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MB1: Principles > Biochem > Flashcards

Biochem Flashcards

1
Q

Name basic biochemical bonds

A 
covalent 
ionic 
h-bonding 
hydrophobic interactions 
van der waals
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2
Q

what is electronegativity

A

attraction of nucleus for electrons, greater the electronegativity the closer atoms van pull electrons to it

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3
Q

Monosaccharide and example

A

6 carbon structure with oxygen binding it into a ring shape
cannot by hydrolysed to a simpler sugar
eg glucose

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4
Q

Disaccharides and examples

A

2 monosaccharides connected by a bond
formed by condensation
safe to consume and transport
fructose, sucrose, lactose and maltose

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5
Q

polysaccharides and examples

A

many monosaccharides connected by a bond

Eg glycogen and cellulose

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6
Q

First and second law of thermodynamics

A

1- Energy cannot be created or destroys

2-when energy is converted from one form to another it is not 100% efficient and some is unable to do work

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7
Q

What is entropy

A

a measure of disorder in a system

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8
Q

what is an exergonic reaction

A

favorable reactions where free energy is negative
total free energy of products is less than that of reactants
can occur spontaneously

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9
Q

what is an endergonic reaction

A

free energy of product is greater than that of reactants

unfavorable reactions where free energy is positive

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10
Q

Define anabolism

A

Synthesizing complex molecules out of smaller ones - energy consuming

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11
Q

Define catabolism

A

Breaking large complex molecules into smaller ones to release energy.
Some exceptions involve energy consuming steps

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12
Q

What is coupling

A

an unfavorable reaction is put together with a favorable reaction to utilise the energy to drive it

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13
Q

Give an example of coupling

A

ATP - provides energy by its dephosphorylation
3 phosphate groups, the negative charges on the phosphates put electrostatic repulsion on the molecule. It splits to become ADP + Pi to partially relieve the strain and as a result releases energy.

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14
Q

what is ΔGo’

A

the change in free energy under standard conditions

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15
Q

what are standard conditions

A

298K, 1atm pressure, pH7 and 1M concn reactants except H ion

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16
Q

Describe the polarity of water

A

it is polar

can form H- bonds with other molecules

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17
Q

define the hydrophobic effect

A

Where water interacts with the water molecules and not other non polar molecules to form a 2 layer system

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18
Q

What branches do amino acids have

A

Carboxyl group
hydrogen group
side chain
amino group

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19
Q

Non polar amino acids

A

hydrophobic side chain

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20
Q

Polar amino acids

A

polar but uncharged side chain

capable of molecular bonding

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21
Q

Acidic amino acids

A

acid functional group on side chain

can be used as buffer

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22
Q

Basic amino acids

A

amine functional group on side chain

also useful as buffer

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23
Q

what is the c terminal

A

carboxyl group

front/joinable end

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24
Q

what is the n terminal

A

amino group

rear direction of travel

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25
Q

How is pKa calculated

A

pKa = -log10[Ka]

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26
Q

what is pH

A

measure of amount of protons in a solution

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27
Q

henderson hasselbalch equation

A

pH=pKa+log10[A−]/[HA]

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28
Q

When can an acid or base act as a buffer

A

when close to its pKa value as pH can remain slightly constant

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29
Q

what is a zwitterion

A

no net charge but can be cationic or anionic depending on whether carboxyl group is reduced or amine group is oxidised

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30
Q

when does a zwitterion have no net charge

A

at its isoelectric point

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31
Q

Primary proteins

A

Sequence of amino acids in a linear line joined by s polypeptide bond

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32
Q

true/false - peptide bonds have rotation

A

false - they display a partial double bond character and rotate between alpha carbon and amino group as well as alpha carbon to carboxyl group

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33
Q

types of structures in secondary proteins and the bonding

A

Hydrogen bonding
Alpha helix
Beta I and II sheet
Collagen triple helix

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34
Q

Alpha helix

A

-CO group forms bond with -NH of amino acid 4 residues away
forms a helical shape
broken by proline

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35
Q

Beta sheets

A

Parallel or antiparallel
glycine and proline turn sheet
Beta II is a zigzag

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36
Q

Collagen triple helix

A

found in bone and connective tissue
superhelix formed by 3 helical chains
covalent inter and intra molecular bonds
repeats X - Y (proline/hydroxyproline) - Gly

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37
Q

What is a fibrous protein

A

large sheets or fibres
mechanical strength
water insoluble

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38
Q

what is a globular protein

A

folded spherically

hydrophobic parts not exposed and so often water soluble

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39
Q

What is tertiary structure and give examples

A

Arrangement of atoms of polypeptide in space
Disulphide bonds
salt bridges
hydrophobic interactions
H-bonds
Formation with metal ions to form prosthetic

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40
Q

What is quaternary structure

A

Proteins containing more than one polypeptide chain

Haemoglobin

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41
Q

DNA runs _____

A

Antiparallel

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42
Q

Name the bases and their nucleosides

A 
Adenine - Adenosine 
Thymine - thymidine 
Uracil - uridine 
Cytosine - cytidine 
Guanine - guanosine
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43
Q

what is a nucleoside and how does it differ from a nucleotide

A

A nucleoside is a base and sugar, whereas a nucleotide is a nucleoside with a phosphate group

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44
Q

How many H-bonds do adenine and thymine form

A

2

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45
Q

How many H-bonds do cytosine and guanine form

A

3

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46
Q

True/false - DNA can only be added to free 3’ end

A

true

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47
Q

True/false - DNA is read 3’ to 5’

A

false - it is read 5’ to 3’

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48
Q

Example of how an analogue can act as a drug

A

retrovir acts as an analogue of thymine to be incorporated into viral DNA and terminates chain elongation due to it lacking OH group on 3’ end

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49
Q

DNA replication is ____

A

semi conservative

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50
Q

Where does DNA replication occur and what unwinds it

A

Replication bubble, Helicase

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51
Q

What catalyses replication

A

DNA polymerase

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52
Q

can DNA polymerase begin replication on its own?

A

No. it requires an RNA primer formed by primase

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53
Q

What are okazaki fragments

A

short fragments of DNA made by replication forks enlargement on lagging strand. these must be joined together by DNA polymerase

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54
Q

Types of RNA

A

mRNA, tRNA, rRNA

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55
Q

What is a stem loop

A

local stretches of intramoleculear base pairing on RNA

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56
Q

What are the stages of transcription

A 
Binding of RNA polymerase 
Chain separation
Transcription initiation 
Elongation
Termination
57
Q

what enzyme unwinds DNA

A

helicase

58
Q

what direction does elongation occur in

A

5’ to 3’

59
Q

how is mRNA terminated

A

Step loop structure, followed by stretch of uracil

this is cleaved to release mRNA

60
Q

how does RNA polymerase bind

A

requires transcription factors on initiation sites, marked by promoters

61
Q

What are promoters

A

DNA sequence marking site of a gene

62
Q

Explain how TATA box helps to induce transcription

A

present 25 nucleotides prior to transcription
TPB binds to it and introduces kink to DNA to determine start of transcription and travel
direction
provides landing platform for Pol II an dother transcription factors

63
Q

True/false - introns removed from mRNA prior to translation

A

true - called splicing

64
Q

What happens to 3’ and 5’ end at end of transcription

A

5’ end capped

sequence of adenosine nucleotides added to 3’ end

65
Q

How is transcription regulated

A

DNA binding proteins, contain a binding domain and a transcription activation/repression domain

66
Q

when do DNA binding proteins bind?

A

Presence of enhancer (promoter)

67
Q

Can DNA be regulated by gene expression?

A

Yes. regulated by specific regulatory proteins to coordinate translation in response to specific stimuli

68
Q

what is a reading frame and how many are there

A

3 reading frames, the reading frame is how genetic code is read in triplets

69
Q

what does unambiguous mean

A

amino acids with once codon coding for them or a stop codon

70
Q

what does degenerate mean

A

amino acids with several codons coding for them

71
Q

How does initiation of transcription occur

A

initiation factors required. GTP hydrolysed to GDP
Small ribosomal unit binds to cap on mRNA
tRNA brings complementary anticodon to start of mRNA in P site, carrying methionine

72
Q

Describe translation elongation

A

Elongation factor brings aminoacyl-tRNA to A site, the anticodon on the tRNA binds to the codon on the mRNA strand. The elongation factor then detaches from tRNA. A second elongation factor regenerates the first to collect the next tRNA. Peptidyl transferase catalyses the peptide bond formation between amino acids in the P and A sites
EF-2 (elongation factor) moves the ribosome along by one triplet. The now empty tRNA moves to E site to exit and reload with a new amino acid
A is now free for next aminoacyl-tRNA, and the tRNA with the growing peptide chain is located in the P region
This is repeated for as long as required

73
Q

Transcription termination

A

‘A’ site encounters stop codon. no tRNA base pairs with it so release factor binds and cleaves from rRNA

74
Q

what is protein degradation

A

discarding of unwanted or damaged proteins

75
Q

what is targeting

A

transport of protein to final destination

76
Q

free ribosome makes proteins for…

A

cytosol, nucleus or mitochondria

77
Q

bound ribosomes makes proteins for….

A

cell membrane, golgi apparatus, ER and secretion

78
Q

types of post translational modification

A

Glycosylation
Formation of disulphide bonds in ER
Proteolytic cleavage in ER, golgi apparatus or secretory vessels

79
Q

what is the transition state

A

maximum of Activation energy and greatest free energy

80
Q

Apoenzyme

A

enzyme without cofactor

81
Q

Holoenzyme

A

Apoenzyme and a cofactor

82
Q

What are cofactors

A

metal ions often with a coordination centre

involve in redox

83
Q

what are coenzymes

A

organically occurring molecules
many derived from vitamins
involved in redox

84
Q

What is the lock and key model

A

active site is specific to substrate conformation and complementary

85
Q

what is the induced fit model

A

active site not really complementary to substrate but upon binding, active site changes conformation and fits substrate complementary.

86
Q

What are isozymes and example

A

isoforms of enzymes - catalyse same reaction but different structure and properties
can be used in clinical testing
eg lactate dehydrogenase

87
Q

What is phosphorylation regulation

A

reversible covalent modification converting enzyme between active and inactive form
carried out by protein kinases

88
Q

what is irreversible covalent modification

A

involved in enzyme activation.

zymogens are irreversibly turned into active form by cleavage of a covalent bond

89
Q

what is K1

A

forward rate constant for enzyme association with substrate

90
Q

What is K-1

A

backwards rate constant for enzyme dissociation with substrate

91
Q

What is K2

A

forward rate constant for enzyme conversion of substrate to product

92
Q

What is Km

A

substrate concentration where initial rate of reaction is half maximal

93
Q

What is Vmax

A

maximum velocity of a reaction

94
Q

What is the michaelis menten equation

A

V=Vmax[S]/Km+[S]

95
Q

How can Vmax and Km be accurately determined

A

lineweaver burk plot

96
Q

What does a low Km suggest

A

little substrate required to make enzyme work at half max rate. more effective at low substrate concentrations

97
Q

What does a high Km suggest

A

higher concentration of substrate required to work at half maximal rate

98
Q

Competitive reversible inhibition

A

binds to active site to block substrate access
Vmax remains constant but Km varies
if a great enough concentration of substrate was added inhibitor could be overcome

99
Q

Non competitive reversible inhibition

A

binds to allosteric site and changes conformation of active site
alters Vmax but keeps Km constant

100
Q

Irreversible inhibition

A

covalent bonds have been added or destroyed

101
Q

True/fasle - allosteric enzymes follow michaelis menten kinetics

A

false - they do not

102
Q

Anabolism is oxidation/reduction

A

reduction

103
Q

Catabolism is oxidation/reduction

A

oxidation

104
Q

what is the structure of glucose

A

6 carbon structure - 5 carbon ring with carbon branch

105
Q

What are the stages of metabolism

A

Stage 1 - Eating
Stage 2 - Acetyl CoA production and glycolysis
Stage 3 - Acetyl CoA oxidation - electron csrriers fully reduced for ETC
Stage 4 - Electron transfer and oxidative phosphorylation

106
Q

What are the uses of glucose

A

oxidation by aerobic glycolysis to yield pyruvate
fermentation by anaerobic glycolysis
oxidation by pentose phosphate pathway - ribose-5-phosphate
Can be stored

107
Q

how is glucose transported into cells

A

Na/Glucose symporter

Glucose transporters - passive GLUT 1-5

108
Q

Action of GLUT 1

A

glucose binds to site extracellular and causes a conformational change to face binding site intracellular and release glucose
then changes conformation again to face outside

109
Q

glucose is phosphorylated to produce _____ then further broken down to ______ and then _____

A

fructose-1,6-bisphosphate
2 triose phosphates
pyruvate

110
Q

Steps of glycolysis

A

glucose trapped and destabilised
Destabilised intermediates split into 2, 3 carbon molecules
ATP generation

111
Q

Glycolysis control points

A

First by hexoinase to ensure cell wants to break glucose down
Second prior to destabilisation by phosphofructokinase (flow rate regulator)
Last before pyruvate formation by pyruvate kinase - exit of products from glycolysis

112
Q

Are glycolysis control points reversible

A

No!

113
Q

How is phosphofructokinase regulated?

A

It regulates the conversion of fructose 6-phosphate to fructose-1,6-biphosphate by use of ATP
it is activated by AMP
inhibited by protons (lactic acid), ATP abundance and citrate

114
Q

What happens in lack of oxygen?

A

NADH ferments pyruvate to lactate to free glycolysis

can be regenerated

115
Q

What is the ATP and NADH yield

A

Net gain of 2 ATP - 4 produced but 2 used

2NAD reduced to NAHD and 2 protons for ETC

116
Q

What is the warburg effect

A

Cancer cells have a low Km so glucose can be metabolized quickly, allowing for rapid energy production and proliferation
due to their inefficient ATP production they have a high glucose demand to comtete with the patient and leave lactate and protons which act as toxins

117
Q

True/false - nad and fad are unlimited

A

False - they must be regenerated and are produced by niacin

118
Q

Where does the TCA occur?

A

mitochondrial matrix

119
Q

how is pyruvate catalysed to Acetyl CoA for TCA?

A

PDC (pyruvate dehydrogenase complex decarboxylates pyruvate to Acetyl CoA in an irreversible reaction

120
Q

Roughly explain the TCA

A

Acetyl CoA added to 4 carbon oxaloacetate to form citrate
citrate is decarboxylated twice to yield 2 molecules carbon dioxide
One GTP is formed
There are 4 oxidation reactions to yield 3 NADH+3protons and one FADH
Oxaloacetate is regenerated

121
Q

True/false - only glucose is converted to acetyl CoA

A

False - carbohydrates, proteins and fats are all broken down to Acetyl-CoA

122
Q

What are the net yields from the TCA

A

10 NADH and 10 protons
2 FADH
4 ATP from glycolysis and 1 from each TCA, 2 lost during glycolysis so net gain 4

123
Q

What are the different control points in the TCA

A

High ATP, NADH and Acetyl CoA suggests abundance of energy and so negatively feeds back on cycle
High NAD and ADP suggest lack of energy so favour cycle

124
Q

What are electrons from NADH and FADH used to do?

A

Reduce oxygen and hydrogen

125
Q

What does the energy from electrons allow for

A

protons to be pumped from mitochondrial matrix to intermembrane space

126
Q

what does the glycerol-3-phosphate and malate-asparate shuttle do and how does it work?

A

allows for indirect crossing of 2 NADH that were formed in cytoplasm

NADH from cytoplasm generates malate from oxaloaceteate. these transport malate to the extracellular matrix where mitochondrial NAD is converted to NADH and malate reverts to oxaloacetate

127
Q

What is the chemosmotic hypothesis

A

coupling of respiration to ATP syntheis, consisting of 2 parts:
Electron transport - where electrons flow from NADH and FADH to oxygen via respiratory chain - while pumping protons out of matrix
ATP synthesis - electrochemical gradient of protons across inner mitochondrial membrane harnesses energy that can be used to make ATP

128
Q

What are the complexes of the resp chain

A

Complex I - NADH electrons
Complex II - FADH electrons
electrons handed to carriers that are increasingly more oxidative
transferred to oxygen, forming water

129
Q

Where does the F1 subinit of ATP synthase lie

A

protruding into the matrix

130
Q

Where does the F0 subunit of ATP synthase lie

A

In the inner membrane

131
Q

How does ATP synthase synthesise ATP

A

Flow of protons turn rotor and conformational change forces ADP and Pi together

132
Q

How does cyanide, carbon monoxide and azide inhibit ATP synthesis

A

inhibit transfer of electrons to oxygen so no protein gradient formed

133
Q

What is the P/O ratio

A

meaure of coupling of ATP synthesis to electron transport

134
Q

What is the overall respiration ATP yield

A

30-32 ATP

135
Q

What factors influence ATP yield

A

depends on P/O ratio

depends on what shuttle is used for transporting cytoplasmic NADH

136
Q

2 functions cholesterol

A

maintains structure and fluidity cell membrane

cell signalling

137
Q

what is the endogenous cycle

A

fat binds to VLDL, leave liver and LPL snips to IDL/LDL to transport cholesterol to cells

138
Q

what is the exogenous cycle

A

fat from portal circulation enter liver and LPL snips fat from chylomicrons

MB1: Principles (10 decks)

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