Biochemistry Flashcards
What is covalent bonding?
Sharing of electron pairs
What is ionic bonding
Attraction of opposite charges
What is hydrogen bonding?
Sharing of a hydrogen atom
What is hydrophobic attraction?
Interaction of non polar substances in the presence of polar substances
What are Van de Waals interactions?
Interactions of electrons of non polar substances
What is electron negativity
The attractive force that an atomic nucleus exerts on electrons
What is the final product of catabolism?
Carbon dioxide
Give some examples of mono, di and poly saccharides?
Mono = Glucose, Ribose Di = Lactose, Sucrose, Fructose and Maltose Poly = Glycogen and cellulose
2 laws of thermodynamics?
1) Energy is neither created or destryed. When energy is converted the total energy before and after is the same
2) When energy is converted, some of that energy becomes unavailable to do work. No energy transfer is 100% efficient
What is enthalpy?
Heat content (H)
What is entropy?
Level of disorder (S)
What is the equation for the change in free energy?
Delta G = deltaH - TxdeltaS
OR free energy change = (enery of products) - (energy if reactants)
What is an exogonic reaction?
Total free energy of the products is less than the total free energy of reactants. Free energy change is negative.
Reactions are fesable and spontaneous.
Drive disease pathways
What is an endogonic reaction?
Total free energy of the products is greater than the total free energy of reactants. Free energy change is positive.
Reactions are unfesable and not spontaneous.
Require an energy input
What are the standard conditions for biochemists?
T = 298K
1 atmosphere of pressure
1mol/litre concentration of reactnts (except H+)
pH = 7
Standard conditions in the body, the temperature is higher
How can you tell if a reaction is reversible or close to equilibrium?
The free energy change should be close to 0
Many cellular processes are unfavourable so how do they happen?
Coupling to to a highly favorable process such as ATP hydrolysis (Free energy change = -30kJ/mol)
Why is ATP less stable than ADP?
The negative phosphate group charges close together create electrostatic repulsion within the molocule
Where is the utilisation energy stored in ATP?
Anhydride bonds between the phosphate groups are high energy bonds
How is ATP regenerated?
Creatinine phosphate or 2ADP ATP + AMP
What is metabolism?
All the reactions taking place in the body
What is anabolism?
Synthesising complex molecules from smaller molecules. Energy consuming
WHat is catabolism?
Breakdown of complex molecules into smaller ones. Releases energy
NB: There are some energy consuming steps within catabolic pathways
What type of reactions are used as control points in metabolic reactions?
Reactions with large negative free energy changes. Not readily reversible reactions. Controlled by enzymes
Where can hydrogen bonding take place?
Covenlent bond between a hydrogen and a more elecronegative atom creates a polarised bond. Bonds tend to be linnear bonds, weaker than covelent bonds individually but strong collectively
What is the hydrophobic effect?
When non polar substances are placed in water they are insoluble. There is a strong attraction between water molecules and water excludes the non polar substance
What is a amphipathic molocule and what do they form in water?
A molocule with a hydrophobic and a hydrophillic part.
they form Micelles in water keeping the hydrophobic parts hidden inside
With a membrane, proteins that span the bilayer are hydrophobic/ampipathic and proteins on the surface are ampipathic/hydrophillic?
Span the bilayer = ampipathic
On the surface = hydrophillic
Proteins are made from L or D amino acids?
20 L amino acids (rotate light anticlockwise)
Some D amino acids are found in bacterial cell walls
In an amino acid what is the alpha carbon bound to and what shape is formed?
Tetrahedral
NH2, H, COOH, R
What are the 8 non polar/hydrophobic amino acids?
Leucine Proline Alenine Valine Methionine Tryptophan Phenylalanine Isoleucine
What are the 7 polar/hydrophilic amino acids?
Glycine Serine Asparagine Glutamine Cysteine Threonine Tyrosine
What are the 2 acidic amino acids?
Aspartic acid and glutamic acid
What are the 3 basic amino acids?
Lysine
Argenine
Histidine
Peptides have a direction- which direction are they read?
N terminus to C terminus
Why do peptides have a partial double bond character?
Pair of unpaired electrons oscillate across the peptide bond => rotation of the peptde bond is restricted. Peptide bonds are strong, planar and ridgid
What is a zwitterion?
An amino acid without a charged side group in a neutral solution with no net charge
Distribution of charge will change as a result of the pH of the surrounding fluid.
How many titratable groups and pKa values do amino acids have?
2 of each
What is the term for the pH at which the amino acid has no net charge?
The isoelectric pH
Why can proteins act as buffers?
Ends and side groups of proteins can be ionised.
How do you measure the strength of an acid?
Acid dissociation constant
What is pH?
A measure of the amount of protons in solutions
What is a buffer?
A soltion to control the pH of a reaction mixture
When does pH=pKa?
When the concentration of acid is equal to the concentration of conjugate base
When will buffers resist a change in pH?
When the pH is close to their pKa value
What is the primary structure of a protein?
A sequence of amino acid residues where polypeptides can rotate around bonds to the alpha cardon but not the peptide bond
What is the secondary structure of a protein?
A hydrogen bonded 3D arrangement of a polypeptide chain which considers the backbone of the polypeptide
What are the 3 types of decondary structure of a protein?
Alpha helix- right handed hydrogen bond between amino acids 4 residues away
Beta sheets- parallel or antiparralel sheets
Colagen triple helix- 3 left handed helix chains twisted to forma a right handed super helix
Which amino acid will cause a right angled bend?
Proline
What is the most common protein found in humans and where is it found?
Collagen- bones and connective tissue. Insoluble in water but soluble in strong alkili
WHat is tropocollagen?
Repeating X-Y-Gly
where X is any amino acid, Y is proline or hydroxyproline
How can a vitamin C defficieny weaken collagen?
The enzyme required to hydroxylate proline requires vitamin C (Ascorbic acid). To maintain health you need hydroxyproline so a vitamin C defficieny will weaken collagen
What is the tertiary structure of a protein?
Arrangement of all amino acids of a polypeptide in space.Fibrous or globular proteins
What is a fibrous protein?
polypeptide chains organised roughly parallel along a single axis. Long fibres, mechanically strong and insoluble in water and salt solution
Eg. Keratin, collagen, cartilage in bone an dteeth
What is a globular protein?
proteins folded into a spherical shape.
Soluble in water and salt solutions, form micelles and have lots of alpha helix and beta sheet.
Eg myoglobin, haemoglobin
What are the bonds found in tertiary protein structures?
Disulphide bonds (redox susceptible)
Electrostatic and hydrophobic attractions
Hydrogen bonds
Complex formation with metal ions
When and where is a disulphide bond usually found?
Between cyctine aminoacids and its formed in reducing conditions
Folding of a protein can occur spontaneously but this is erroneous. What molecules are used to help fold proteins?
Chaperones
What will denatre a protein structure?
Heat: increases vibrations in a protein
pH: electrostatic attraction interrupted
Detergents/urea: disrpt hydrophobic interaction
Thiol agents/reducing agents: Disrupt the disulphide bonds
What is myoglobin?
A globular protein which stores oxygen in muscles
What subunits does haemoglobin contain?
2 alpha and 2 beta subunits
What happens in stage one of glycolysis?
Glucose is trapped and stabalised
What are the control points in stage 1 of glycolysis?
Only the irreversible reactioncatalysed by hexokinase (controls substrate entry) and phosphofructokinase (controls rate of flow)
What happens in stage 2 of glycolysis?
2 interconvertable 3 carbon molecules are formed
What happens in stage 3 of glycolysis?
Generation of ATP
What is the contraol point in satge 3 of glycolysis?
Pyruvate kinase which controls the product exit
What are the products of glycolysis?
2 pyruvate, 2NADH + 2H+ and 2ATP
What happens if there is no oxygen for respiration?
No terminal electron acceptor therefore the electron transport chain and TCA cycle stop. But electrons are dangerous and you must continure to generate ATP
Pyruvate –> lactate catalysed by lactate dehydrogenase and NAD+ is produced to be used in glycolysis for ATP production
What ion can be used to neutralise the charge on lactate?
Ca++
Which enzyme catalyses the pyruvate –> lactate reaction?
Lactate dehydrogenase
What are the activators and inhibators of phosphofructokinase?
Activators: AMP, Fructose 2-6 bisphosphate
Inhibators: ATP, Citrate, H+ (too much lactic acid produced)
When is the cell charges and discharged?
Charged when adenylate nucleotides are in ATP
Discharged when adenylate nucleotides are in AMP + Pi
Which enzyme catalyses the reaction of 2ADP -> AMP + ATP
Adenylate kinase
Which cell types require glucose as an energy source?
Erythrocytes, renal medulla, retina, brain, all cancer cells
WHat can happen to glucose in the cell?
Storage
Oxidation through aerobic glycolysis
Fermentation by anaerobic gylcolysis
Oxidation through the pentose phosphate pathway
What is involved in the pentose phosphate pathway?
Ribose 5 phosphate
pre-cursor for nucleotide synthesis and DNA repair
Essential for growth
How is glucose transported into cells
Na+/glucose symporters
Passive facilitated diffusion glucose transporters (GLUT 1-5)
Where are the fallowing found? GLUT1 = GLUT2 = GLUT3 = GLUT4 = GLUT5 =
GLUT1 = Brain (low Km) GLUT2 = Liver and beta cells of the pancreas (high Km) GLUT3 = Brain (low Km) GLUT4 = Muscle and adipose tissue GLUT5 = Small and large intestine (fructose transport)
What is the Warburg effect?
Upregulation of anaerobic gylcolysis
Cancer cells produce energy by a high rate of glucose metabolism to lactate as cancer cells have a hexokinase with a low Km
What are the advantages and disadvantages of the Warburg effect for cancer cells?
+ Rapid energy production
+ Supports other pathways needed for nucleotide synthesis
+ Supports rapid proliferation
+ tumour core is very hypoxic or anoxic so anaerobic is important
- Produces H+ and lactate
- very inefficient ATP synthesis
- High glucose consumption demand- cancer patients loose weight
How can 2 deoxyglucose be used to treat cancer patients?
Initially phosphorylated to 2 deoxyglucose-6-phosphate which competitively inhibits phophoglucose isomerase and non competitively inhibits hexokinase.
Blocks further metabolism of glucose-6-phosphate
How can 3 bromopyruvate be used to treat cancer patients?
Competitive inhibator or glyceraldehyde-3-phosphate dehydrogenase. Prevents production of 1,3-bisphosphate
How can Dichloroacetate be used to treat cancer patients?
Promotes conversion of lactic acid to pyruvate by re-engaging mitochondrial metabolism and then slows the glycolytic rate.
Cells can no longer sustain nucleotide synthesis.
The ribose-5-phosphate production through pentose phosphate pathway is inhibited
What is PDC?
Pyruvate dehydrogenase complex
What happens during the PDC reactions?
1) Pyruvate is decarboxylated and CO2 is formed with hydroxyethyl TTP
2) Hydroxyethyl group is transferred to lipoic acid and oxidises to form acetyl dihydrolipoamide
3) Acetyl group is transferred to CoA
4) Dihydrolipoamide is reoxidised to form lipoic acid
What can inhibit the PDC reactions?
ATP, Acetyl CoA and NADH
What are the intermediates in the TCA cycle?
A Clown In Kilimanjaro Sings Songs For Money Only Acetyl CoA Cirtate Isocitrate Ketoglutarate (alpha) Succinyl-CoA Succinate Fumerate Malate Oxaloaccetate
Where are the 3 control points of the TCA cycle?
1) Oxaloaccetate –> Citrate (citrate synthase)
Inhibited by ATP, NADH, succinyl CoA and citrate
2) Isocitrate –> alpha ketoglutarate (Isocitrate dehydrogenase)
Inhibited by ATP and NADH and stimulated by ADP and NAD+
3) Alpha ketoglutarate –> Succinyl CoA (alpha ketoglutarate dehydrogenase)
Inhibited by ATP and NADH and Succinyl CoA
Where does the TCA cycle occur and why?
Mitochondrial matrix as it contains all the enzymes for the TCA cycle except succinate dehydrogenase which is integrated into the inner mitochondrial membrane
How does pyruvate enter the mitochondrial matrix?
H+ gradient from cyctol to matrix and there is a H+/pyruvate symport protein which uses facilitated diffusion. NB: Pi also enters coupled with H+.
Can pyruvate be converted back to accetyl CoA?
No the reaction is irreversible
What are the products of the TCA cycle?
2CO2
3NADH + 3H+
1FADH2
1GTP (substrate level phosphorylation)
What is the yield from one glucose at the end of the TCA cycle?
6ATP, 10H+, 10NADH, 2FADH2 and 6CO2
What is PDC deficiency?
X linked neurological disease in children. Gene for pyruvate dehydrogenase is on the X chromosome. Female carriers get adolescent onset and males result in a still birth
What are the symptoms of PDC deficiency?
Poor muscle tone and lack of coordination, retardation and seizures, persistent lactic acidosis and respiratory problems
What is fumerase deficiency and Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC)
Defect in fumerase => multiple system benign and malignant tumours particularity in the kindey
In the respiratory chain their are 4 multisubunit complexes. Where do electrons form NADH and FADH2 enter?
NADH enter at complex 1 and FADH2 enter at complex 2
In the respiratory chain, do electrons move from higher to lower or lower to higher redox potentials?
Higher to lower and the energy released is used to actively transport H+ across the membrane
What is the terminal electron acceptor?
Oxygen and it is reduced to water
What is UQ in oxidative phosphorylation?
Ubiquinone co-enzyme Q which is hydrophobic and shuttles rapidly in the membrane
What is CytC in oxidative phosphorylation?
Soluble protein which contains a haem group as a functional cofactor which contains a FE++ group which can take up ad release electrons
In oxidative phosphorylation Transport of electrons through the respiratory chain is coupled to what?
Transport of H+ from the matrix to the intermembrane space. Requires energy released form electrons moving from a higher to lower redox potential
Which 3 multi subunit complexes pump H+ in oxidative phosphorylation?
1, 3 and 4
What happens when there are more protons in the intermembrane space than the matrix?
Protons diffuse back into the matrix and this is coupled to ATP synthesis.
NADH is produced in glycolysis but cannot cross the mitochondial membrane for oxidative phosphorylation. How is this overcome?
Malate- Aspartate shuttle
1) NADH is used to generate malate from oxaloacetate in cystol
2) Malate transporters transfer malate into the mitochondrial matrix
3) Malate conversion to oxaloacetate in the TCA cycle generates NADH in addition to the malate that arises from fumerate.
What does a negative and positive edution potential imply?
Negative implies a lower affinity for electrons than hydrogen (reducing agent)
Positive implies a higher affinity for electrons than hydrogen (oxidising agent)
What makes up ATP synthase?
F1 subunit- round and protrudes into the mitochondrial matrix
F0 subunit is a hydrophobic complex in the inner membrane
a, b, alpha, beta and delta form the stator
c, gamma and epsilon form the rotor (mostly F0)
Flow of protons turns the rotor and a conformational change leads to ATP synthesis
What substances can inhibit oxidative phosphorylation?
Cyanide, azide and CO inhibit the transfer of electrons to oxygen meaning no proton gradient is formed and no ATP synthesised
What happens with uncoupling of electron transport and phosphorylation?
Protons return to the matrix via UCP uncoupling protein rather than ATP synthase
=> non shivering thermogenesis and maintains body temperature in hibernating mammals and newborns.
Brown adipose tissue contains UCP. This proton leas consumes oxygen and generates heat and requires fatty acids. ?Obesity therapy
What is the P/O ratio?
Number of molecules of Pi incorporated into ADP per atom of oxygen used
What is the P/O for NADH and FADH2?
NADH is 2.5 and FADH2 is 1.5
How many ATP are generated through 1 glucose in aerobic respiration?
30-32
