BioChem Flashcards
The most strong type of bond is…
Covalent
The five main types of bonds are…
Covalent Ionic Hydrogen Hydrophobic PD-PD interaction LDFs/ Van der Waals - interaction of electrons in non-polar substances
Electronegativity is…
The attractive force that an atomic nucleus exerts on electrons
EN carbon is greater than EN hydrogen. Which is reduced?
Carbon has a greater attractive force for electrons, so it gains electrons, therefore it is reduced and hydrogen is oxidised
Reducing agents are themselves oxidised. True/False?
True`
First law of thermodynamics?
Energy is neither created or destroyed
Second law of thermodynamics?
When energy is converted to another form, some of it is lost (never 100% efficient)
∆G = the change in free energy = ?
∆H - T∆S ∆G°’ + RTln([C][D]/[A][B])
Exergonic reactions are where…
Products have less free energy than the reactants ∆G is -ve
Reaction can occur spontaneously
Endergonic reactions are where…
Products have greater free energy than the reactants ∆G is +ve
Reaction cannot occur spontaneously
The difference between normal standard conditions and biochemical standard conditions is…
pH = 7
At equilibrium ∆G = 0. This is characteristic of readily reversible reactions. True/False?
True
Reaction spontaneity can be achieved by…
Changing concn of reactants/products
Coupling with highly favourable processes (e.g. with hydrolysis of ATP)
Both of the above help ∆G become -ve (EXERGONIC IS FAVOURABLE)
Distinguish between catabolism and anabolism
Breaking down complex molecules into smaller ones to give out energy (favourable)
Synthesise complex molecules out of smaller ones, requires energy
What is the hydrophobic effect?
Tendency of non-polar substances to aggregate in aqueous solutions (in centre) and exclude water molecules
Amino acids are subdivided into 4 groups, which are?
Non-polar hydrophobic
Polar uncharged
Acidic (-COOH)
Basic (-NH)
The N-terminal of a peptide chain is -ve. True/False?
False It is +ve due to NH3
The C-terminal of a peptide chain is -ve. True/False?
True due to COO-
A zwitterion has which type of charge?
None! No net charge - AA with charged side groups in neutral solutions
Ka = acid dissociation constant = ?
[H+][A-]/[HA]
pH = measurement of how many H+ in a solution = ?
-log10[H+]
Henderson Hasselbach Equation connects Ka of a weak acid with the pH of a solution containing this acid. The equation is…
pH = pKa + log[A-]/[HA] pKa - pH = log[HA]/[A-]
Primary protein structure describes…
The specific sequence of amino acids in a chain
Secondary protein structure describes…
The hydrogen-bonded 3D arrangement of the chain α-helix (one peptide chain spiralled; right-handed) B-stranded-sheet or B-pleated-sheet
Tertiary protein structure describes…
The arrangement of the chain in space and forces stabilising the structure - H bonds, salt bridges, covalent disulphide bonds
Quaternary protein structure describes…
Association of non-protein groups to the chain e.g. haemoglobin, myoglobin with multiple subunits
Give the number of bonds between bases A?T and C?G…
A-T = 2, C-G = 3
What is the central dogma?
DNA is transcribed to RNA, which is translated into protein
A nucleoside has…
5C sugar + organic base
A nucleotide has…
5C sugar + organic base + phosphate group(s)
Pol II synthesises only stable RNA. True/False?
False Pol II (specific promotor - binds to TATA box creating a kink in DNA — transcription) synthesises all RNA. Pol I and III synthesise only stable RNA
DNA polymerase has 3 important characteristics
Can only add to existing nucleic acids
Cannot start synthesis on its own
Requires an RNA primer to start replication
Differentiate between leading and lagging strands of DNA
Leading = 3-5, free 3 end for next nucleotide Lagging = 5-3, uses short okazaki fragments
Nucleotides only add to the free 3’ end of a strand? True/False
True
Describe the structure of ribosomes
4 rRNA molecules - EXIT, PEPTIDYL (peptides held), AMINOACYL (where tRNA goes to bind) area
Enzymes can affect the equilibrium position of a reaction. True/False?
False
How do enzymes lower the activation energy of a reaction?
Bind to and stablise the transition state and provide alternative reaction pathways
Enzyme without a cofactor is called a…
Apoenzyme
What is a cofactor?
Inorganic metal ions e.g. Zn, Fe, Cu that stabilise transition states
Enzyme with a cofactor is called a…
Holoenzyme
What are coenzymes?
Organic molecules derived from vitamins
Induced fit model describes enzyme-substrate interaction by…
Binding of substrate induces a conformational change in the enzyme, resulting in complementary fit
Trypsin and chymotrypsin work in the ____ and have an optimum pH of _
Small intestine, 7
What are isozymes?
Catalyse same reactions as enzymes but have different properties and structure
CK is an isozyme. The M form is produced in ____ and the B form is produced in the ___. MB form is produced in the ___
Skeletal muscle, brain, heart
Which enzymes carry out phosphorylation?
Kinases
What are zymogens?
Inactive precursors of an enzyme
Where are trypsinogen and chymotrypsinogen formed? Why is it important they are produced inactive?
Pancreas
They would digest the pancreas if active
Which enzyme activates trypsinogen? Where does this occur?
Enteropeptidase
Small intestine
Vmax is?
The maximal rate of reaction at unlimited substrate concn
Km is?
The concn of substrate which gives 50% maximal rate, i.e. 0.5Vmax
A low Km means…
An enzyme only needs a little substrate to work at 0.5Vmax (it has high affinity)
Vmax can be obtained from a Lineweaver-Burk plot by looking at the interesection with the X axis. True/False?
False
Intersection with X (horizontal) axis is Km; intersection with Y (vertical) axis is Vmax
In competitive inhibition, Vmax is ___ and Km is ___
The same, increased
In non-competitive inhibition, Vmax is ___ and Km is ___
Decreased, the same
Orthosteric enzymes follow M-M kinetics and the curve is shaped like a ____
Hyperbola
Allosteric enzyme do not follow M-M kinetics and the curve is shaped like a ___
Sigmoid
Hexokinase has a low Km (0.5) for glucose while glucokinase had a Km of 5. What does this tell you about their affinity for glucose?
Hexokinase has a higher affinity for glucose than glucokinase - needs less enzyme to work at 50% of Vmax
GLUT3 is located in the…
Brain
GLUT5 is located in the…
Gut
In glycolysis, glucose (6C) is converted into…
2 x pyruvate (3C each)
In glycolysis, there is a net gain of how many ATP?
2 ATP (4 gained, 2 lost)
The _, _ and _ reactions in glycolysis are control points (irreversible as they are very exergonic)
1st, 3rd and final
3 enzymes involved in the glycolysis control points
Hexokinase (GLUCOSE), phosphofructokinase (FRUCTOSE), pyruvate kinase (PYRUVATE)
We must reoxidise NADH to form __ in order to continue ATP synthesis after glycolysis
NAD+
Pyruvate conversion to lactate occurs when?
Low oxygen - muscle cells work very hard to allow glycolysis to continue NAD+ is regenerated by oxidation of NADH
What is Warburg effect?
Upregulation of anaerobic glycolysis in cancer cells
What is the substrate for the TCA cycle?
Acetyl-CoA
Where does TCA cycle occur?
Mitochondria (mainly central matrix and then cristae)
What is the fate of pyruvate before TCA cycle?
Enters mitochondria, where PDC catalyses oxidative decarboxylation of pyruvate to acetyl-CoA 2CO2 released in total
Citric acid (6C) is formed by the combination of which 2 molecules?
Oxaloacetate (4C) + Acetyl-CoA (2C)
How many cofactors are reduced in total in TCA cycle?
4 - 3x NAD+ and 1x FAD+
How does pyruvate enter the TCA cycle?
Via the H+ gradient from the cytosol into the matrix of the mitochondria
GDP conversion to GTP is known as…
Substrate level phosphorylation
Succinate hydrogenase uses FAD+ as a cofactor. It is the one enzyme of TCA cycle that is located in the central matrix. True/False?
False It is the only enzyme located in the cristae - all others located in the central matrix
Lipids are converted to ______ and then ____ which enters TCA cycle
Fatty acids, Acetyl-CoA
Each turn of TCA cycle involves the uptake and release of how many carbon atoms, and in what form?
C uptake as Acetyl-CoA, 2C released as 2CO2
Glycolysis + PDC + TCA cycle reactions = _NADH, _H+, _FADH2
10NADH, 10H+, 2FADH2
Each NADH and FADH2 molecule contains how many electrons?
2
A -ve electron transfer potential means…
Substance is more likely to donate electrons than hydrogen
What is the function of Co-enzyme Q?
Pick up electrons from Complex 1 or 2 and donate them to Complex 3
Transfer of electrons through the respiratory chain is coupled to transport of _ from the mitochondrial matrix to the intermembrane space
H+
Key point of oxidative phosphorylation: Electrons from NADH and FADH2 reduce O2 to __ e- energy is used to pump protons from the matrix to the _____, causing matrix pH to ____ Protons follow their concn and flow across the membrane - this energy is used to phosphorylate ___ to ___
H2O
Intermembrane space,
pH to increase (and intermembrane space pH to decrease)
ADP to ATP
1 glucose molecule yields how many ATP molecules in total?
30-32 ATP
How does NADH from cytoplasm enter mitochrondia to be oxidised into NAD+?
Using shuttles - glycerol 3 phosphate, malate aspartate
Electron transport and ATP synthesis happens ______ using ____ pumps
Simultaneously
(Seperate) H+
Explain the process of uncoupling electron transport and phosphorylation…
Brown adipose tissue contains uncoupling protein thermogenin
