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Biochem Flashcards

1
Q

What are the bond strengths strongest to weakest

A

covalent–>ionic–>hydrogen–>hydrophobic interactions–>vanderwaals

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2
Q

Redox reations

A

OILRIG- one molecule is reduced and one is oxidised

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3
Q

what is electronegativity

A

the attractive force that an atomic nucleus exerts on electrons

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4
Q

talk about the electronegativity of carbon and hydrogen

A

carbon>hydrogen.. carbon has a greater attractive force for electrons, so it gains electrons, therefore it is reduced and hydrogen is oxidised

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5
Q

Carbohyrates

A

monosaccharides- glucose
disaccharides- lactose
polysaccharides-cellulose, glycogen (alpha 1-4 occationally alpha 1-6)

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6
Q

1st law of thermodynamics

A

energy neither created nor destroyed

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7
Q

2nd law of thermodynamics

A

energy converted from one form to another, some of that energy become unavailable to do the work (ie energ is lost and never 100% effective)

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8
Q

Change in free energy (Kj/mol) DeltaG

A

DeltaG = (energy of products {delta H}) - (energy of reactants {T delta S} )

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9
Q

if free energy is negative

A

exergonic (can occur spontaneously) ie products have less fre energy than reactants

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10
Q

if free energy is positive

A

endergonic (cannot occur spontaneously - requires energy e.g. walking upstairs) ie products have more free energy than the reactants

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11
Q

at equlibrium delta G=0 what does this mean

A

readily reversible reactions

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12
Q

Ka=

A

acid dissociation constant

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13
Q

pH=

A

measurement of how many H+ ions in a solution

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14
Q

Reaction spontaneity can be achieved by

A
  • change in conc of a reactant
  • coupling with highly favourable processes
  • both of the above help delta G become neg
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15
Q

protein structures

A

Primary - sequence of amino acids

Secondary - formation of backbone (polypeptide)

Tertiary - 3d structure

Quaternary - Spatial arrangement of multiple subunits (disulphide bonds hold proteins together)

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16
Q

The N terminal of a peptide chain is +ve due to NH3

A

…

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17
Q

The C terminal of a peptide chain is -ve

A

..

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18
Q

what is a prokaryote

A

microscopic single cell organism that does not have a defined nucleus

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19
Q

what is a eukaryote

A

normal cell with nucleus

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20
Q

nucleoside

A

base+sugar

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21
Q

nucleotide

A

nucleoside+ phosphate

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22
Q

Purines

A

adenine and guanine

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23
Q

Pyrimidines

A

uracil, thymine and cytosine

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24
Q

what are phosphodiester bonds

A

bonds between 3’ OH groups and 5’ triphosphate

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25
Q

base pairing

A

a-t

c-g

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26
Q

DNA polymerase

A

can only add to existing nucleic acids, cannot start sythesis on its own, requires RNA primer to start replicatoin

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27
Q

rRNA (ribosomal)

A

combines with proteins to form ribosomes where protein synthesis takes place

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28
Q

tRNA (transfer)

A

carries amino acids to be incorporated into proteins, anticodons consist of 3 nucleotides

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29
Q

mRNA (messanger)

A

stable RNA, carries genetic information for protein synthesis

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30
Q

poll II

A

synthesises all mRNA

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31
Q

transcription

A

RNA polymerase binding
oDetects initiation sites on DNA (promoters)
oRequires transcription factors

DNA chain separation
oUnwinding of DNA

Transcription initiation
oSelection of first nucleotide of growing RNA
oRequired additional general transcription factors

Elongation
oAddition of further nucleotides to RNA chain
oRNA synthesised in 5’ - 3’ direction

Termination
oRelease of finished RNA

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32
Q

what is TFIID

A

general transcription factor required for all Pol II transcribed genes

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33
Q

exons

A

coding regions

34
Q

introns

A

non-coding regions

35
Q

Translation

A
  • Anticodons of tRNA form base pairs with codons of mRNA
  • AUG is the start codon

Initiation
oGTP provides energy
oRibosomal subunit binds to 5’ end of mRNA, moves along until start codon found
oInitiator tRNA pairs to start codon
oLarge subunit joins assembly and initiator tRNA is located in P site

Elongation
oElongation factor brings aminoacyl-tRNA to A site
oGTP
oSecond elongation factor regenerates the first to pick up next aminoacyl-tRNA

Peptidyl transferase catalyses peptide bond formation between amino acids in P and A sites

Termination
oOccurs when A site of ribosome encounters a stop codon (UAA, UAG, UGA
oFinished proteins cleaves off tRNA

36
Q

Ribosomes

A
  • 3 tRNA binding sites - Exit, Peptidyl, Aminoacyl
  • Free ribosomes in cytosol proteins for - cytosol, nucleus, mitochondria - Post translational
  • Bound ribosomes on rough ER - plasma membrane, ER, Golgi, secretion - Co-translational
37
Q

enzymes

A
  • biological catalysts
  • speeds up the rate at which a reaction reaches equilibrium doesnt affect the position of equilibrium
  • lower the activation energy and stablise the transition state and provides alternatice reaction pathways
38
Q

apoenzymes

A

Enzymes without a cofactor

39
Q

holoenzymes

A

enzymes with a cofactor

40
Q

Induced fit

A

binding of the substrate induces a conformational change in the shape of the enzyme, resulting in a complementary fit

41
Q

what carries out phosphorylation

A

protein kinases

42
Q

Trypsin and chymotrypsin

A

work in the small intestine at an optimum pH of 7

43
Q

Trypsinogen and Chymotrypsinogen

A

produced in the pancreas and are produced in an inactive form so that they dont digest the pancreas. Enteropeptidase activates the trypsinogen in the small intestine.

44
Q

CK is an isozyme. The M form is produced in the skeletal muscle and the B form is produced in the brain. The MB form is produced in the heart.

45
Q

Vmax=

A

maximal rate at unlimited substrate conc

46
Q

Km=

A

Michaelis constant = 50% Vmax

47
Q

low Km=

A

an enzyme only needs a little substrate to work at 0.5Vmax (it has a high affinity)

48
Q

oVmax is the intersection of the straight line with the Y axis
oKm is the line’s intersection with the X axis

49
Q 
Competitive 
o	Binds to active site
o	Vmax remains the same 
o	Km increased 
(where both lines cross the y axis at same point)
50
Q

myoglobin

A

Michaelis Menten regulation

hyperbolic

51
Q

Haemoglobin

A

allosteric regulation

sigmoidal

52
Q

GLUT3

53
Q

GLUT5

54
Q

anabolism

A

required energy- endergonic and reductive

55
Q

catabolism

A

breakdown of molecules to yield energy-exergonic and oxidative

56
Q

glucose is oxidised to form what

A

co2 and h2o

57
Q

Glucose gets into cell via Glucose Transporters (GLUT) by facilitated diffusion

58
Q

glycolysis

A

the initial pathway for the conversion of glucose to pyruvate (net gain of 2 ATP ie uses 2 ATP but gains 4 ATP)

59
Q

hexokinase

A

phosphorylates glucose

60
Q

Phosphofructokinase

A

phosphorylates fructose-6-phosphate

61
Q

The 1st, 3rd and final reactions in glycolysis are control points and are irreversible and very exergonic.

62
Q

what are the 3 enzymes in the glycolysis control points

A

Hexokinase, phosphofructokinase, pyruvate kinase

63
Q

after glycolysis NADH must what?

A

by reoxidised to form NAD+ in order to continue ATP synthesis

64
Q

Pyruvate is converted into lactate when there is low oxygen- muscle cells work v hard to allow glycolysis to continue

A

which forms lactic acid (anaerobic)

65
Q

NAD

A
  • Only limited amounts of NAD+ are present in cell
  • NAD+ reduced to NADH + H+ in glycolysis
  • NAD+ is regenerated through the oxidative metabolism of pyruvate
66
Q

pyruvate

A
  • Anaerobic - alcoholic fermentation, lactic acid formation in humans
  • Aerobic - further oxidised in the Citric Acid Cycle
67
Q

aerobic metabolism of pyruvate

A
  • Enters mitochondria matrix
  • Converted to acetyl-coA (catalysed by Pyruvate Dehydrogenase Complex PDC)
  • Condenses with 4C compound to form 6C compound
  • 6C compound decarboxylated twice - yields CO2
  • 4 oxidation reactions - yield NADH + H+ and FADH2
  • GTP formed
  • 4C compound recreated
68
Q

for each Acetyl CoA the TCA cycle generates…

A
  • 3 NADH + H+
  • 1 FADH2
  • 1 GTP
  • 2 CO2
69
Q

TCA facts:

A

substrate= Acetyl CoA

  • occurs in the mitochondria
  • Oxaloacetate+ acetyl-CoA= citric acid
  • 3xNAD+ and 1x FAD+ are reduced in the cycle
  • Lipids are converted into fatty acids and then Acetyl- CoA which enters the TCA cycle
70
Q

Electrons from NADH and FADH2 reduce O2 to H2O. Electron energy is used to pump protons from the matrix to the intermembrane space, causing matrix pH to increase. Protons follow their conc and flow across the membrane- this energy is used to phosphorylate ADP-ATP

71
Q

what does negative electron transfer mean

A

substance more likely to donate electons than ydrogen

72
Q

Phosphoryl transfer potential

A

free energy change for ATP hydrolysis

73
Q

Electron transfer potential

A

measured by redox potential of a compound

74
Q

The standard redox potential of a substance is a measure of how readily it donates an electron

A

Negative = reduced form of X has lower affinity for electrons than hydrogen

Positive = reduced form of X has higher affinity for electrons than hydrogen

75
Q

oxidative phosphorylation

A

electron transport and ATP synthesis

76
Q

what occurs in the electron transport phase:

A

electrons from NADH enter complex 1, electrons fromFADH2 enter at complex 2 (TCA), electrons are handed down from high to lower redox potentials, and transferred onto O2 to form H2O
Transfer of electrons through respiratory chain is coupled to H+ transport from mitochondrial matrix to intermembrane space
3/4 complexes pump H+

77
Q

what is the electrochemical gradient

A

more protons in intermembranous space than matrix, matrix side more negative, protons attracted to matrix - coupled to ATP synthesis

78
Q

inhibition of oxidative phosphorylation

A
  • Cyanide, azide and CO inhibit transfer of electrons to O2

- No proton gradient formed, no ATP synthesised

79
Q

basic Oxidative phosphorylation

A
  • Electrons from NADH and FADH2 used to reduce O2 to H2O
  • Their energy used to pump protons from mitochondrial matrix to intermembrane space
  • Protons flow back across membrane
  • Energy of proton flow used to phosphorylate ADP to ATP
80
Q
  • Glycolysis - 2 ATP
  • TCA cycle (2 GTP) - 2 ATP
  • Glycolysis, PDH, TCA cycle (10 NADH + H+) - 25 ATP
  • TCA cycle (2 FADH2) - 3 ATP
  • 1 glucose molecule yields 30-32 ATP molecules
  • Transfer of electrons through the respiratory chain is coupled to transport of H+ from the mitochondrial matrix to the intermembrane space

Principles (Y1) (9 decks)

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