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Principles > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

bond strengths strongest to weakest

A

covalent > ionic > hydrogen > hydrophobic > van der waals

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2
Q

major classes of biomolecules

A

peptides and proteins, lipids, nucleic acids, carbohydrates

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3
Q

monosaccharide, disaccharide and polysaccharide examples

A 
monosaccharide = glucose
disaccharide = lactose 
polysaccharide = cellulose and glycogen
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4
Q

1st law and 2nd law of thermodynamics

A 
1st = energy cannot be created or destroyed 
2nd = when energy converted from one form into another, some becomes useless (eg lost as heat)
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5
Q

Change in free energy = ?

A

Delta G = (energy of products) - (energy of reactants)

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6
Q

exergonic reactions

A

have negative deltaG, can occur spontaneously

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7
Q

endergonic reactions

A

have positive deltaG, cannot occur spontaneously as require energy

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8
Q

how is free energy related to equilibrium

A

DeltaG near zero characteristic of readily reversible reactions

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9
Q

structure of proteins

A 
primary = sequence of amino acids 
secondary = result of hydrogen bonding along backbone 
tertiary = 3d structure 
quaternary = arrangement of multiple subunits
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10
Q

secondary structures and quaternary structures

A

Alpha = NO and COOH of amino acids 4 apart bond together
Beta sheets = can be parallel or antiparallel
Triple helix = tropocollagen, abundant in connective tissues

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11
Q

smooth ER and Rough ER

A

smooth ER = synthesis of steroid hormones, cholesterol, lipid synthesis
Rough ER = studded with ribosomes. synthesis of polypeptides/proteins

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12
Q

golgi apparatus

A

comprised of flattened, membrane-bound cisternae.

  • receives material from ER and distributes
  • modify proteins
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13
Q

nucleoside and nucleotide

A 
nucleoside = base + sugar
nucleotide = nucleoside + phosphate
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14
Q

DNA structure

A
  • purines = A and G (2 carbon-nitrogen ring)
  • pyrimidine = U, T,C
  • phosphodiester bonds between 3’ OH and 5’ triphosphate
  • CG is a triple bond
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15
Q

how does DNA replication happen

A
  • helicase unwinds
  • primase adds RNA primers
  • DNA polymerase makes strand
  • Leading strand = continuous as has free 3’ end
  • Lagging strand = Okazaki fragments sealed with ligase
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16
Q

Types of RNA

A 
rRNA = combines with protein to form ribosome 
tRNA = carries amino acids for protein synthesis 
mRNA = carries genetic information
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17
Q

how many types of RNA in eukaryotes and prokaryotes and what synthesises all mRNA

A

prokaryotes = 1 type
eukaryotes = 3 types
- pol || synthesises all mRNA

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18
Q

transcription requires transcription factors. what is the general one used for all pol || transcribed genes

A

TFIID

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19
Q

how many amino acids and combinations are there

A

64 amino acids and 20 combinations

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20
Q

how does translation occur

A
  • requires energy from GTP
  • ribosome moves along mRNA until start codon found.
  • tRNA with anticodon binds
  • Elongation: elongation factor brings aminoacyl-tRNA to A site. GTP hydrolysed and factor released.
  • 2nd elongation factor resynthesises 1st one to pick up next aminoacyl-tRNA
  • Peptidyl transferase catalyses bonds between amino acids in P and A sites.
  • ‘empty’ tRNA moves to E site and growing peptide moves from A to P site
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21
Q

what are the 3 tRNA binding sites

A

Exit, Peptidyl, Aminoacyl

22
Q

what do free ribosomes and bound ribosomes make proteins for

A

free: cytosol, mitochondria, nucleus
bound: Golgi, ER, plasma membrane

23
Q

what’s the difference between degenerate and unambiguous in genetic code

A

degenerate: amino acid has more than one codon
unambiguous: one codon for one amino acid

24
Q

what do enzymes do

A

they speed up rate reaction reaches equilibrium but don’t change its position. Also lower Ea.

25
Q

What are co factors and co enzymes

A

metal ions. enzymes with cofactor called holoenzymes and enzymes without cofactor called apoenzymes. coenzymes are organic molecules which bind tightly (prosthetic groups)

26
Q

what is Vmax and Km

A 
Vmax = maximal rate at unlimited substrate conc. 
Km = Michaelis constant = 50% of this rate 
Vmax = y axis intercept
Km = x axis intercept
27
Q

the lower the Km then…

A

the the faster the enzyme is at converting substrate at lower substrate conc.

28
Q

what does competitive enzyme inhibition do to graph

A

Km varies, Vmax stays same

29
Q

what does non-competitive enzyme inhibition do to graph

A

Vmax changes, Km stays same

30
Q

what relationship do allosteric enzymes show

A

sigmoidal

31
Q

what are the stages of glycolysis

A

glucose > fructose1,6biphosphate > 2 triose molecules > 2 pyruvate

32
Q

what are the products after glycolysis

A

2 ATP, 2NADH, 2 pyruvate

33
Q

what does hexokinase do

A

phosphorylates glucose

34
Q

what does phosphofructokinase do

A

it phosphorylates fructose-6-phosphate (to form fructose1,6,biphosphate)

35
Q

what does the pyruvate dehydrogenase complex catalyse

A

the decarboxylation of pyruvate to acetyl-coA

36
Q

what are the products of PDC (happens twice)

A

2 CO2, 2 NADH

37
Q

what happens in the TCA cycle

A

acetyl-coA joins with a 4 carbon molecule to form a 6-carbon molecule which is decarboxylated twice

38
Q

what are the products of ONE cycle of the TCA cycle

A

3NADH, 1ATP, 1FADH, 2CO2

39
Q

what are the products of the TCA for one mole of glucose

A

6NADH, 2ATP, 2FADH, 4CO2

40
Q

what is the only enzyme of the TCA cycle which isn’t located in the matrix

A

succincte dehydrogenase

41
Q

how do the NADH formed from glycolysis cross the membrane to matrix

A

using ‘shuttles’ of malate and G3P (glycerol-3-phosphate)

42
Q

what does a negative standard redox potential mean

A

reduced form of compound has lower affinity for electrons than hydrogen

43
Q

what is oxidative phosphorylation

A

coupling of respiration to ATP synthesis

44
Q

what happens in the 1st stage of oxidative phosphorylation

A

electron transport: electrons from NADH and FADH are handed down from higher to lower redox potentials as they are transferred onto O2 to form H2O.

  • electron transfer coupled to H+ transport from MATRIX to INTERMEMBRANE SPACE.
  • 75% of complexes pump H+ (1,3,4)
  • electrochemical gradient formed so H+ move back into matrix through ATP synthase
45
Q

what happens in 2nd stage of oxidative phosphorylation

A

ATP synthesis

46
Q

how can oxidative phosphorylation be inhibited

A

cyanide, azide, carbon monoxide

47
Q

what is the final balance from glycolysis to oxidative phosphorylation

A

10NADH, 2FADH, 6CO2, 30-32 ATP

48
Q

what complex do electrons from NADH enter at

A

complex 1

49
Q

what complex do electrons from FADH enter at

A

complex 2

50
Q

which complex DOES NOT PUMP Hydrogen ions

A

Complex 2

Principles (10 decks)

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