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Year 1 MBChB > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

First law of thermodynamics?

A

Energy is neither created or destroyed

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2
Q

Second law of thermodynamics?

A

When energy is converted from one form to another, some of it becomes unavailable for work

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3
Q

2 formulas for ΔG?

A

ΔH – TΔS or (energy of the products) – (energy of the reactants)

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4
Q

2 things ΔG represents?

A

Energy available to do work and how close a reaction is to equilibrium

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5
Q

What ΔG value would a reaction close to equilibrium have?

A

ΔG = 0

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6
Q

Highly +ve or -ve ΔG values are readily reversible reactions? True or False?

A

False

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7
Q

4 key points of an exergonic reaction + an example?

A
  • free energy of products is less than reactants
  • ΔG is negative
  • reaction can occur spontaneously
  • reactions like these are used for control points
  • ATP hydrolysis is a negative ΔG reaction
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8
Q

3 key points of an endergonic reaction?

A
  • free energy of the products is more than reactants
  • ΔG is positive
  • reaction needs input of energy
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9
Q

What is coupling of reaction?

A

Reactions with +ve ΔG are coupled with a -ve ΔG reaction to make them occur more spontaneously

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10
Q

Do cells store a lot of ATP?

A

No

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11
Q

Is ATP or ADP more unstable and why?

A

ATP due to repulsion of 3 phosphates

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12
Q

Name of bonds that join phosphate groups?

A

Anhydride bonds

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13
Q

Is water polar or non-polar + shape?

A

Polar + bent

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14
Q

What types of substances can water dissolve and how?

A

Ionic and polar via dipole-dipole interactions

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15
Q

Polarity of hydrophic, hydrophillic and amphipathic molecules?

A

Non-polar, polar and both

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16
Q

Example of amphipathic molecules?

A

Phospholipids in the cell membrane and micelles

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17
Q

How many amino acids are there + how many bases in amino acid?

A

20 + 3

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18
Q

What is the alpha carbon?

A

The carbon that has 4 different groups bound to it

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19
Q

What is the shape of an amino acid?

A

Tetrahedral

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20
Q

D and L amino acids are + what does that mean?

A

Sterioisomers + they are non-superimposable versions of eachother

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21
Q

Name the components of an amino acid?

A

Alpha carbon, NH2 (amino) group, COOH (carboxyl) group, H and an R side chain

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22
Q

Direction of an amino acid + charges of each side?

A

N-terminal (+ve) to C-terminal (-ve)

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23
Q

Key feature of peptide bonds + what they join?

A

They are planar + amino acids

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24
Q

How do amino acid chains rotate?

A

Around the alpha carbons

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25
Q

Describe how amino acids form resonance structures?

A

The 2 free electrons of the N of a peptide bond are given to the nearby oxygen to form a C=N

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26
Q

4 key features of zwitterions?

A
  • 2 titratable end groups
  • act as buffers for acids and bases
  • 2 pKa values
  • no net charge
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27
Q

Acids …. protons to form …. and bases accept ….. to form …..?

A

Give, conjugate bases, electrons and conjugate acids

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28
Q

What does Ka + pKa mean?

A

How readily an acid loses protons + value at which pH does not change upon addition of OH

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29
Q

What is pH a measure of + change in x pH = ?

A

Protons in a solution + 10 to the power of x

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30
Q

As an acid strengthens its Ka value ….. and pKa value …..?

A

Increases and decreases

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31
Q

Primary protein structure?

A

Sequence of amino acids

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32
Q

Bonding that holds secondary structure?

A

Hydrogen bonding

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33
Q

3 types of secondary structures?

A

Alpha helix, beta sheets 1 & 2 and triple helix

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34
Q

What are alpha helices + what molecule breaks them?

A

Single stands where a C-O binds an N-H 4 residues away + proline residues

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35
Q

2 types of beta sheets?

A 
1 = parallel and anti-parallel
2 = zigzag pleated sheets
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36
Q

What are triple helices + where are they found?

A

3 chains of collagen made from proline residues + connective tissue

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37
Q

What is tertiary structure + additional feature?

A

Final 3D shape of the polypeptide + prosthetic group

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38
Q

Describe fibrous vs globular proteins + examples?

A

Fibrous are insoluble sheets (kertain) and globular are soluble spheres (haemoglobin)

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39
Q

What is quaternary structure?

A

Binding of subunits together

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40
Q

Amino acid substitution in sickle cell anaemia?

A

Valine (hydrophobic) for glutamic acid

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41
Q

Examples of disease that arise from incorrect protein folding?

A

Parkinson’s and Alzheimer’s

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42
Q

Examples of prion diseases?

A

Mad cow and Creutzfeldt-Jacob

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43
Q

3 differences between DNA and RNA?

A

DNA (deoxyribose sugar, ACTG and double stranded) vs RNA (ribose sugar, AUCG and single stranded)

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44
Q

How to differentiate between ribose and deoxyribose?

A

Ribose has an OH on carbon 2 and deoxyribose has an H

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45
Q

Building blocks of bases?

A

dATP/TTP/CTP/GTP (DNA) vs ATP/UTP/GTP/CTP (RNA)

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46
Q

A nucleoside + nucleotide is made of a?

A

Base and sugar + nucleoside and phosphate

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47
Q

A nucleic acid is?

A

RNA and DNA

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48
Q

5 step summary of DNA replication?

A
  • Helicase unwinds
  • RNA primer joins 3’ end
  • Nucleotides added
  • DNA polymerase fills gaps on leading strand
  • DNA ligase bonds Okazaki fragments on lagging strand
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49
Q

2 steps in how nucleotides added in DNA replication?

A
  • Triphosphate breaks leaving base + monophosphate

- 5’ phosphate forms phosphodiesterase bond with 3’ OH of DNA chain

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50
Q

What is essential for DNA replication?

A

A 3’ end

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51
Q

Bonding between A and T + C and G?

A

A=T and C≡G

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52
Q

Enzyme that adds TTAGGG repeat?

A

Telomerase

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53
Q

Extra function of DNA polymerase?

A

Exonuclease activity removes incorrect nucleotides

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54
Q

General structure of RNA?

A

Stem-loop with intramolecular pairing

55
Q

Most unstable RNA?

A

mRNA

56
Q

Structure of tRNA?

A

Anticodon (3 bases) determines which amino acid binds to attachment site on opposite side of molecule

57
Q

What is RNA made by?

A

RNA polymerase (Pol)

58
Q

How many Pols in prokaryotes vs eukaryotes?

A

1 vs 3

59
Q

What Pol is needed to synthesise mRNA?

A

Pol II

60
Q

Transcription + splicing summary?

A
  • TATA BBP (part of TFIID) binds TATA box and kinks DNA to provide landing platform
  • Pol II binds TATA promoter region and unwinds DNA within itself
  • Nucleotides added to form mRNA complimentary to DNA template
  • Introns are removed leaving exons
  • Addition of 5’ cap and 3’ poly A tail
61
Q

What are the 2 essential components needed for translation?

A

Initiation factors and GTP hydrolysis

62
Q

Three binding sites of a ribosome?

A

APE

63
Q

Start and tRNA initiator codon?

A

AUG and UAC

64
Q

7 step translation summary?

A
  • IF binds ribosome and GTP hydrolysis occurs
  • A binds mRNA 5’ end of mRNA and finds start codon
  • Initiator tRNA binds start codon which moves to P
  • EF-1 alpha brings next tRNA into A
  • GTP is hydrolysed and EF-1 alpha dissociates
  • EF-2 moves mRNA along one triplet
  • Continues until stop codon is reached
65
Q

Role of EF-1 and 2 in transcription + which molecule regenerates EF-1?

A 
1 = bring tRNA in to A site
2 = move mRNA along ribosome + EF-alpha beta
66
Q

Role of GTP hydrolysis in translation?

A

Allows EF-1 alpha to be released from tRNA

67
Q

Enzyme that bonds tRNA and amino acid?

A

Aminoacyl-tRNA synthetase

68
Q

Energy released from GTP, ATP and UTP is different? True or False?

A

False - energy is the same

69
Q

Enzyme that forms peptide bonds?

A

Peptidyl transferase

70
Q

Where does post-translational modification take place?

A

In the ER and golgi apparatus

71
Q

What is glycosylation and when does it take place?

A

Adding carbohydrates to proteins during post-translational modification

72
Q

Disease of incorrect lysosome protein sorting?

A

Mucolipidosis

73
Q

Disease of alpha-1 antitrypsin (A1AT) incorrect folding?

A

Emphysema

74
Q

How are enzymes activated?

A

Phosphorylation via kinases

75
Q

What is a zymogen?

A

Inactive enzyme precursor that is activated via cleaved covalent bond

76
Q

How do enzymes lower activation energy?

A

Bind to intermediate complex and stabilise it

77
Q

Examples of cofactors vs coenzymes?

A

Iron/zinc vs NAD/FAD/vitamins

78
Q

Enzyme - cofactor?

A

Apoenzyme

79
Q

Enzyme + cofactor?

A

Holoenzyme

80
Q

Name of an enzyme in a cofactor metal coordination complex?

A

Metalloprotein

81
Q

Coenzymes can tightly bind to form?

A

Prosthetic groups

82
Q

What is an isoenzyme + example?

A

Different structure but same reaction

Lactate dehydrogenase is H in the heart (promotes aerobic) and M in the muscle

83
Q

What is Vmax and Km + name of graph used to determine their values + what the graph compares?

A
  • Vmax = max velocity of a rection
  • Km = 0.5 Vmax
  • Line-weaver burk graph plots substrate concentration vs rate of reaction
84
Q

How are Vmax and Km determined on a graph?

A 
Vmax = Y axis intersection
Km = X axis intersection
85
Q

Change in Vmax and Km with competitive inhibition + give an example?

A

Vmax = no change and Km = increased + methanol poisoning

86
Q

Change in Vmax and Km with non-competitive inhibition?

A

Vmax = decreased and Km = no change

87
Q

2 key points about allosteric enzymes + an example?

A
  • Do not follow Michaelis-Menten kinetics
  • Produce sigmoidal curve
  • Haemoglobin
88
Q

2 ways glucose enters the cell?

A

Na/glucose symport or GLUT transporters

89
Q

Control points of glycolysis?

A

Hexokinase, PFK and pyruvate kinase

90
Q

Hexokinase catalyses?

A

Glucose to glucose-6-phosphate

91
Q

PFK catalyses?

A

Fructose-6-phosphate to frucotse-1,6-biphosphate

92
Q

What activates and inhibits PFK?

A

AMP + fructose-2,6,-biphsophate and ATP + citrate + H

93
Q

Where is ATP used in glycolysis?

A

Hexokinase + PFK reactions

94
Q

2 triose phosphates to 2 pyruvates produces?

A

4 ATP + 2 NADH + 2 H

95
Q

Products of anaerobic glycolysis?

A

2 ATP + 2 NADH + NAD

96
Q

Function of NADH in anaerobic glycolysis?

A

Converts pyruvate to lactic acid

97
Q

All enzymes for CAC in matrix except what + function?

A

Succinate dehydrogenase + makes FADH2

98
Q

How does pyruvate enter the martix?

A

H/pyruvate symport

99
Q

Enzyme that converts pyruvate to acetyl co-A?

A

Pyruvate dehydrogenase complex

100
Q

Irreversible step of the CAC?

A

Pyruvate 3C to acetyl co-A 2C

101
Q

Summary of the CAC complexes?

A

Pyruvate (3C) -> acetyl co-A (2C) -> citrate (6C) -> oxaloaceteate (4C)

102
Q

Products of the CAC?

A

3 CO2, 1 FADH, 3 NADH, 2 H, 1 GTP (which forms 1 ATP)

103
Q

Yield per glucose molecule from glycolysis + CAC?

A

4 ATP, 10 NADH, 10 H, 2 FADH2, 6 CO2,

104
Q

How many electrons do NADH or FADH2 carry?

A

2

105
Q

Purpose/journey of electrons from NADH/FADH2 carriers?

A

Transferred along the ETC to reduce O2 to H2O which provides energy for H to cross the inner membrane

106
Q

How does NADH cross the mitochondrial membrane?

A

Glycerol and malate shuttles

107
Q

Eo’ = ?

A

The redox potential - how readily X loses electrons

108
Q

NADH electrons enter at?

A

Complex I

109
Q

FADH2 electrons enter at?

A

Complex II

110
Q

Complex IV is a?

A

Cytochrome

111
Q

What is a cytochrome?

A

A protein with a haem group (cofactor) that takes up/releases electrons

112
Q

Which complexes are H pumps in the ETC?

A

I, III and IV

113
Q

2 step ETC summary?

A
  • Complex I, II and IV couple H transfer across inner membrane with electron transfer along membrane
  • H moves back in through ATP synthase
114
Q

1 glucose molecule produces .. ATP ?

A

30-32

115
Q

Explain uncoupling of the ETC?

A

H is redirected back through uncoupling protein/thermogenin instead of ATP synthase to produce heat instead of energy

116
Q

Where is uncoupling seen?

A

In newborn adipose tissue

117
Q

How does cyanide inhibit the ETC?

A

Stops electron transfer to O2

118
Q

Electrons are moves from …. to ….. energy but ….. redox potential?

A

Higher to lower and higher

119
Q

Coenzyme Q is …. and shuttles between which complexes?

A

Ubiquinone and I, II and III

120
Q

Which complex is part of the CAC?

A

II

121
Q

Why do allosteric enzymes produce a sigmoidal curve?

A

They have more than one active site

122
Q

Term for 3 bases on DNA, mRNA and tRNA?

A

Triplet, codon and anticodon

123
Q

Protons are pumped …. the inner mitochondrial membrane/ETC and electrons are pumped …. the inner mitochondrial membrane/ETC?

A

Across and along

124
Q

Hydrophillic signal molecules like ….. and ….. do/do not cross the cell membrane easily?

A

Peptide hormones and Ach + do not

125
Q

Hydrophobic signal molecules like …… and …… do/do not cross the cell membrane easily?

A

Glucocorticoids and thyroid hormones + do

126
Q

Molecule used in muscles for short-term energy production?

A

Creatine phosphate

127
Q

What is Von Gierke’s disease + how it it treated?

A

Failure to break down glycogen into glucose + slow release glucose foods and small portions

128
Q

Does GLUT 1 in the brain have a high or low Km?

A

Low

129
Q

Diagnostic test for prostate cancer + disadvantage?

A

Prostate specific antigen (PSA) + some men with benign prostatic hyperplasia also have raised PSA

130
Q

Gland that controls calcium levels?

A

Parathyroid

131
Q

Hypercalcaemia does what to kindeys?

A

Increases urine and Na loss

132
Q

Give an example of a monsaccharide, disaccharide and polysaccaharide?

A

Glucose, lactose and glycogen

133
Q

4 amino acid groups + examples?

A

Non-polar hydrophobic, polar uncharged, acidic (COOH) and basic (NH)

Year 1 MBChB (10 decks)

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