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Biochemistry > Principles > Flashcards

Principles Flashcards

1
Q

What are biomolecules made up of?

A

Atoms

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2
Q

What are atoms made up of?

A
  1. Proton (positive)
  2. Neutron
  3. Electron (negative
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3
Q

What is a covalent bond?

A

Shared pair of electrons between non-metal atoms

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4
Q

What is an ionic bond?

A

Attraction of opposite charges

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5
Q

What is a hydrogen bond?

A

Sharing of a H atom (intermolecular)

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6
Q

What are hydrophobic interactions?

A

Interactions of non-polar substances in the presence of polar substances (especially water)

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7
Q

What are Van der Waals forces?

A

Interaction of electrons of a non-polar substances

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8
Q

What is the electronegativity of an element?

A

The attractive force that an atomic nucleus exerts on the electrons of another atom.

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9
Q

What is phosphorylation?

A

Addition of a phosphate group

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10
Q

What is dephosphorylation?

A

Removal of a phosphate group?

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11
Q

What is acylation?

A

Addition of an acytl group (carbon with double bond to oxygen)

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12
Q

What is carboxylation?

A

Addition of a carboxyl group

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13
Q

What is esterification?

A

Reaction of an alcohol and a carboxylic acid to form an ester

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14
Q

What is a condensation reaction?

A

Joining compounds together by removing water

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15
Q

What is hydrolysis?

A

Breaking up a compound by adding water

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16
Q

What is oxidation?

A

Loss of electrons

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17
Q

What is reduction?

A

Gain of electrons

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18
Q

What is a redox reaction?

A

When one molecule is oxidised and the other is reduced.

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19
Q

What is a reducing agent?

A

Molecule that causes another molecule to be reduced by itself being oxidised

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20
Q

What is an oxidising agent?

A

Molecule that causes another molecule to oxidise by being reduced itself.

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21
Q

What are the oxidation stated of carbon?

A

Alkane–> alcohol–>aldrehyde–>carboxylic acid–>carbon dioxide

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22
Q

What are main functions of biomolecules?

A
  1. Information storage eg DNA
  2. Structural eg teeth, bones
  3. Energy generation eg glycolysis, TCA cycle
    4.Energy currency eg ATP
    Recognition/communication eg receptors, hormones and enzymes
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23
Q

What are the major classes of biomolecules?

A

PEPTIDES AND PROTEINS- made from amino acids
LIPIDS- made from trigycerides, phospholipds and steroids
NUCLEIC ACIDS- DNA and RNA
CARBOHYDRATES -mono/di/trisaccharides

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24
Q

Give an example of a monosaccaride.

A

Glucose

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25
Q

Give 4 examples of disaccarides.

A

Lactose
Maltose
Sucrose
Cellobiose

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26
Q

Give two examples of polysaccharides.

A

Cellulose

Glycogen

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27
Q

What is the first law of thermodynamics?

A

Energy is neither created nor destroyed only transferred

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28
Q

What is the second law of thermodynamics?

A

When energy is converted from one form to another, some of that energy becomes unable to do work

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29
Q

What is enthalpy?

A

Heat content

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30
Q

What is entropy?

A

Disorder

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31
Q

How do you calculate the free energy of a reaction?

A

ΔG = ΔH – TΔS

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32
Q

How do you calculate the change in free energy?

A

ΔG = (energy of the products) – (energy of the reactants)

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33
Q

When is a reaction feasible?

A

If the free energy change is -ve

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34
Q

What is an endergonic reaction?

A

Reactions in which the total free energy of the products is more than the total free energy of the reactants. Free energy change is +ve

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35
Q

What is an exergonic reaction?

A

Free energy of the products is less than the reactants.Free energy change is -ve.

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36
Q

What is the equation for determining free energy of a reaction?

A

ΔG = ΔGo’ + RTln([C][D]/[A][B])

unit is kJ/mol

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37
Q

What are standard conditions?

A

T=298K
1atm pressure
1M concentration

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38
Q

What is ΔGo?

A

ΔGo’ is the change in free energy under standard conditions

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39
Q

What is ATP?

A

Used as a universal energy currency because its breakdown has a very negative standard free energy
The reaction
ATP + H2O → ADP + Pi + H+
has a very negative ΔGo’ (-30 kJ/mol)

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40
Q

Why is ATP less stable than ADP?

A

The negative charges close together in ATP put a strain (electrostatic repulsion) on the molecule that makes it less stable than ADP
Strain is relieved (partially) by removing one or more phosphate groups
Anhydride bonds are ‘high energy’ bonds

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41
Q

What is metabolism?

A

All the reactions taking place in the body

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42
Q

What is catabolism?

A

Breakdown of complex molecules into smaller ones to release energy

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43
Q

What is anabolism?

A

Synthesizing complex molecules out of smaller ones in energy consuming reactions

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44
Q

What is glycolysis?

A

Initial breakdown of glucose for the generation of ATP
Uses two ATP molecules
Generates Four ATP–>net gain of TWO

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45
Q

What is gluconeogenisis?

A

Making new glucose from non carbohydrate precursors eg pyruvate
Anabolic reaction

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46
Q

What is meant by a polar molecule?

A

The electrons are not shared equally in the molecule due to it’s electronegativity

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47
Q

Describe the molecular shape of water.

A

Water is bent and forms a dipole- it is therefore tetrahedral shaped.

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48
Q

What does hydrophilic mean?

A

‘Water-loving’ i.e. a substance that dissolves in water

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49
Q

What makes a molecule hydrophilic?

A

It must be ionic or polar.

Like dissolves like.

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50
Q

Describe the formation of hydrogen bonds in water.

A

A covalent bond between hydrogen and a more electronegative atom (e.g. oxygen) creates a polarized bond
hydrogen has partial positive charge

This hydrogen can interact with unshared electrons from another electronegative atom

This interaction is called a hydrogen bond

Individually much weaker than covalent bonds but can be strong collectively

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51
Q

What substances are hydrophobic (insoluble in water)?

A

Non-polar substances

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52
Q

Why are non polar molecules hydrophobic?

A

Hydrogen bonds BETWEEN water molecules prefer to interact with each other than the non-polar substance

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53
Q

What is the hydrophobic effect?

A

When non-polar substances are not dissolved when mixed with water eg hydrocarbons and water do not mix

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54
Q

What are amphipathic molecules?

A

Molecules that are both hydrophilic and hydrophobic.

They have a hydrophilic head and a hydrophobic tail

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55
Q

How does water interactions affect the organisation of amphipathic molecules?

A

Hydrophilic head interacts with water and is in contact.

Hydrophibic tail does not, it is sequestered from the water–>forming MICELLES

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56
Q

Give an example of an amphipathic molecule.

A

Sodium palmitate (a fatty acid)

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57
Q

What is the importance of cell membranes?

A

They act as a selective and controllable barrier to the outside world
Aid compartmentalization by isolating organelles.

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58
Q

What is contained within the cell membrane?

A

Lipids- phospholipid bilayer

Proteins

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59
Q

Describe the general structure of amino acids.

A 
The building blocks of proteins.
An alpha carbon bonded to either:
-an amino group
-a carboxyl group
-a hydrogen
-a side chain
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60
Q

What is the classifications of amino acids?

A

Polar
Non-polar
Basic
Acidic

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61
Q

Describe the steriochemistry of amino acids.

A

Comes in D and L forms which are non superimposable mirror images.

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62
Q

What is a peptide bond?

A

Bond between two amino acids.

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63
Q

Describe the characteristics of a peptide bond.

A

Unidirectional (N to C)
Partial double bond character
Planar
Strong and rigid

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64
Q

What is an acid?

A

Molecule that donates a proton

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65
Q

What is a base?

A

Molecule that accepts a proton

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66
Q

How is the strength of an acid measured?

A

By how well is dissociates ie. its acid dissociation constant

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67
Q

What is the equation for measuring the amount of protons in a solution in strong acids?

A

pH = -log10[H+]

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68
Q

Give an equation for calculating the pKa of an acid.

A

pKa=-log10[Ka]

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69
Q

What is the Henderson-Hasselbalch equation used to measure?

A

The pH of weak acids

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70
Q

What is the Henderson-Hasselbalch equation?

A

pH=pKa +log [A-]/[HA]

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71
Q

What is a buffer?

A

A solution in which the pH remains constant when small amounts of acid or base are added.

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72
Q

What happens close to the pKa value during a titration of an acid with a base?

A

pH remains relatively unchanged

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73
Q

What is the isoelectric pH (pI) of a molecule?

A

the pH at which a molecule has no net charge

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74
Q

Explain why an uncharged amino acid has two titratable groups.

A

Uncharged amino acids exist as zwitterions in a neutral solution- no net charge
Contain two titratable groups- therefore have two pH pKa values.

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75
Q

Explain how proteins can act as buffers.

A

The ends of proteins can be ionised.

They can therefore act as buffers eg haemoglobin in blood

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76
Q

Explain the impact of pH of amino acids and thus proteins.

A

Changes in pH can change the ionisation in amino acids and thus proteins which can lead to changes in the structure and function of that protein

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77
Q

What is the primary structure of a protein?

A

The sequence of amino acids

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78
Q

What is the secondary structure of a protein?

A

The localised conformation of the polypeptide backbone. IMPORTANT ONLY CONSIDERS BACKBONE.

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79
Q

What is the tertiary structure of a protein?

A

The 3D structure of an entire polypeptide, including all of its side chains
Arrangement of all atoms of a polypeptide in space
Consists of local regions with distinct secondary structure

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80
Q

What is the quaternary structure of a protein?

A

The spatial arrangement of polypeptide chains in a protein with multiple subunits

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81
Q

What are the three types of secondary protein structures?

A

Alpha helix
Beta strands and sheets
Triple Helix

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82
Q

Describe the alpha helix in secondary protein structures.

A 
Rod-like
One polypeptide chain
Mostly right-handed
-C-O group of one amino acid forms a hydrogen bond with the -N-H group of an amino acid four residues away
Proline residues break alpha helices
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83
Q

Describe the beta sheets structure of secondary proteins.

A 
Polypeptide backbone almost completely extended
Can involve more than one chain
Two directions possible:
parallel
antiparallel
Turns between strands (glycine and proline
Repeated ‘zigzag’ structure
also called pleated sheet)
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84
Q

Give an example of secondary protein structures.

A

Phosphoglycerate kinase
Contains both alpha helix and beta sheets.
Can have more than one type in one protein

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85
Q

Give an example of a molecule with a triple helix secondary protein structure.

A

Collagen.
Three left-handed helical chains twisted around each other form a right-handed superhelix
Tropocollagen
Repeating sequence of X-Y-Gly in all strands
X = any amino acid
Y = proline or hydroxyproline
also contains hydroxylysine
Inter-chain H-bonds (no intra-chain)
involving hydroxylysine and hydroxyproline
Covalent inter- and intra-molecular bonds

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86
Q

Why is collagen relevant clinically?

A

Influences the strength of connective tissue
Weakened collagen results in bleeding gums
Covalent crosslinking increases with age
Scurvy-bleeding gums, skin discolouration
the enzyme which hydroxylates proline requires ascorbic acid (vitamin C)
dietary deficiency of vitamin C results in reduction in hydroxyproline
results in weakened collagen

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87
Q

What are the two types of tertiary proteins?

A

Fibrous

Globular

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88
Q

Describe fibrous proteins

A

Contain polypeptide chains organized approximately parallel along a single axis. They
consist of long fibers or large sheets
tend to be mechanically strong
are insoluble in water and dilute salt solutions
play important structural roles in nature

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89
Q

Give examples of fibrous proteins.

A

Keratin- hair and wool

Collagen- bones, teeth, skin. blood vessels

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90
Q

Describe globular proteins

A

Proteins which are folded to a more or less spherical shape
they tend to be soluble in water and salt solutions
most of their polar side chains are on the outside and interact with the aqueous environment by hydrogen bonding and ion-dipole interactions
most of their nonpolar side chains are buried inside
nearly all have substantial sections of alpha-helix and beta-sheet

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91
Q

Give examples of globular proteins

A

Myoglobin

Haemoglobin

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92
Q

What forces interact between tertiary protein structures?

A 
Covalent disulphide bonds
Electrostatic interactions = salt bridges
Hydrophobic interactions
Hydrogen bonds
backbone
side chain
Complex formation with metal ions
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93
Q

Give an example o how changing of a single nucleotide can result in altered protein function

A

Sickle cell anaemia

results in the change in haemoglonin in low oxygen- rigid, sickle shaped cells

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94
Q

What can happen when proteins fold too slowly?

A

protein may begin to fold incorrectly before it is completely synthesised
it may associate with other proteins before it is folded properly

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95
Q

Give examples of clinical conditions resulting from slow protein folding.

A

Alzheimer’s
Parkinsons
CJD

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96
Q

What are chaperones?

A

Specialised proteins which aid the folding process

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97
Q

Give examples of clinical diseases caused by incorrect protein folding

A

Mad cow disease- infection
Creutzfeld-Jacob Disease
Prion protein diseases

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98
Q

What can denature a protein?

A

Heat- increased vibrations
Extreme pH- interupt elextrostatci interactions
Detergents, urea, guanidine hydrochloride- disrupt hydrophobic interactions
Thiol agent, reducing agents- disrupt disulphide bonds

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99
Q

Name an example of a tertiary structure.

A

Lysosyme

Myoglobin

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100
Q

Describe the structure of myoglobin

A 
Globular protein
Contains a haem group
which contains an iron ion, Fe(II)
prosthetic group
haem group binds oxygen
one oxygen molecule per myoglobin protein
Stores oxygen in muscle
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101
Q

Name and describe a quaternary protein structure example.

A 
Haemoglobin
Proteins which contain more than one polypeptide chain
between 2 and more than a dozen subunits
identical or different subunits
Haemoglobin
four subunits
two  and two  chains
each contains a haem group
each subunit can bind one oxygen molecule
Binding of one oxygen changes affinity of the other subunits
see allosteric regulation
Transports oxygen in blood
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102
Q

What is the central dogma?

A

DNA–>RNA–>PROTEIN

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103
Q

What is the chemical structure of the nucleic acid in DNA?

A

Deoxyribose
Base
Phosphate group

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104
Q

What is a nucleoside?

A

Base + sugar

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105
Q

What is the chemical structure of RNA?

A

Ribose sugar
Base
Phosphate group

106
Q

What is a nucleotide?

A

Base + phosphate group

107
Q

What four bases occur in DNA?

A

Adeninie
Guanine
Cytosine
Thymine

108
Q

What are the four bases in RNA?

A

Adenine
Guanine
Cytosine
Uracil

109
Q

What is the nucleoside for the bases of DNA and RNA?

A 
Adenosine
Cytosine
Guanosine
Thymidine
Uridine
110
Q

What bond is formed between nucleic acids?

A

Phosphodiester

111
Q

What are the details of a phosphodiester bond?

A

A phosphodiester bond is formed between a free 3’ OH group and a 5’ triphosphate
Consumes two high-energy bonds!

112
Q

What direction is DNA synthesized?

A

5 to 3

New nucleotides are only added to the free 3 end

113
Q

Describe the structure of the DNA double helix?

A

Two antiparallel nucleotide strands
One is 5 to 3, the other 3 to 5
Sugar phosphate backbone
Base pairs on inside

114
Q

How many bonds are formed between A and T?

A

Two -double bond

115
Q

How many bonds are formed between C and G?

A

Three

triple bond

116
Q

Why is DNA replication important?

A

So that daughter cells have a complete genome

117
Q

What are the features of DNA replication?

A

Semi conservative

118
Q

What is the catalyst in DNA replication?

A

DNA polymerase

119
Q

What is require before DNA replication can occur

A

Existing nucleic acid

RNA primer

120
Q

Explain the origins of replication in eukaryotes?

A

Have many origins of DNA replication

Bidirectional to ensure DNA replication finishes in a reasonable amount of time

121
Q

What is the leading strand?

A

ALways has a free 3 end

122
Q

What is the lagging strand

A

Has to be replicated in short segments called okazaki fragments

123
Q

What are the steps of DNA replication?

A 
Helicase unwinds DNA
DNA polymerase synthesises a complementary strand
Primase synthesises an RNA primer
Gaps are filled by DNA polymerase
Primers are degraded
124
Q

How does DNA polymerase ‘proof read’ the DNA?

A

has a 3 to 5 exonuclease activity

removes incorrect nucleotide

125
Q

Describe the general structure of RNA.

A

single stranded
can create stem-loops= local streches of intramolecular basepairing
contains uracil instead of T

126
Q

What are the three main clases of RNA?

A

ribosomal
transfer
messenger

127
Q

What is the function of rRNA?

A

combines with proteins to form ribosomes where protein synthesis takes place

128
Q

What is the function of tRNA?

A

carries the amino acids to be incorporated into the protein

129
Q

What is the function of mRNA?

A

carries the genetic information for protein synthesis

130
Q

What are the stable RNAs?

A

rRNA

tRNA

131
Q

What enzyme makes RNA?

A

RNA polymerase

132
Q

How many types of RNA polymerazes are there in eukaryotes?

A

three

Pol 1, poll II and poll III

133
Q

How can RNA polymerases be distinguished?

A

By their sensitivity to toxins like alpha amanitin

134
Q

WHich RNA polymerase synthesises mRNA?

A

Pol II

135
Q

What is tRNA?

A

Adapter between nucleic acid code and amino acid code

136
Q

What is an anti codon?

A

Three nucelotides

specific amino acids attach to it at the 3 end

137
Q

What is the shape of tRNA?

A

three dimensional

cloverleaf when flattened

138
Q

What are the steps of transcription?

A 
RNA polymerase binds
DNA chain separate
Transciption initiated
Elongation
Termination
139
Q

What is the TATA box?

A

present about 25 nucelotides before transcrition starts

site for binding of promoters

140
Q

What is TBP?

A

TATA box binding protein

141
Q

What is TFIID?

A

a general transcription factor

rquired for all Pol II transcibed genes

142
Q

What is the role of TBP?

A

Introduces kink into DNA- determines transciptional start and direction
Provides a landing platform for furthur transcription factors and for RNA polymerase

143
Q

What is required to initiate transcription?

A

general transcription factors
precise order of assembly
Pol II and TFIIF extend transcript of their own
TFIID allows transcription at low basal rates

144
Q

Describe the process of transcription elongation.

A

RNA synthesised 5 to 3
New RNA complementary to template
Identical to the coding strand

145
Q

Describe transcription termination.

A

Newly synthesised RNA makes a stem-loop structure
followed by a stretch of Us
A specific enzyme cleaves the (now finished) RNA
RNA is released
polymerase dissociates

146
Q

Name a specific example of a transciption regulator.

A

Steroid receptors

147
Q

Where are steroid receptors located?

A

Cytoplasm (inactive)

148
Q

How are steroid hormones transported in the blood?

A

Bound to albumin or specific transport proteins

149
Q

Describe the process of how steroids regulate transcription?

A

Free steroids enter target cells by diffusion
Bind to inactive steroid receptor in cytoplasm
Activates receptor
Translocates to nucleus
Binds to response elements
usually as homodimer
Coordinated regulation of a set of genes

150
Q

Where does the steroid bind to the DNA?

A

At steroid response elements (SRE’s)

151
Q

What is an exon?

A

Coding region of DNA

152
Q

What is an intron?

A

Non-coding region of DNA

153
Q

Describe the process of slicing

A

Extrons and introns are transcribed

Introns have to be removed before translation into protein

154
Q

How are the ends of mRNAs processed?

A

Addition of poly(A) tail

addition of 5’ cap

155
Q

What is the function of an anticodon?

A

Forms base pairs with codons

156
Q

How many nucleotides are in codons and anticodons?

A

Three

157
Q

What is the name for the three nucleotides on a codon or anticodon?

A

Triplets

158
Q

What do the anticodons code for?

A

Amino acids

159
Q

What is meant by the face that amino acids are degenerate?

A

Amino acids can have more than one codon

160
Q

What is meant by the fact that each codon is unambiguous?

A

Each codon codes for only one amino acid

161
Q

What are the components of translation?

A 
Amino acids
tRNAs
Aminoacyl-tRNA synthetases
A specific set of protein factors for each of
initiation of protein synthesis
elongation of polypeptide chain and translocation
termination
ATP and GTP as sources of energy
Ribosomes
mRNA
162
Q

What is the function of Aminoacyl-tRNA synthetase?

A

Binds amino acids to their corresponding tRNA molecule

163
Q

What kind of bond is between the amino acid and its tRNA?

A

covalent- requires ATP

164
Q

How many rRNA molecules are contained within a ribosome?

A

four

three in bacteria

165
Q

How many tRNA binding sites are present on a ribosome?

A

three

166
Q

Describe the initiation of translation.

A

Requires initiation factors (IFs)
GTP is hydrolysed to provide energy for initiation
Small ribosomal subunit binds to 5’ end of mRNA
Moves along the mRNA until AUG (start codon) is found (ATP-dependent)
Special ‘initiator’ tRNA with UAC anticodon base-pairs with the start codon
carries methionine
Large subunit joins assembly and initiator tRNA is located in P site

167
Q

Describe the elongation process of translation.

A

An elongation factor (EF-1a), brings the next aminoacyl-tRNA to the A site
anticodon (here: CGU) base-pairs with codon (here: GCA)
GTP is hydrolysed, EF is released from tRNA
A second elongation factor (EFbg) regenerates EF1a to pick up the next aminoacyl-tRNA

168
Q

What enzyme catalyses peptide bond formation between the amino acids in the P and A sites?

A

Peptidyl tranderase

169
Q

What are the names of the tree different binding sites for tRNA?

A 
A= acceptor
P= peptidly
E= exit
170
Q

Describe peptide bond formation and translocation.

A

Peptidyl transferase catalyses peptide bond formation between amino acids in the P and A sites
peptide now located in A site
Elongation factor EF-2 moves ribosome along the mRNA
by one triplet
‘Empty’ tRNA moves to E site
can exit and become reloaded with an amino acid
tRNA with the growing peptide moves from the A to the P site
A site is free for the next aminoacyl-tRNA

171
Q

Describe the process of termination of translation.

A

Occurs when the A site of the ribosome encounters a stop codon
UAA, UAG or UGA
No aminoacyl-tRNA base-pairs with stop codons
Release factor RF binds stop codon
GTP hydrolysis
Finished protein is cleaved off tRNA
The components – rRNA, mRNA and tRNA – dissociate from one another
Whole process starts all over again with small subunit being bound by IF ready for translation of a new protein

172
Q

What is a polysome?

A

Cluster of ribosomes bound to an RNA molecule

173
Q

Name the five possible overall mutations.

A 
Point 
Missense
Nonsense
SIlent
Frameshift
174
Q

What is a point mutation?

A

Change in a single base in DNA

175
Q

What is a missense mutation?

A

Results in a change of amino acid sequence which can change protein function

176
Q

What is a nonsense mutation?

A

Created new termination codon

Changes length of protein

177
Q

What is a silent mutation?

A

No change in amino acid sequencw
DUe to degeneracy of the genetic code
No effect on protein

178
Q

What is a frameshift mutation?

A

Addition of deletion of a base (or two)

Changed the reading frame of translation into protein

179
Q

Name the four types of base mutation.

A

Insertion
Deletion
Altered base- single amino acid change
Altered base- no amino acid change

180
Q

Name the four chromosomal mutations.

A

Deletions
Duplication
Inversions
Translocation

181
Q

What is protein targeting?

A

Moving a protein to its final cellular destination

182
Q

What is protein modification?

A

Addition of further functional chemical groups

183
Q

What is protein degradation?

A

Damaged or unwanted proteins must be removed

184
Q

What is the difference between a free and a bound ribosome?

A

Free ribosomes are in the cytosol whereas bound ribosomes are on the rough ER

185
Q

Where do free ribosomes make proteins for?

A

Cytosol
Nucleus
Mitochondria
Translocated post translationally

186
Q

Where do bound ribosomes make proteins for?

A 
Plasma membrane
ER
Golgi apparatus
Secretion
Translocation co-translationally
187
Q

Giv examples of post-translational modifications.

A

Glycosylation- addition of a carbohydrate

Formation of disulphide bonds

188
Q

What condition can be caused by a post-translational misfolding of the alpha- antitrypsin protein

A

Emphysema

189
Q

Name and describe a disease caused by incorrect protein targeting?

A

I cell disease (mucilipidosis II)
inherited recessive disorder of protein targeting
proteins normally destined for lysosomes are not properly sorted in the Golgi
end up secreted from cell
lysosomes can not properly digest material, become clogged

death before age 8

190
Q

What are enzymes?

A 
Catalysts
Proteins- exception ribozymes
Efficient
Specific
Potent
191
Q

What is a cofactor?

A

‘Helper’ molecules for enzymes

192
Q

What is the name for an organic cofactorr?

A

Coenzyme

193
Q

What is the name for a tightly bound enzyme?

A

Prosthetic group eg. haem in haemoglobin

194
Q

What is the name for an enzyme without a cofactor?

A

Apoenzyme

195
Q

What is the name for an enzyme with cofactor?

A

Holoenzyme

196
Q

Give an example of a metal ion cofactor

A

Zinc, iron, copper

Involved in redox reactions

197
Q

Give an example of a Coenzyme

A

Many are dervived from vitamins and are involved in redox reactions
NAD+, FAD
Others involved in group transfer processes eg CoA transfers acetyl groups
ATP transfers phosphate groups

198
Q

How does coenzymes relate to vitamin deficiency?

A

Most vitamins function as coenzymes- symptoms of vitamin deficiencies reflect the loss of specific enzyme activities.

199
Q

What is the difference between dietary and functional deficiency?

A

Dietary- inadequate intake

Functional- caused by drugs or toxins which inhibit co enzyme synthesis

200
Q

What does NAD+ stand for?

A

Nicotinamide adenine dinucleotide

201
Q

Where does the substrate bind to?

A

Active site eg a cleft or crevice

202
Q

What are the features of an active site?

A

Contains amino acids which are specific and essential for catalytic activity.

203
Q

What is the lock and key model?

A

Active site of unbound enzyme is complementary to the shape of the substrate

204
Q

What is the induced fit model?

A

Binding of substrate induces a conformational change in enzyme, results in complementary fit

205
Q

Name an example of an induced fit enzyme?

A

Hexokinase

206
Q

What effect do enzymes have on the transition state?

A

Bind to it and stabilize it

207
Q

What is the transition state?

A

Reaction intermediate that has the greatest free energy

208
Q

What effect to enzymes have on the activation energy of the reaction?

A

Reduce it by providing alternative reaction pathways

209
Q

Describe the bonding specific to the chymotrypsin active site?

A

Hydrophobic pocket binds aromatic amino acids

210
Q

Describe the bonding specific to trypsin active sites?

A

Negatively charges Asp interacts with positively charged Lys or Arg

211
Q

Describe the bonding at elastase active sites

A

Active site partially blocked, only amino acids with small or no side chains can bind

212
Q

Why is the trypsin acive site affected so greatly by pH?

A

Trypsin active site – carboxyl group part of active site – essential that this is charged – reduction in pH would reduce the extent of ionisation of this functional group and therefore decrease efficacy of active site.

213
Q

What is an isozyme?

A

Isozymes are isoforms of enzymes, they catalyse the same reaction but have different properties and structure (and sequence)

214
Q

Give an example of a developmental varying isozyme?

A

Haemoglobin

Different during various stages of development- foetal and embryonic varieties have a higher affinity for oxygen

215
Q

Give an example of tissue specific isoforms

A 
Lactate dehydrogenase (LDH)
Two types- one in heart and one in muscle 
Tetramer- five possible combinations
216
Q

What does an increase in LDH suggest?

A

Myocardial infarction

217
Q

Describe how the isozyme, creatine kinase is useful clinically?

A

Dimeric protein that binds to muscle sacromere
M form on skeletal muscle
B form in brain
Heart has both in a heterodimer (MB)
Appearance of brain type in blood- STROKE
Appearance of heart type suggest -MI

218
Q

Name an example of reversible covalent modification.

A

Phosphorylation- can convert inactive for to active form

219
Q

Which enzymes carry out phosphorylation?

A

Protein kinases

220
Q

What is a zymogen?

A

Inactive presursor of an enzyme

221
Q

Describe what is meant by irreversible covalent modification

A

Zymogens are irreversibly transformed into active enzymes by cleavage of a covalent bond

222
Q

Describe examples of irreversible covalent modification

A

in pancreas: trypsinogen and chymotrypsinogen, inactive precursors, are formed
in small intestine: enteropeptidase cleaves trypsinogen to form active trypsin which cleaves chymotrypsinogen to form active chymotrypsin
Other examples:
digestive enzymes, blood-clotting enzymes, clot-dissolving enzymes

223
Q

Why is the trypsin acive site affected so greatly by pH?

A

Trypsin active site – carboxyl group part of active site – essential that this is charged – reduction in pH would reduce the extent of ionisation of this functional group and therefore decrease efficacy of active site.

224
Q

What is an isozyme?

A

Isozymes are isoforms of enzymes, they catalyse the same reaction but have different properties and structure (and sequence)

225
Q

Give an example of a developmental varying isozyme?

A

Haemoglobin

Different during various stages of development- foetal and embryonic varieties have a higher affinity for oxygen

226
Q

Give an example of tissue specific isoforms

A 
Lactate dehydrogenase (LDH)
Two types- one in heart and one in muscle 
Tetramer- five possible combinations
227
Q

What does an increase in LDH suggest?

A

Myocardial infarction

228
Q

Describe how the isozyme, creatine kinase is useful clinically?

A

Dimeric protein that binds to muscle sacromere
M form on skeletal muscle
B form in brain
Heart has both in a heterodimer (MB)
Appearance of brain type in blood- STROKE
Appearance of heart type suggest -MI

229
Q

Name an example of reversible covalent modification.

A

Phosphorylation- can convert inactive for to active form

230
Q

Which enzymes carry out phosphorylation?

A

Protein kinases

231
Q

What is a zymogen?

A

Inactive presursor of an enzyme

232
Q

Describe what is meant by irreversible covalent modification

A

Zymogens are irreversibly transformed into active enzymes by cleavage of a covalent bond

233
Q

Describe examples of irreversible covalent modification

A

in pancreas: trypsinogen and chymotrypsinogen, inactive precursors, are formed
in small intestine: enteropeptidase cleaves trypsinogen to form active trypsin which cleaves chymotrypsinogen to form active chymotrypsin
Other examples:
digestive enzymes, blood-clotting enzymes, clot-dissolving enzymes

234
Q

What is the michaelis constant?

A

The substrate concentration where the initial reaction rate is half maximal

235
Q

What is Vmax?

A

The maximum velocity of a reaction in infinite substrate concentrations

236
Q

What is Vo?

A

The initial reaction rate

237
Q

What is equilibrium?

A

The rate at which there is no net change of substrate to product

238
Q

What are the units of Km?

A

concentration (m)

239
Q

What does a low Km mean?

A

Enzyme has a high affinity for the substate

240
Q

What does a high Km mean?

A

Enzyme has a low affinity for the substrate

241
Q

How do you determine Vmax on a linewearver-burk plot?

A

Intersection of the straight line with the Y axis

242
Q

How do you determine the Km for a lineweaver-burk plot?

A

Intersection with the X axis

243
Q

Give an example of an enzyme with a low Km?

A

Hexokinase- can work at near Vmax even when blood glucose level is very low
Glucokinase is an isozyme- activity increases as glusose levels rise

244
Q

What is MODY?

A

MODY (maturity-onset diabetes of the young)
caused by mutations in pancreatic glucokinase which affect KM or Vmax
reduced glucokinase activity results in reduced insulin secretion for a given blood glucose level

245
Q

What is the difference between a reversible and irreversible enzyme inhibitor?

A

Reversible inhibitors are substances which bind to an enzmye but can be released- irreversible inhibitors cannot be released

246
Q

What is the difference between a competitive and non competitive inhibitor?

A

competitive inhibitor: binds to the active (catalytic) site and blocks access to it by substrate
noncompetitive inhibitor: binds to a site other than the active site, inhibits the enzyme by changing its conformation

247
Q

How can a competitive inhibitor be ‘out- competed’?

A

By the addition of lots of substrate

Non competitice inhibitors cannot be out competed in this way

248
Q

What is a common mechanism of allosteric control.

A

In feedback inhibition- where by the product of a biochemical pathway can act as an allosteric inhibitor of a rate limiting enzyme nearer the beginning of the pathway

249
Q

What is the shape of an allosteric enzymes rate curve?

A

Sigmoidal

They do not follow the Michaelis-menten kinetics- not a hyperbola

250
Q

How can allosteric enzymes be controlled

A

Allosteric inhibitors

Allosteric activators

251
Q

What is co-operativity?

A

The influence that the binding of a ligand to one protomer has on the binding of ligand to another protomer in an oligomeric protein

252
Q

What is an allosteric site?

A

BInding site on an enzyme disctinct from the active site

253
Q

Give an example of allosteric regulation

A

Binding of oxygen to haemoglobin

254
Q

Describe the allosteric actions of oxygen and haemoglobon

A

Positive co-operativity- as oxygen increases haemoglobins affinty for oxygen in its other subunits increases

255
Q

What is the R form of an enzyme?

A

Relaxed- binds substrate tightly- ACTIVE

256
Q

What is the T form of an enzyme?

A

Tight- binds substrate less tightly- INACTIVE

257
Q

When are more enzymes in the T from?

A

In the absence of substrate- activate in the presence of substrate

258
Q

What is the sequential model of allosteric regulation?

A

The binding of substrate induces a conformational change from the T form to the R form
The change in conformation is induced by the fit of the substrate to the enzyme
Other subunits subsequently change as well

259
Q

How do allosteric inhibitors work?

A

By locking the subunits of the enzyme in the T form

260
Q

How do allosteric activators work?

A

By locking the enzyme subunit in the R form

Biochemistry (4 decks)

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