ion, into the matrix
* highly toxic to the liver
* can cause respiratory acidosis and hyperthermia
47
What are some distinct difference between the Nuclear and Mitochondrial genome?
- mt has a higher gene density
- mt doesn't contain introns
- has significantly higher % of coding DNA
- exclusively maternal
- not associated with histones
- mutates faster due to more damage from ROS and less correcting of mt DNA
48
How do defects in oxidative phosphorylation present themselves?
- involve tissues most reliant on OXPHOS
- occur later in life
- progressive with age
- show progressive enrichment in mutated mtDNA's
49
What are the two phenotypic/ variable penetrance that governs the presentation of a mt disease?
* Threshold effect (homoplasmy and heteroplasmy of mt)
* a certain amount of mutated or dysfunction mt is needed for the disease to be present
* during cell division, the progenitor cell with heteroplasmy could divide to give normal or a diseased cell
* Mt Genetic Bottleneck
* if the mature oocyte has a high level of mutation
50
Give 5 biochemical classifications of Mt myopathies
_Defects of_
* **Mitochondrial transport systems**
* ****CPT I and II ( can't use certain fat for energy)
* **Substrate utilisation**
* ****Pyruvate Dehydrogenase Complex deficiency
* Fatty acid oxidation defects
* **TCA cycle**
* ****Fumarase deficiency/ alpha-ketoglutarate dehydrogenase deficiency
* **OXPHOS coupling**
* ****Luft's syndrome: hypermetabolism, heat intolerance, polydipsia without polyuria
* **Oxidative phosphorylation**
* ****deficiency in the Complexes I toV
51
Give 4 key Mt Myopathies
* Lebers Herideritary optic neuropathy: **LHON**
* Myoclonus epilepsy with ragged fibre: **MERRF**
* Mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes: **MELAS**
* Kearns-Sayre syndrome: **KSS**
52
# Lebers hereditary optic neuropathy
Give more detail on LHON syndrome and its impact
* SNP in mt change ND4
* Arg to His in a polypeptide of Complex I
* can also be an SNP in mt gene for cut b in complex III
* there is a defect in é transport from NADH to ubiquinone
* not enough ATP produced in mt for neurons
* results in a damaged optic nerve
53
# Myoclonus epilepsy with ragged-red fibre
Give more detail on MERRF syndrome and its effect
* point mutation in mt gene encoding tRNALys
* disrupts the synthesis of proteins essential for OXPHOS
* in 80% of cases occurs at position 8344 in the mt genome
* effects other genes, mtTK, mtTL1, mtTH, mtTF
* skeletal muscles fibres are abnormally shaped
* the ragged-red fibres are clumps of defective mitochondria that accumulate in aerobic skeletal muscle fibres
* appear red when stained with **Gomeri modified Trichrome**
54
# Mitochondrial encephalomyopathy
Give more detail on MELAS syndrome and its effects
* effects the mtND5 gene - complex I
* also affects mtTH, mtTL1 and mtTV - all involved with tRNA
* mainly affects the brain/SNF and skeletal muscle
* symptoms appear in childhood
* lactic acidosis
* stroke-like episodes
* seizures --\> loss of vision
* movement difficulties + myoclonus
* dementia
55
# Kearns-Sayre syndrome
Give more detail on KSS and its effects
* from a 5kb deletion of the mt genome
* onset before age 20
* short stature and often have multiple endocrinopathies including diabetes
* Symptoms: dementia and retinitis pigmentosa
* lactic acidosis
* heart conduction defects
* raised cerebrospinal fluid protein content
56
What are some treatments of mt myopathies and how are they diagnosed?
* Diagnosed
* biochemical tests
* histology
* genetic testing
* Treatment and Prognosis
* prognosis is variable depends on the individual's metabolism
* occupational/physical therapy- help with muscle movement
* vitamin therapies: riboflavin, creatine, CoQ, C, K, carnitine
there is no specific treatment apart from the development of genetic strategies
