Biochemistry

Question 1

bond strengths strongest to weakest

Answer 1

covalent > ionic > hydrogen > hydrophobic > van der waals

Question 2

major classes of biomolecules

Answer 2

peptides and proteins, lipids, nucleic acids, carbohydrates

Question 3

monosaccharide, disaccharide and polysaccharide examples

Answer 3

monosaccharide = glucose
disaccharide = lactose 
polysaccharide = cellulose and glycogen

Question 4

1st law and 2nd law of thermodynamics

Answer 4

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

Question 5

Change in free energy = ?

Answer 5

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

Question 6

exergonic reactions

Answer 6

have negative deltaG, can occur spontaneously

Question 7

endergonic reactions

Answer 7

have positive deltaG, cannot occur spontaneously as require energy

Question 8

how is free energy related to equilibrium

Answer 8

DeltaG near zero characteristic of readily reversible reactions

Question 9

structure of proteins

Answer 9

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

Question 10

secondary structures and quaternary structures

Answer 10

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

Question 11

smooth ER and Rough ER

Answer 11

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

Question 12

golgi apparatus

Answer 12

comprised of flattened, membrane-bound cisternae.

• receives material from ER and distributes
• modify proteins

Question 13

nucleoside and nucleotide

Answer 13

nucleoside = base + sugar
nucleotide = nucleoside + phosphate

Question 14

DNA structure

Answer 14

• 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

Question 15

how does DNA replication happen

Answer 15

• 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

Question 16

Types of RNA

Answer 16

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

Question 17

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

Answer 17

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

Question 18

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

Answer 18

TFIID

Question 19

how many amino acids and combinations are there

Answer 19

64 amino acids and 20 combinations

Question 20

how does translation occur

Answer 20

• 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

Question 21

what are the 3 tRNA binding sites

Answer 21

Exit, Peptidyl, Aminoacyl

Question 22

what do free ribosomes and bound ribosomes make proteins for

Answer 22

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

Question 23

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

Answer 23

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

Question 24

what do enzymes do

Answer 24

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

Question 25

What are co factors and co enzymes

Answer 25

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

Question 26

what is Vmax and Km

Answer 26

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

Question 27

the lower the Km then...

Answer 27

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

Question 28

what does competitive enzyme inhibition do to graph

Answer 28

Km varies, Vmax stays same

Question 29

what does non-competitive enzyme inhibition do to graph

Answer 29

Vmax changes, Km stays same

Question 30

what relationship do allosteric enzymes show

Answer 30

sigmoidal

Question 31

what are the stages of glycolysis

Answer 31

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

Question 32

what are the products after glycolysis

Answer 32

2 ATP, 2NADH, 2 pyruvate

Question 33

what does hexokinase do

Answer 33

phosphorylates glucose

Question 34

what does phosphofructokinase do

Answer 34

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

Question 35

what does the pyruvate dehydrogenase complex catalyse

Answer 35

the decarboxylation of pyruvate to acetyl-coA

Question 36

what are the products of PDC (happens twice)

Answer 36

2 CO2, 2 NADH

Question 37

what happens in the TCA cycle

Answer 37

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

Question 38

what are the products of ONE cycle of the TCA cycle

Answer 38

3NADH, 1ATP, 1FADH, 2CO2

Question 39

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

Answer 39

6NADH, 2ATP, 2FADH, 4CO2

Question 40

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

Answer 40

succincte dehydrogenase

Question 41

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

Answer 41

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

Question 42

what does a negative standard redox potential mean

Answer 42

reduced form of compound has lower affinity for electrons than hydrogen

Question 43

what is oxidative phosphorylation

Answer 43

coupling of respiration to ATP synthesis

Question 44

what happens in the 1st stage of oxidative phosphorylation

Answer 44

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

Question 45

what happens in 2nd stage of oxidative phosphorylation

Answer 45

ATP synthesis

Question 46

how can oxidative phosphorylation be inhibited

Answer 46

cyanide, azide, carbon monoxide

Question 47

what is the final balance from glycolysis to oxidative phosphorylation

Answer 47

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

Question 48

what complex do electrons from NADH enter at

Answer 48

complex 1

Question 49

what complex do electrons from FADH enter at

Answer 49

complex 2

Question 50

which complex DOES NOT PUMP Hydrogen ions

Answer 50

Complex 2