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Biochemistry Flashcards

1
Q

What three atoms are biomolecules made up of?

A

Protons, neutrons and electrons

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2
Q

What is the nucleus composed of?

A

Protons and neutrons

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3
Q

What is the mass and charge of a proton?

A

Mass of 1
Positive charge

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4
Q

What is the mass and charge of a neutron?

A

Mass of 1
No charge

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5
Q

What is the mass and charge of an electron?

A

Mass is negligible
Charge is negative

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6
Q

Where are electrons found?

A

Orbiting the nucleus in an orbital shell

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7
Q

Each colum in the periodic table is known as a group. Provide 3 facts about groups

A
  • Each group has shared chemical properties
  • Increasing no. of electron orbitals from top to bottom
  • Increasing no. of electrons that can be lost, gained or shared (Valence)
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8
Q

Each row in the periodic table is called a period. Give 2 facts about periods

A
  • Each period has the same number of electron shells
  • Total number of electron shells increases from period 1 to period 7.
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9
Q

What does the atomic number, denoted above an element, tell you?

A

How many protons are in the nucleus of that particular atom

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10
Q

Where can you find the mass of an atom on the periodic table?

A

Below an element. The atomic mass tells you the number of protons and neutrons and negligible mass of electrons.

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11
Q

What does the difference between the mass and the atomic number tell you?

A

The number of neutrons in the nucleus of an atom.

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12
Q

Define the ionization energy

A

The energy input needed to discharge an electron.

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13
Q

What is the electron affinity?

A

The energy released when electron is attached to a neutral atom.

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14
Q

Provide 3 metal characters

A
  1. malleable
  2. conduct heat and electricity
  3. mostly solid at room temp (except mercury)
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15
Q

The atomic radius __________ down a group.

A

Increases

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16
Q

The electronegativity ___________ down a group.

A

Decreases

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17
Q

The ionisation energy __________ down a group.

A

Decreases

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18
Q

Is ionisation low or high in very reactive elements?

A

Low, they also tend to have a low electronegativity,

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19
Q

Does ionisation energy increase or decrease across a period?

A

Increases

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20
Q

Does electron affinity increase or decrease across a period?

A

Increase

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21
Q

Where can elements with the strongest metal properties be found in the periodic table?

A

Bottom left

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22
Q

Where can elements with the most non-metal characteristics be found?

A

Top right of the periodic table

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23
Q

What determines the reactivity of an atom?

A

The number of electrons

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24
Q

How are electons orbitting the same orbital shown?

A

As pairs

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25
Q

How do we know if atoms are reactive or stable?

A
  • Atoms whose outermost shells contain unfilled orbitals (unpaired electrons) are reactive.
  • When all the orbitals in the outermost shell are filled, the atom is stable.
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26
Q

Why is the charge balance of helium neutral?

A

Helium has a pair of electrons and a pair of protons

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27
Q

What is the basis of a covalent bond?

A

Sharing of electron pairs

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28
Q

What is the basis of an ionic bond?

A

Attraction of opposite charges

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29
Q

What is the basis of a hydrogen bond?

A

Sharing of a H atom

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30
Q

What is the basis of a hydrophobic interaction?

A

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

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31
Q

What are van der Waals interactions?

A

Interaction of electrons of non-polar substances

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32
Q

Define bond energy

A

The amount of energy needed to separate two bonded or interacting atoms under physiological conditions.

This is how the strength of a bond is measured/described

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33
Q

What is the strongest type of bond?

A

Covalent, ionic bonds (the next strongest) are much weaker.

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34
Q

What is the usual number of covalent bonds a single atom can make the same as?

A

The number of reactive (unpaired or single pair in unfilled orbital) electrons in the outer shell.

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35
Q

Why is the number of covalent bonds an atom can make biochemically important?

A

Defines the role atoms can play in life.

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36
Q

How many covalent bonds can carbon make and what shape does this produce?

A

4, forms a tetrahedral shape/form

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37
Q

Carbon compounds can form complex structures. As well as covalent bonds with itself carbon can also form bonds with Hydrogen, Nitrogen and Oxygen atoms. What does this produce/allow?

A

Variability

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38
Q

Name 4 complex structures formed by carbon compounds

A
  1. Linear ampiphatic e.g. stearic acid
  2. Cyclic e.g. cholesterol
  3. Branched e.g. ß-Carotene
  4. Planar e.g. chlorophyll
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39
Q

Define electronegativity

A

The attractive force that an atomic nucleus exerts on electrons

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40
Q

The addition and removal of the following group is known as….

A

Phosphorylation and de-phosphorylation (a common way of changing a proteins function).

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41
Q

Acylation is the addition of which group?

A

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42
Q

Carboxylation is the addition of which group?

A

Carboxylation may alter the ability of a terminal part of a protein to interact with another structure.

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43
Q

What is the name of the following type of reaction?…

A

Esterification- esters are formed when an alcohol and an acid interact with eachother.

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44
Q

What happens during a condensation reaction?

A

Water is removed

anabolism is the assembly of monomers into a polymer, often involves the removal of water - condensation.

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45
Q

What happens during a hydrolysis reaction?

A

Water is added

Catabolism is when a biological polymer is broken down to produce water.

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46
Q

What happens during oxidation-reduction (Redox) reactions?

A

Electrons are transferred from one molecule to another

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47
Q

What is oxidation?

A

Oxidation is loss of electrons

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48
Q

What is reduction?

A

Reduction is gain of electrons

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49
Q

As one molecule is oxidised another is reduced, what is this known as?

A

A redox pair

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50
Q

AH + B ⇔A +BH

Which molecule is oxidised, electron donor, reducing agent?

A

A

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51
Q

AH + B ⇔ A + BH

Which one is reduced, electron acceptor, oxidising agent?

A

B

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52
Q

Why are redox reactions biologically important?

A

They are fundemental to almost all biochemical reactions.

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53
Q

What are the 5 oxidation states of carbon?

A
  1. Alkane (in fats)
  2. Alcohol (in carbohydrates)
  3. Aldehyde
  4. carboxylix acid
  5. carbon dioxide (final product of catabolism)
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54
Q

Name 6 common functional groups in biological molecules

A
  1. Methyl groups
  2. Methylene groups
  3. Amino groups and amides
  4. Carboxyl groups and esters
  5. Carbonyl groups and aldehydes
  6. Phophates
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55
Q

The ability of carbon to form ___________ shapes in combination with biologically important elements gives structural and reactive diversity to biochemical molecules.

A

Tetrahedral

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56
Q

Redox reactions define the movement of __________ between reactive groups on biomolecules.

A

electrons

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57
Q

Metabolism and, thus life, is a fundementally net ________ process in which carbon moves from a fully __________ (stable carbon structure) to fully _________ state (carbon dioxide)

A

Oxidative

Reduced

Oxidised

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58
Q

Name 5 functions of biomolecules

A
  1. Information storage- DNA
  2. Structural- teeth, bones, cartilage
  3. Energy generation- glycolysis, citric acid cycle, electron transport chain
  4. Enery currency/storage-ATP
  5. Recognition/communication/specificity- receptors, hormones, enzymes
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59
Q

Name the 4 major classes of biomolecules

A
  1. Peptides and proteins- consists of amino acids
  2. Lipids- triglycerides, phospholipids, steroids
  3. nucleic acids- DNA, RNA
  4. carbohydrates- mono-, di-, polysaccharides
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60
Q

Give one example of a monosaccharide, the building blocks of carbohydrates

A

Glucose

An O atom in glucose between carbon 1 and 5 circulises the molecule and creates a reducable target which releases energy. Glucose molecule is cleaved into two 3 carbon molecules in the first step of the glycolytic pathway.

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61
Q

What do carbohydrates do?

A

Store combustible or metabolic energy in the cell in the form of carbon chains which are linked to oxygen and hydrogen.

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62
Q

How are disaccharides formed?

A

By covalent bonds between carbon 1&4 or 1&2 positions.

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63
Q

What do disaccharides do?

A

Provide your body with a rapid source of energy as the O atom linking the moleucles is readily reduced by enzymes to generate readily metabolised monosaccharides.

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64
Q

Give 4 examples of disaccharides

A
  1. Latcose
  2. Maltose
  3. Sucrose
  4. Cellobiose
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65
Q

What do polysaccharides do in the body?

A

Provide large, onboard stores of stored metabolic energy in the form of polymeric glucose known as glycogen.

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66
Q

Give 2 examples of polysaccharides

A
  1. Cellulose
  2. Glycogen
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67
Q

In all chemical reactions, matter and energy are neither __________ or __________.

A

Created , destroyed

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68
Q

What is thermodynamics?

A

Biophysical discipline which deals with the question of whether a process is energetically favourable.

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69
Q

State the first law of thermodynamics

A

Energy is neither created nor destroyed-when energy is converted from one form to another, the total energy before and after the conversion is the same.

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70
Q

What is the second law of thermodynamics?

A

When energy is converted from one form to another, some of that energy becomes unavailable to do work- no energy transformation is 100% efficient.

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71
Q

What happens if there is no energy to apply order to a system?

A

Unless energy is applied to a system, it will be randomly arranged or disordered.

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72
Q

What is enthalpy and its symbol?

A

Heat content

H

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73
Q

What is entropy and its symbol?

A

Randomness, disorder

S

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74
Q

What is the most important change in a reaction? How do we calculate it?

A

The most important change is in free energy:

change in free energy = change in enthalpy - T x change in entropy

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75
Q

What is another way to calculate the free energy change?

A

Change in free energy = (energy of the products) - (energy of the reactants)

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76
Q

In exergonic reactions the total free energy of the product(s) is ______ than the total free energy of the reactant(s)

So the free energy change is ________.

A

Less

Negative

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77
Q

Can exergonic reactions occur spontaneously?

A

Yes

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78
Q

Give two examples of how the energy liberated in an exergonic reaction can be used to do work

A
  • conversion of glycogen to glucose
  • generation of body heat
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79
Q

Give 4 facts about endergonic reactions

A
  1. The total free energy of the product(s) is more than the total free energy of the reactant(s).
  2. Free energy change(delta G) is positive
  3. Cannot occur spontaneously
  4. need input of energy to proceed
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80
Q

What is delta Gº’ ?

A

The change in free energy under standard conditions.

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81
Q

What does R stand for?

A

The universal gas constant (8.3JK¯¹mol¯¹)

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82
Q

What does T stand for?

A

T is the absolute temperature (in degrees Kelvin)

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83
Q

What are standard conditions in the human body?

A
  • T=298K
  • 1 atmosphere pressure
  • 1 M(1mol/l) concentration of reactants (except for H+)
  • Delta Gº’
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84
Q

Why is it not 1M of Hydroegn ions used for standard conditions in the human body?

A

In the body 1M of hydrogen ions is difficult (pH=0, which is extremely acidic) pH=7 is preferred.

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85
Q

How is free energy related to equilibrium?

A

The further towards completion the point of equilibrium is, the more free energy is released.

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86
Q

What kind of free energy values are characteristic of readily reversible reactions?

A

Delta G values near 0.

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87
Q

Define the equilibrium of a reversible reaction

A

When the concentration of products is equal to the concentration of reactants, forwards and backwards reactions are balanced.

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88
Q

Are reactions with a negative delta Gº’ i.e. reactions going from high energy reactants to low energy products favourable?

A

Yes

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89
Q

What does increasing the concentration of reactants [A][B] relative to products [C][D] do to the change in free energy?

A
  • [C][D]/[A][B] becomes smaller than 1
  • The ln of a number smaller than 1 is negative
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90
Q

Which enzyme catalyses the reaction Glucose-6-phosphate ⇔ Glucose-1-phosphate?

A

Phosphoglucomutase

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91
Q

Glucose-6-phosphate ⇔ Glucose-1-Phosphate

What are the forward and backward reactions involved in?

A
  • Forward reaction is involved in glycogen synthesis
  • Back reaction is involved in glycogen breakdown
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92
Q

Give 3 reasons why many cellular processes are unfavourable

A
  1. Have to proceed in the direction of a positive delta G
  2. transport against a gradient
  3. synthesis of large molecules
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93
Q

How can cellular processes which are unfavourable be driven?

A

By coupling them to a highly favourable process.

Usually the generartion of pyruvate and inorganic phosphate which is exergonic

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94
Q

Is the reaction of ATP + water → ADP +Pi + H+ favourable?

A

Yes it has a very negative deltaGº’ (-30kJ/mol)

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95
Q

How do many reactions in the body occur?

A

By coupling an unfavourable reaction (positive deltG) with a very favourable reaction like the breakdown of ATP.

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96
Q

What is ATP used for?

A

It is used as a universal energy currency for driving many different cellular processes.

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97
Q

What are anhydride bonds?

A

High energy bonds

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98
Q

What do the negative charges close together in ATP do to make it less stable than ADP?

A

Put a strain (electrostatic repulsion) on the molecule.

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99
Q

How is the strain created by negative charges close together on ATP partially relieved?

A

By removing one or more phosphate groups

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100
Q

Do cells store much ATP?

A

No, cells do not store large amounts of ATP- concentrations < 10mM

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101
Q

Give 2 reasons why ATP is constantly regenerated

A
  1. Cells do not store large amounts of ATP
  2. Active muscle cells (for example) use it at a high rate
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102
Q

Provide 2 examples of ways we can regenerate ATP

A
  1. using creatine phosphate
    * standard free energy of hydrolysis = -43kJ/mol
  2. using 2 ADP ⇔ATP + AMP
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103
Q

What does metabolism encompass?

A

All of the reactions taking place in the body, divided into Catabolism + Anabolism

(all exergonic and endergonic reactions although it is important not to assume all catabolic reactions are exergonic and anabolic endergonic)

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104
Q

What is catabolism?

A

Breaking down complex moleucles into smaller ones and releasing energy

THERE ARE ENERGY CONSUMING STEPS IN SOME CATABOLIC PATHWAYS

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105
Q

What is anabolism?

A

Synthesizing complex molecules out of smaller ones in energy consuming reactions.

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106
Q

Describe glycolysis as an example for a catabolic pathway in four points.

A
  1. Initial breakdown of glucose for the generation of ATP
  2. Early steps use two ATP molecules
  3. Later steps generate four ATP molecules
  4. Net gain of two ATP molecules per glucose molecule
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107
Q

Describe glucogenesis as an example for an anabolic pathway in 3 points

A
  • Making new glucose from non-carbohydrate precursors, e.g. pyruvate
  • costs energy- which could for example come from fat metabolism
  • this pathway is NOT simply the reverse of glycolysis
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108
Q

Which reactions are not used as control points?

A

Reactions close to equilibrium (delta G close to 0)

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109
Q

Which reactions are useful control points?

A

Reactions with large negative delta G values are useful control points.

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110
Q

Define flux

A

The rate of turnover of molecules through a metabolic pathway.

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111
Q

How is flux through control points in metabolic pathways controlled?

A

By altering the activity of the enzyme involved

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112
Q

What are carbohydrates composed of?

A

Carbon chains that are primarily linked to hydrogen and oxygen atoms.

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113
Q

Why is the oxidation of carbohydrates important in metabolic pathways?

A

Provides an important source of energy release.

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114
Q

Why are carbohydrates as polymers (disaccharides/polysaccharides) useful?

A

They provide an important form of stored energy which can be held within cells or moved between organs.

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115
Q

What do the laws of thermodynamics do?

A

Place limits on biochemical processes. The tendency of sequential reactions to convert energy to unusable forms ultimately sets a limit to life.

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116
Q

Describe water molecules

A
  • Water is polar
  • electrons are shared unequally
  • depends on electronegativity of atoms
  • oxygen has a high positive electronegativity at 3.5, hydrogen has a lower positive one of 2.2. Charge difference caused by an unequal share of covalently bonded electrons. This is called a dipole moment, negative charge is nearer the oxygen.
  • Water molecule is bent
  • forms a dipole
  • tetrahedral shape
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117
Q

Which type of substances dissolve in water?

A
  • Ionic and polar substances dissolve in water
  • hydrophilic, greek for ‘water loving’
  • Based on electrostatic interactions
  • ion-dipole interactions
  • dipole-dipole interactions
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118
Q

Describe how a hydrogen bond forms

A
  • A covalent bond between hydrogen and a more electronegative atom (e.g. oxygen) creates a polarized bond- hydrogen has a partial positive charge.
  • This hydrogen can interact with unsharred electrons from another electronegative atom.
  • This interaction is called a hydrogen bond.
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119
Q

Are hydrogen bonds stronger than covalent bonds?

A

Individually much weaker than covalent bonds but can be stronger collectively

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120
Q

Where are hydrogen bonds important?

A

In water and biological structures

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121
Q

Describe hydrogen bonds in biomolecules

A

Hydrogen atoms are shared between two electronegative atoms. Bonds tend to be linear.

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122
Q

Are non-polar substances soluble in water?

A

No they are insoluble in water- hydrophobic

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123
Q

Why are non-polar substances insoluble in water?

A
  • Powerful attraction between water molecules- they prefer to interact with themselves instead of non-polar molecules.
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124
Q

Are hydrocarbons polar molecules?

A

No, they are very non-polar and hydrophobic- compounds consisting only of carbon and hydrogen.

Water tends to exclude hydrocarbons- non-polar solid does not dissolve, non-polar liquids form a two-layer system with water.

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125
Q

Oil and water _______ mix.

Often called the _______ effect.

A
  1. do not
  2. hydrophobic
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126
Q

What are amphipathic molecules?

A

Ones which are both hydrophilic and hydrophobic, also called amphiphilic

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127
Q

Describe the two elements of amphipathic molecules

A
  • Polar (hydrophilic) ‘head’ group (at one end)- different types e.g. the choline group, carboxylic acid group; interact well with water
  • Non-polar (hydrophobic) ‘tail’ (at other end)- hydrocarbon, do not interact well with water
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128
Q

How do amphipathic molecules behave in water?

A

Form miscelles in water

  • ‘head’ groups in contact with water
  • ‘tail’ groups sequestered from the water
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129
Q

What do cell membranes do?

A

Selective and controllable barrier to the outside world which aid compartmentalixation by isolating organelles.

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130
Q

What are cell membranes composed of?

A

Lipids of various types

  • structural (lipid bilayer)
  • precursors of signalling molecules (DAG, IP3)

Proteins of various types

  • confer selectivity
  • involved in recognition
  • and more
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131
Q

Proteins and polypeptides are made up of how many L-amino acids?

A

20

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132
Q

What does D and L refer to in relation to amino acids?

A

Their stereochemistry

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133
Q

All amino acids contain an alpha carbon bonded to which 4 components?

A
  • An amino group (NH2)
  • A carboxyl group (-COOH)
  • A hydrogen (-H)
  • A side chain (-R)
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134
Q

D- and L- forms of amino acids are known as what?

A

Stereoisomers

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135
Q

What are stereoisomers?

A

Non-superimposable mirror images

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136
Q

Name 8 non-polar, hydrophobic amino acids

A
  1. Leucine
  2. Proline
  3. Alanine
  4. Valine
  5. Methionine
  6. Trytophan
  7. Phenylalanine
  8. Isoleucine
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137
Q

Name 7 polar, uncharged amino acids

A
  1. glycine
  2. serine
  3. asparagine
  4. glutamine
  5. threonine
  6. cysteine
  7. Tyrosine
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138
Q

What are acidic amino acids? Name 2

A

Acidic amino acids have side chains with a hydrogen ion that can dissociate in solution,they ionise to create acidic regions in a protein.

e.g. aspartic acid, Glutamic acid

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139
Q

What are basic amino acids? Name 3

A

Basic amino acids have side chains with ammonia like side groups that tend to bind hydrogen ion and gain a positive charge in solution. They can create basic regions in a protein.

Three examples

  • Lysine
  • Arginine
  • Histidine
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140
Q

How is a peptide bond formed?

A

Two amino acids are combined in a condensation reaction where water is removed. A peptide bond is formed CO-NH

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141
Q

Peptides have a direction, what is the direction of the peptide chain?

A

They run from the N-terminal residue to the C-terminal residue.

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142
Q

State three facts about Peptide bonds

A
  1. Peptide bonds partial double bond character
  2. Peptide bonds are planar
  3. Peptide bonds are strong and rigid-important for folding
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143
Q

What are acids?

A

Molecules which can donate a proton (hydrogen ion, H+)

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144
Q

What are bases?

A

Bases are proton acceptors

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145
Q

What does the strength of an acid depend on?

A

How readily it loses a proton

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146
Q

How is the strength of an acid measured?

A

By the acid dissociation constant, Ka

HA ⇔ H+ + A-

Ka= [H+][A-] / [HA] or pKa= -log10[Ka]

HA = acid A-= conjugate base

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147
Q

What is pH? How do we calculate it?

A

A measurement of the amount of protons in a solution.

pH= -log10[H+]

logarithm to the base 10 of the proton concentration.

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148
Q

What would you term a solution with pH=7?

A

Neutral

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149
Q

What would you term a solution with pH<7?

A

Acidic

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150
Q

What would you term a solution with pH >7?

A

Basic (alkali)

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151
Q

What is the Henderson-Hasselbalch equation and what does it do?

A

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

  • Connects the Ka of a weak acid with the pH of a solution containing this acid.
  • Lets us calculate the properties of buffer solutions- depending on the concentrations of acid and conjugate base.
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152
Q

What is a buffer?

A
  • A solution to control the pH of a reaction mixture.
  • At their pKa value buffers tend to resist a change of pH on addition of moderate amounts of acid or base.
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153
Q

What do we plot for a titration curve?

A

Plots pH as a function of base added to an acid.

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154
Q

Close to pKa what happens to pH if base is added?

A

It remains relatively unchanged

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155
Q

Describe zwitterions

A
  • Amino acids without charged side groups exist as zwitterions in neutral solution- no net charge.
  • Contain two titratable groups
  • Isoelectric
  • If acid is added- cationic form
  • If base is added-amionic form
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156
Q

What is the isoelectric pH?

A

The pH at which a molecule has no net charge is called the isoelectric pH, pI

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157
Q

What is the significance of uncharged amino acids having two titratable groups?

A

They have two pKa values

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158
Q

Explain why proteins can act as buffers

A
  • The ends of proteins can be ionised
  • Several of the amino acid side chains can be ionised
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159
Q

A change in ____ can change ionisation of a protein. This can lead to changes in ________ and thereby function.

A
  1. pH
  2. structure
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160
Q

Differences in the ____________ properties of atoms in water molecules create dipoles which promote _________ bond interactions between biomolecules.

A
  1. electronegative
  2. hydrogen
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161
Q

Why do hydrogen bonds have an important role in biochemical reactions and transitional stabilisation of molecular interactions?

A

They are weak but readily reversible

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162
Q

How is it possible for amphipathic molecules which contain hydrophilic and hydrophobic domains to span polar and non polar environments.

A

As non-polar molecules cannot form hydrogen bonds.

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163
Q

Amino acids have unique properties which can confer hydrophobic, __________, acid or ______ properties to peptide chains and proteins.

A
  1. hydrophilic
  2. basic
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164
Q

The ___________ properties of the amino acid backbone can confer unique buffering properties to proteins which influence their function.

A

zwitterionic

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165
Q

Name 3 important consequences on protein function from protein buffering characteristics

A
  1. impact their ability to interact with other binding partners
  2. protein structure
  3. protein distribution within the cell
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166
Q

Name the four levels of protein structure

A
  1. primary structure
  2. secondary structure
  3. tertiary structure
  4. quaternary structure
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167
Q

What is the primary structure of a protein?

A

The sequence of amino acid residues

168
Q

Define the secondary structure of a protein

A

The localised conformation of the polypeptide backbone.

Folding of the backbone which depends on the chemical properties of neighbouring amino acids.

169
Q

What is the tertiary structure of a protein?

A

The three-dimensional structure of an entire polypeptide, including all its side chains, includes multiple secondary structures.

  • 3D arrangement of all atoms and side chains of a polypeptide in space.
  • Consists of local regions with distinct secondary structure.
170
Q

Define the quaternary structure of a protein

A

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

Proteins which contain more than one polypeptide chain- between 2 and more than a dozen subunits, identical or different subunits.

171
Q

Polypeptides can rotate around the angles between which two points?

A
  • The alpha carbon and the amino group
  • The alpha carbon and the carboxyl group

Can rotate by as much as 180 degrees in either direction

Composition of neighbouring side chain groups determines how and when a fold occurs

172
Q

The secondary structure of a protein is localised and only considers the backbone of the polypeptide. Which bonds are involved in this 3D arrangement?

A

Hydrogen bonds

173
Q

Name the three types of secondary protein structures

A
  1. Alpha helix
  2. Beta (ß) strands and sheets
  3. Triple helix
174
Q

Describe the alpha helix secondary structure

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
175
Q

How are proline residues able to break alpha helixes?

A

The amide plane is at an acute angle to the side chain so this disrupts hydrogen bonding sequence. Prolines are therefore one of a group of amino acids that can produce kinks in the secondary sequence.

176
Q

Describe the secondary structure ß sheets

A
  • polypeptide backbone almost completely extended.
  • can invole more than one chain
  • Two possible directions
    • parallel
    • anti-parallel
  • turns between strands (glycine and proline)
  • formed by carboxy to amide hydrogen bonds which form between peptide chains-this folds them into a flattened sheet like structure.
177
Q

Describe ß pleated sheets

A

Repeated zig-zag structure, where glycine or proline create turns this is when a pleated sheet is created.

178
Q

Is it possible for different secondary structure elements to occur within one protein e.g. an alpha helix and a ß sheet

A

Yes

179
Q

Describe the collagen triple helix

A
  • component of bone and connective tissue
  • most abundant protein in vertebrates
  • water-insoluble fibres
  • 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)
  • covalent inter- and intra-molecular bonds
180
Q

Why is collagen important?

A
  • influences strength of connective tissue
  • weakened collagen results in bleeding gums
181
Q

What are the two types of tertiary structures?

A

Fibrous proteins and globular proteins

182
Q

Why is meat from older animals tougher?

A

Covalent crosslinking increases with age.

183
Q

How do people get scurvy: bleeding gums, skin discoloration?

A
  • the enzyme which hydroxylates proline requires ascorbic acid (Vitamin C)
  • Dietary deficiency of vitamin C results in reduction in hydroxyproline
  • results in weakened collagen
184
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.
185
Q

Name 2 examples of fibrous proteins

A
  1. Keratin of wool and hair
  2. collagen of connective tissue of animals including cartilage, bones, teeth, skin and blood vessels
186
Q

Describe globular proteins

A

Proteins which are folded into a more or less spherical shape

  • they tend to be soluble in water and salt solutions
  • most of their polar size chains are on the outside and interact with the aqueous environment by hydrogen bonding and ion-dipole interactions.
  • most of their non-polar side chains are buried inside.
  • nearly all have substantial sections of alpha-helix and beta-sheet
187
Q

Give 2 examples of globular proteins

A
  1. myoglobin
  2. haemoglobin
188
Q

Name the 5 forces which stabilise tertiary structures

A
  1. covalent disulphide bonds
  2. electrostatic interactions= salt bridges
  3. hydrophobic interactions
  4. hydrogen bonds
    • backbone
    • side chain
  5. Complex formation with redox sensitive metal ions
189
Q

What can happen when environmental events cause the forces holding the tertiary structure together to change?

A

This can influence the behaviour and biochemical function of the protein considerably.

190
Q

Why are disulphide bonds important?

A
  • Can create links which can be lost if the disulphide bridge is reduced
  • oxidation of the groups will recreate the double bonds
  • reduction or oxidation of disulphide bonds often contributes to regulated change in protein conformation.
191
Q

State the three electrostatic interactions in proteins

A
  1. positive charges attract negative charges
  2. salt bridges
  3. Repulsion between similar charges
192
Q

Where are charged (polar) side groups normally located on a proteins structure?

A

On the outside of proteins- interact with water.

193
Q

Hydrophobic interactionss have a strong organizing influence in proteins. What is this called?

A

The hydrophobic effect

194
Q

List the following in order of decreasing strength of interaction

  • Hydrocarbon-Hydrocarbon (Van der Waals)
  • Hydrogen bonds between water molecules
  • Attraction between water and hydrocarbon
A
  1. Hydrogen bonds between water molecules
  2. Attraction between water and hydrocarbon
  3. Hydrocarbon-hydrocarbon (Van der Waals)
195
Q

Where do hydrophobic amino acid side chains tend to cluster in globular proteins?

A

In the centre

196
Q

Which type of bond determines the solubility and cellular location of proteins?

A

Hydrogen bonds

197
Q

Do amino acid substitutions effect protein structure and thus function?

A

Mutations that alter the normal sequence of amino acids can have major effect on protein structure and therefore function.

Can lead to significant functional changes.

198
Q

How does single cell anaemia occur and manifest?

A

Single nucleotide sequence change

  • In coding region of the ß chain of haemoglobin A

Results in altered protein

  • Valine instead of glutamic acid

Under low oxygen conditions, haemoglobin polymerises

  • results in rigid, sickle shape cells

Can block blood flow in capillaries

199
Q

Describe the folding of polypeptide chains

A
  • primary structure of a protein contains all the info needed for its 3D shape
  • proteins may fold spontaneously into their correct shape
  • But this can be a slow and erroneous process taking part in several compartments
  • sometimes folding process is aided by other specialized proteins called chaperones.
200
Q

What is the name of specialized proteins which may assist in protein folding?

A

Chaperones

201
Q

Why can protein folding be a slow and erroneous process?

A
  • protein may begin to fold incorrectly before it is completely synthesised.
  • It may associate with other proteins before it is folded properly
  • examples: Alzheimer’s, Parkinson’s, CJD
202
Q

What is the name given to disruption of the protein structure?

A

Denaturation

203
Q

What types of physical condition or chemical agent(s) will disrupt the various protein structures and how?

A
  • Heat- increase in vibrations in a protein
  • Extremes of pH- electrostatic interactions interrupted
  • Detergents, Urea, guanidine, hydrochloride- disrupt hydrophobic interactions
  • Thiol agents, reducing agents- reduce and thereby disrupt disulphide bonds
204
Q

Describe myoglobin as an example of a tertiary structure

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
205
Q

Describe haemoglobin as an example of a quaternary structure of a protein

A
  • four subunits
  • two alpha and two ß chains
  • each contains a haem group
  • each subunit can bind one oxygen molecule
  • binding of one oxygen changes affinity of the other subunits-allosteric
  • transports oxygen in blood
206
Q

The properties of amino acids confer shape, form and function to _________ .

A

Proteins

207
Q

How many levels of structural hierarchy are there from single polypeptide chains to multimeric proteins?

A

4

208
Q

Changes in protein conformation can arise from redox interactions. How does this happen?

A

The redox interactions affect the state of metal ion centres or disulphide bridges, and also through electrostatic interactions, salt bridging and hyrophobic interactions.

209
Q

Changes in amino acid sequence that affect structurally sensitive parts of a protein will alter its __________. These drive gain or loss of function effects which may have evolutionary significance. In the clinical context however, such mutations are freqeuntly a significant cause of ____________.

A
  1. function
  2. disease
210
Q

What does the total DNA in each cell constitute which carries the information required for making the whole organism?

A

The genome

211
Q

Where is the information required for making the whole organism stored in the genome?

A

In the nucleotide sequence

212
Q

What does the DNA nucleotide sequence determine?

A

The amino acid sequence of polypeptide chains.

213
Q

Describe the central dogma and what it concerns

A

The central dogma is concerned with the flow of information from DNA to protein via RNA.

This occurs via transcription and translation

214
Q

How does the type of sugar determine whether a molecule is RNA or DNA?

A
  • Ribose sugar in RNA
  • Deoxyribose in DNA
215
Q

What is a nucleoside composed of?

A

Base and sugar

216
Q

What is a nucleotide composed of?

A

Nucleoside (base & sugar) + phosphate group(s)

217
Q

Which 4 bases occur in DNA?

A
  1. Adenine (A)
  2. Thymine (T)
  3. Cytosine (C)
  4. Guanine (G)
218
Q

Which 4 bases occur in RNA?

A
  1. Adenine (A)
  2. Uracil (U)
  3. Cytosine (C)
  4. Guanine (G)
219
Q

Which 2 bases are purines and how many rings are their molecules comprised of?

A
  • Adenine
  • Guanine
  • 2 rings
220
Q

Which 3 bases are pyrimidines and how many rings are their structures comprised of?

A
  • Uracil
  • Thymine
  • Cytosine
  • 1 ring
221
Q

What are the nucleosides of the following bases…

  • Adenine
  • Cytosine
  • Guanine
  • Thymine
  • Uracil
A

Adenosine

Cytidine

Guanosine

Thymidine

Uridine

222
Q

Name the DNA building blocks- dATP, dGTP, dCTP, dTTP

A
  • deoxy-adenosine-triphosphate
  • deoxy-guanosine-triphosphate
  • deoxy-cytidine-triphosphate
  • deoxy-thymidine-triphosphate
223
Q

Name the RNA building blocks- ATP, CTP, GTP, UTP

A
  • adenosine triphosphate
  • cytidine triphosphate
  • guanosine triphosphate
  • uridine triphosphate
224
Q

How is DNA polymerised?

A
  • A phosphodiester bond is formed between a free 3’ OH group and a 5’ triphosphate
  • consumes 2 high energy bonds
  • so the connection is made between the phosphate connected to the sugar and the free 3’ end of the preceding C and will extend this by one base.
  • Reaction is catalysed by DNA polymerase 3 which releases the pyrophosphate ion
225
Q

How are nucleotides polymerised is another way to ask how DNA is polymerised?…

A

Nucleotides are polymerised by the addition of a nucleotide onto the 3’ hydroxyl groups of an existing chain of nucleotides

226
Q

What is the direction of nucleic acids and what does this mean when new nucleotides are added?

A
  • 5’ to 3’
  • beginning has a free 5’ carbon connected to a phosphate
  • end has a free 3’ emd which allows nucleotides to join
  • new nucleotides are only added to a free 3’ end
227
Q

The two nucleotide strands run as follows:

  • One 5’ to 3’
  • one 3’ to 5’

What is this called?

A

Anti-parallel, as they run in opposite directions

228
Q

Describe the DNA double helix and it’s base pairing

A
  • anti-parallel strands
  • sugar-phosphate backbone on the outside
  • base pairs in the inside
  • hydrogen bonded base pairs
    • A double bond T
    • C tripple bond G
229
Q

Why does DNA have to be replicated (duplicated) before cell division?

A

So that the daughter cells have a complete complement of the genome

230
Q

DNA replication is semi-conservative, what does this mean?

A

Semi-conservative means when a double-stranded DNA molecule is replicated the new DNA contains one new strand of DNA and one of the old strands which has acted as a template.

231
Q

DNA replication is catalysed by DNA polymerase, what are its limitations?

A
  • can only add nucleotides to existing nucleic acids
  • can not start DNA synthesis on their own
  • require an RNA primer to start replication
232
Q

Eukaryotic genomes have many origins of replication. Replication starts simultaneously at several points in the genome and is bidirectional. Why is this?

A

Ensures that replication can be finished in a reasonable time.

233
Q

Why is DNA replication discontinuous?

A
  • Nucleotides can only be added to free 3’ ends
  • No problem on one strand
    • leading strand always has a free 3’ end
  • Other strand has to be replicated in short segments
    • lagging strand
    • okazaki fragments
234
Q

What is the fate of RNA primers?

A

Eventually get degraded and replaced by DNA.

235
Q

Which enzyme is responsible for unwinding the DNA and stopping it from rewinding?

A

Helicase

236
Q

Which enzyme is responsible for synthesizing the RNA primer?

A

Primase

237
Q

What are the 4 building blocks in DNA replication?

A
  1. dATP
  2. dTTP
  3. dCTP
  4. dGTP
238
Q

What is the fate of the three phosphate groups when a nuclotide is added to the chain?

A
  • one phopshate group forms phosphodiester bond
  • two leaves as PPi (pyrophosphate)-energy supply
239
Q

What happens if the wrong nucleotide is incorporated into a DNA strand?

A
  • This can create mutations
  • They may be deleterious or advantageous
  • occurs once every 10^4 to 10^5 base pairs
  • mutations are heritable
240
Q

DNA polymerase has 3’ > 5’ exonuclease activity, what does this repair mechanism do?

A
  • removes incorrect nucleotide
  • improves error rate to one in 10^9 to 10^10 base pairs
241
Q

Describe RNA-ribonucleic acid

A
  • usually single stranded
  • can contain local stretches of intramolecular base-pairing
  • 3 main classes
    • ribosomal(rRNA)- combines with proteins to form ribosomes where protein synthesis takes place
    • transfer RNA (tRNA)- carries the amino acids to be incorporated into the protein
    • messenger RNA (mRNA)- carries the genetic information for protein synthesis
  • Contains U (uracil) instead of T
242
Q

Which are the 2 types of stable RNA?

A
  1. rRNA
  2. tRNA

These are typically much shorter than mRNA which is typically hundreds of thousands of base pairs long.

243
Q

Give an example of the use of Nucleotide analogues as drugs

A
  • ZDV(zidovudine)= AZT(azidothymidine)= Retrovir
  • analogue of thymidine
  • is incorporated into the growing viral DNA
  • lacks 3’ OH group, therefore, chain elongation is terminated
  • Only works because viral reverse transcriptase has higher affinity for ZDV than human DNA polymerases
  • It effects the HIV virus but not the human
244
Q

What is tRNA?

A

An adapter between the nucleic acid code and the amino acid code.

245
Q

How many nucleotides does the tRNA anticodon consist of?

A

Three nucleotides

246
Q

All tRNA molecules have a distinct ____ ____________ structure.

A

Three dimensional

247
Q

What does a tRNA molecule resemple when it is flattened into two dimensions?

A

cloverleaf structure

248
Q

When tRNA attaches to the nucleic acid, a specific amino acid is attached to the 3’ end, what does this depend on?

A

The anticodon sequence

249
Q

What is RNA made by?

A

RNA polymerases

250
Q

RNA polymerases are ______-_________ complexes.

A

Multi-subunit

251
Q

What do RNA polymerases do?

A

Use one DNA strand as template to copy the nucleotide sequence into RNA.

252
Q

How many types of RNA polymerase do prokaryotic cells have?

A

one

253
Q

How many types of RNA polymerase do eukaryotic cells have and what are they called?

A
  • Three
  • Pol I, Pol II, Pol III
254
Q

How can RNA polymerases in eukaryotic cells be distinguished?

A

By their sensitivity to toxins like alpha-amanitin

255
Q

What does pol II explicitly synthesise?

A

mRNA

256
Q

Can RNA polymerase initiate transcription from an empty space?

A

Yes

257
Q

Name the 5 steps of transcription

A
  1. RNA polymerase binding
  2. DNA chain separation
  3. Transcription initiation
  4. Elongation
  5. Termination
258
Q

Explain the process of RNA polymerase binding

A
  • detection of initiation sites (promoters) on DNA
  • requires transcription factors
259
Q

Describe DNA chain separation

A
  • local unwinding of DNA
  • to gain access to the nucleotide sequence
260
Q

What is transcription initiation?

A

Selection of the first nucleotide of the growing RNA.

261
Q

What happens during elongation?

A

Addition of further nucleotides to the RNA chain

262
Q

What is termination?

A

Release of finished RNA

263
Q

What are promoters?

A
  • A site in the genome which tell RNA where to bind.
  • promoters are specific DNA sequences that sit upstream of the initiation of transcription site of various genes.
  • all protein coding regions have a promoter
264
Q

Describe the role of the TATA box

A
  • RNA pol II specific promoter
  • transcription starts at nucleotide +1
  • TATA box is present about 25 nucleotides before the transcriptional start (-25)
265
Q

What is the role of the TATA box binding protein (TBP)?

A
  • Recognises TATA box
  • Part of TFIID
    • TFIID is a general transcription factor
    • required for all pol II transcribed genes
  • introduces kink into DNA
    • determines transcriptional start and direction
  • Provides a landing platform for further transcription transcription factors and for RNA polymerase
266
Q

Describe the 5 stages of initiation of transcription

A
  1. The first transcription factor, TFIID, binds to the promoter at the TATA box.
  2. and another transcription factor joins it
  3. RNA polymerase II binds only after several transcription factors are already bound to DNA.
  4. more transcription factors are added in a presice order of assembly
  5. and the RNA polymerase is ready to transcribe RNA
267
Q

What does initiation of transcription require?

A

Additional general transcription factors

268
Q

Which two proteins extend the transcript on their own during initiation of transcription?

A
  • Pol II
  • TFIID
269
Q

What happens to TFIID after initiation has begun and what does this allow?

A
  • TFIID remains at the promoter, a new initiation complex can assemble.
  • allows transcription at low, basal rates
270
Q

What are the 5 key points of trascription elongation?

A
  • A transcription ‘bubble’ moves in one direction along the DNA
  • DNA is unwound in front of the polymerase, and rewound behind it.
  • RNA chain is synthesised in a 5’ to 3’ direction
  • New RNA sequence is complementary to the template strand
  • It is identical to the coding strand- but don’t forget: U instead of T
271
Q

Can polymerase be recycled after transcription?

A

Yes

272
Q

What happens during 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
273
Q

How is transcription regulated?

A
  • requires ‘specific’ transcription factors
    • DNA-binding proteins
    • contain 2 functional domains which can be physically separated
  • bind to specific DNA sequences in the vicinity of a promoter
    • enhancers
  • regulate trascription positively or negatively
274
Q

What are the two functional domains of ‘specific’ transcription factors?

A
  • DNA-binding domain
  • Transcriptional activation domain
275
Q

DNA bending can bring an ________ ________, bound to an enhancer element far from the promoter, into contact with the ___________ complex.

A
  • activator protein
  • transcription
276
Q

When does coordinated gene expression occur?

A

In response to specific stimuli, e.g. hormones, cellular stress…

277
Q

Describe how coordinated gene expression would occur in response to a stressor

A
  1. A stressor (e.g. drought) activates transcription of a regulatory protein through a drought-sensitive transcription factor
  2. Binding of the regulatory protein to the stress response element (SRE) stimulates transcription of genes A,B and C…
  3. which produces different proteins participating in the stress response.
278
Q

Explain how steroid receptors produce co-ordinated gene expression

A
  • family of transcription factors, subset of (much larger) family of nuclear hormone receptors
  • structurally similar
  • DNA-binding and ligand-binding domains highly conserved
  • located in cell cytoplasm (inactive)
  • on binding ligand (steroid) move to nucleus and bind to DNA at steroid-response elements (SREs)
279
Q

Explain how glucocorticoid receptors are an example of coordinated gene expression

A
  • steroids are transported in the blood
    • bound to albumin or specific transport proteins
  • 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
280
Q

Eukaryotic genes have coding and non-coding sequences, what are these called?

A

Coding regions (exons) are interrupted by non-coding regions (introns)

  • between 1 and more than 50 introns per gene
281
Q

Are exons and introns both transcribed together?

A

Yes

282
Q

Introns have to be removed before translation into a protein, how does this occur?

A

splicing

283
Q

The primary transcript is known as pre-mRNA, what does it contain?

A

Introns and exons, introns need to be spliced out before mRNA is made

284
Q

How are the ends of an mRNA molecule processed?

A
  • addition of 5’ cap of modified GTP- capping
  • addition of a poly(A) tail- polyadenylation
285
Q

Transcription and translation are _____________ in eukartoyic cells, unlike in prokaryotes where they all occur in the same place.

A

compartmentalised

286
Q

Where do DNA replication, transcription, processing of the primary mRNA transcript and translation occur?

A
  • DNA replication, transcription, processing of the primary transcript= nucleus
  • Translation= ribosomes in the cytoplasm
287
Q

During translation, ______________ of tRNA molecules form base pairs with ________ on mRNA.

A
  • anti-codons
  • codons
288
Q

How many nucleotides do anticodons and codons consist of?

A

Each consist of 3 nucleotides

289
Q

What is the genetic code based on considering each codon and anticodon consists of three nucleotides?

A

Triplets

290
Q

There are four nucleotides available which leads to how many possible combinations and codes for how many amino acids?

A
  • 64 possible combinations
  • code for 20 amino acids
291
Q

What are the 3 key features of the genetic code?

A
  • degenerate- many amino acids have more than one codon
  • unambiguous-each codon codes for only one amino acid (or a stop)
  • nearly universal
292
Q

Each tRNA molecule can be translated into how many different reading frames depending on where translation starts?

A

3

293
Q

Name the 7 components of translation

A
  1. amino acids
  2. tRNAs
  3. aminoacyl-tRNA synthetases
  4. a specific set of protein factors for each of
    • initiaion of protein synthesis
    • elongation of peptide chain and translocation
    • termination
  5. ATP and GTP sources of energy
  6. ribosomes
  7. mRNA
294
Q

What do aminoacyl-tRNA synthetases do?

A

Bind amino acids to their corresponding tRNA molecule(s)- highly specific

295
Q

How many aminoacyl-tRNA molecules are there for each amino acid?

A

At least one

296
Q

What provides the energy for formation of a covalent bond between amino acids and tRNA molecules?

A

ATP

297
Q

How many different rRNA molecules do ribosomes contain?

A

4

(3 in bacteria)

298
Q

What else do ribosomes contain besides rRNA molecules?

A

They also contain protein components

  • 55 polypeptides in prokaryotic cells
299
Q

Ribosomes have three tRNA binding sites, what are they?

A
  • E=exit
  • P=peptidyl
  • A=aminoacyl
300
Q

What is requried for initiation of translocation?

A

Initiation factors (IFs)

GTP which is hydrolysed to provide energy for initiation

301
Q

Describe the steps which occur during initiation of translocation

A
  • small ribosome 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
302
Q

What happens during the elongation stage of translocation?

A
  • An elongation factor (EF-1a), brings the next aminoacyl-tRNA to the A site
    • anticodon base pairs with codon
  • GTP is hydrolysed, EF is released from tRNA
  • A second elongation factor (EFßY) regenerates EF1a to pick up the next aminoacyl-tRNA
303
Q

Which enzyme catalyses the peptide bond formation between amino acids in the P and A sites so that the peptide becomes located in the A site?

A

Peptidyl transferase

304
Q

During peptide bond formation in translocation the elongation factor EF-2 moves the ribosome along the mRNA by how far?

A

One triplet

305
Q

What happens when a tRNA molecule becomes ‘empty’?

A

It moves to the E site where it can exit and become reloaded with an amino acid.

306
Q

What happens during elongation once a peptide bond has been formed to the tRNA with the growing peptide?

A

It moves moves from the A site to the P site. A site is free for the next aminoacyl-tRNA.

307
Q

When does termination occur during translocation?

A

When the A site of the ribosome encounters a stop codon.

308
Q

Name 3 possible stop codons

A

UAA

UAG

UGA

309
Q

How many aminoacytl-tRNA can base-pair with stop codons?

A

None

310
Q

What binds with the stop codon during termination causing GTP hydrolysis?

A

Release factor, RF

311
Q

What happens during termination of transcription?

A
  • Release factor RF binds to stop codon
  • 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.
312
Q

Name the 5 types of mutation

A
  1. Point mutation
  2. Missense mutation
  3. Nonsense mutation
  4. Silent mutation
  5. Frameshift mutation
313
Q

What is a point mutation?

A

Change in a single base in DNA

314
Q

What is a missense mutation?

A
  • results in a change of amino acid sequence
  • can change protein function, e.g. altered haemoglobin in sickle cell anaemia
315
Q

What is a nonsense mutation?

A
  • Creates a new termination codon
  • changes length of protein due to premature stop of translation
316
Q

What is a silent mutation?

A
  • no change of amino acid sequence
  • due to degeneracy of the genetic code
  • no effect on protein function
317
Q

What is a frameshift mutation?

A
  • addition or deletion of a single base or (two!)
  • changes reading frame of translation into protein
318
Q

What is the difference between gene mutations and chromosomal mutations?

A

Chromosomal mutations affect larger portions of the genome.

319
Q

Name the 4 types of chromosomal mutations

A
  • deletions
  • dublications
  • inversions
  • translocations
320
Q

What are the three things which can happen to a finished protein?

A
  • Targeting
  • modification
  • degradation
321
Q

What is targeting?

A
  • moving a protein to its final cellular destination
  • many possible locations within a cell
  • depends on the presence of specific amino acid sequences within the translated protein.
322
Q

what is modification of a protein?

A

Addition of further functional chemical groups

323
Q

What is degradation?

A

unwanted or damaged proteins have to be removed.

324
Q

Free ribosomes in the cytosol make proteins destined for which 3 places? These are translocated _______- transationally.

A
  • cytosol
  • nucleus
  • mitochondria
  • translocated post-translationally
325
Q

Bound ribosomes on the rough endoplasmic reticulum make proteins destined for which 4 places. These are translocated __-translationally.

A
  • plasma membrane
  • ER
  • golgi apparatus
  • secretion
  • translocated co-translationally
326
Q

Give 5 examples of post translational modification

A
  • glycolysation= addition and processing of carbohydrates in the ER and the golgi, adding sugars is important for targetting and recognition
  • formation of disulphide bonds in the ER
  • folding and assembly of multisubunit proteins in the ER
  • specific proteolytic cleavage in the ER, golgi and secretory vesicles allows the fragments to fold into different shapes
  • phosphorylation- added phosphate groups alter the shape of the protein
327
Q

Describe the clinical relevance of protein targetting using the example of I-cell disease (mucolipidosis II)

A
  • inherited recessive disorder of protein targetting
  • proteins normally destined for lysosomes are not properly sorted in the golgi
  • end up secreted from the cell
  • lysosomes cannot properly digest material, become clogged
  • death before age 8
328
Q

How are many enzymes regulated?

A

By the addition or removal of phosphate

329
Q

Methylation regulats the compaction of what in the nucleus?

A

chromatin

330
Q

Why is phosphorylation as the most studied post-translational modification clinically relevant?

A
  • Kinases (enzymes that catalyse phosphorylation) are the second most targetted group of drug targets
  • > 40 kinase inhibitors received FDA approval for the treatment of malignancies, ~150 more in clinical trial- multi-billion dollar industry.
  • attractive due to “drugability”: common features (ATP binding) but distinct 3D structure and specificity
  • kinase inhibitor drugs you will hear more about include Gleevec (Imatinib), Zelboraf (Vemurafineb)
  • imatinib targets the kinases Abl (mutated in CML)
  • vemurafenib inhibits a mutated form of Raf( V600E) often mutated in melanoma.
331
Q

Enzymes catalyse the many chemical reactions which together make up the process of ____________.

A

metabolism

332
Q

What does an enzyme do?

A

Speeds up the rate at which a reaction reaches equilibrium.

333
Q

Do enzymes affect the equilibrium position for a reaction?

A

Reactions reach equilibrium when the forward and backward reaction have an equal velocity- Enzymes DO NOT affect the the equilibrium position of a reaction. The equilibrium position does not change, only the speed at which it is reached.

334
Q

Give 5 qualities of enzymes

A
  • catalysts
  • mostly proteins- exceptions: some types of RNA-ribozymes-are catalysts
  • efficient
  • specific- each enzyme has a limited range of substrates, some can distinguish stereoisomers
  • potent-each enzyme molecule can convert many substrate molecules into product per second
335
Q

Why are enzymes efficient?

A
  • work at body temperature, in aqueous solution, near neutral pH
  • can increase the rate of a reaction by a factor of up to 10^20
336
Q

In most of biology we encounter __-proteins and L amino acids

A

D

337
Q

What is the activation energy?

A

The minimum amount of energy required for a reaction to occur.

338
Q

What is the transition state?

A

The reaction intermediate species which has the greatest free energy.

339
Q

What do enzymes do to the transition state?

A

Specifically bind and stabilise the transition state.

340
Q

What do enzymes do to the activation energy?

A

Reduce the activation energy by providing alternative reaction pathways.

341
Q

What is glycogen storage disease?

A

Enzyme deficiency that results in failure of glycogen to enter transition “phosphorylated” state.

342
Q

What is the cause of glycogen storage disease?

A

defective glycogen synthesis/breakdown in muscle, liver and kidney.

11 variants arising from defects in 12 glycogen or glucose metabolising enzymes

Most common- Vin Gierke’s disease

343
Q

What are the sympotms of glycogen storage disease?

A
  • hypoglycaemia
  • hapatomegaly (liver swelling)
  • skin & mouth ulcers
  • bacterial & fungal infection
  • bowel inflammation & irratibility
344
Q

What are the treatments for glycogen storgae disease and why?

A
  • slow release glucose meal (eg corn starch)
  • feed little and often= ‘mimic’ glycogen conversion to glucose.
    • Do not want them to have huge glycogen stores.
345
Q

Describe Von Gierke’s disease in relation to enzymes

A
  • glycogen is a polymer of glucose molecules
  • glucose-6-phosphase can directly partake in glycolysis
  • in the liver glucose-6-phosphate is de-phosphorylated by the enzyme glucose-6-phosphatase which removes the phosphate from carbon 6 of glucose-c-phosphate and makes glucose. this is then released into the blood stream to circulate and feed other tissues.
  • mutation in glucose-6-phosphatase
  • when glucose-6-phosphate is generated in the liver, it cannot be de-phosphorylated to provide glucose for the blood- leads to a deficit of glucose in the blood- VG
  • Do not want them to have
346
Q

Catalytic activity of many enzymes depends on the presence of small molecules, called _________ or _______________.

A
  • cofactors
  • coenzymes
347
Q

What are the two types of small molecules enzymes depend on?

A
  • metal ions (inorganic, termed cofactors)
  • organic molecules (organic origin, termed coenzymes)
348
Q

Metal cofactors form a metal co-ordination centre in the enzyme. What is the enzyme referred to as _____________.

A

Metalloprotein

349
Q

Describe the action of coenzymes?

A
  • coenzymes mostly associate with the enzyme only transiently.
  • coenzymes change charge or structure during the course of the reaction but are re-generated.
  • tightly bound coenzymes are called prosthetic group e.g. haem in haemoglobin and cytochromes.
350
Q

What is the name of an enzyme without a coenzyme?

A

apoenzyme

351
Q

What is the name of an enzyme with a cofactor?

A

holoenzyme

352
Q

Apoenzyme + cofactor = _____________

A

holoenzyme

353
Q

Give examples of metal ions as cofactors

A
  • zinc, iron, copper
  • involved in redox reactions
  • stabilise transition states
354
Q

Describe the features of coenzymes

A
  • many are derived from vitamins
  • many involved in redox reactions (also carry electrons)
    • NAD+, FAD
  • others involved in group transfer processes
    • coA(=coenzyme A) transfers acetyl group
    • ATP transfers phosphate groups
355
Q

What do most vitamins function as?

A

coenzymes

356
Q

What do symptoms of vitamin deficiencies reflect the loss of?

A

Specific enzyme activities. May be dietary or functional (eg drug or diseass-induced deficiencies)

357
Q

Describe the function of Nicotinamide adenine dinucleotide (NAD+)

A
  • common coenzyme for redox reactions
  • May donate or receive electrons during enzyme catalysis
  • easily re-generated
358
Q

What is an active site?

A
  • a cleft or crevice
  • contains amino acids essential for catalytic activity
  • contains amino acids for highly specific interactions
359
Q

Where does a substrate bind to an enzyme?

A

The active site

360
Q

What is the induced fit model for the active site of an enzyme?

A

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

361
Q

How do temperature and pH affect enzyme activity?

A
  • humans have a working optimum of about 37 degrees and so do their enzymes
  • enzymes become denatured at higher temperatures
  • each enzyme has specific requirements around temp and pH e.g. those responsible for breakdown in the stomach would need to tolerate acidic conditions.
  • environment dictates how well the reaction takes place
362
Q

What are isozymes?

A

isoforms of enzymesm they catalyse the same reaction but have different properties and structure (and sequence)

363
Q

You can have 2 isozymes which can be doing the exact same job in the same way but their gene expression is regulated in a different way. Give 3 ways this can happen

A

Different isozymes can be

  • synthesised during different stages of foetal and embryonic development
  • present in different tissues
  • present in different cellular locations
364
Q

Give two examples of the clinical use of isozymes

A
  • relative amounts of isozymes in tissues are useful in diagnostic properties.
  • relative amounts of isozymes in blood are useful for diagnostic properties
365
Q

Explain how creatine kinase isozymes can be used for diagnosis purposes

A

Creatine Kinase (CK) is a dimeric protein which binds to the muscle sacromere

  • M form is produced in skeletal muscle (MM)
  • B form is produced in the brain (BB)
  • heart produces both types, forms a heterodimer (MB)
  • appearance of brain type in blood sucggests stroke or a tumour
  • appearance of heart type suggests heart attack
366
Q

What proteins carry out phosphorylation reactions?

A

Protein kinases

367
Q

What is regulation of enzyme activity by phosphorylation an example of?

A

Reversible covalent modification, generally occurs on the side groups

368
Q

Can phosphorylation activate an enzyme?

A

Phosphorylation can convert enzymes to an active or inactive form.

369
Q

Which enzymes cause dephosphoralation?

A

Phosphatases

370
Q

What are zymogens?

A

Inactive precursors of an enzyme

371
Q

How are zymogens irreversibly transformed into active enzymes?

A

By cleavage of a covalent bond.

  • In the pancreas: trypsinogen and chymorypsinogen, inactive precursors are formed
  • in small intestine: enteropeptidase cleaves trypsinogen to form active trypsin which cleaves chymotrysinogen to form active chymotrypsin.
  • other examples: digestive enzymes, blood-clotting enzymes, clot-dissolving enzymes
372
Q

True or false:-enzymes alter the equilibrium of a reaction

A

False

373
Q

True or false:- enzymes reduce the time for a chemical reaction to reach equilibrium

A

True

374
Q

True or false:- enzymes stabilise intermediates that are formed as substrates are converted to products

A

true

375
Q

True or false:- enzymes catalyse reactions to avoid loss of free energy when substrates are converted into products

A

False, the only effect the activation energy by lowering it

376
Q

Enzymes are _________. Small changes in their abundance, efficacy or ___________ in tissue can have major implications for disease.

A
  • catalysts
  • distribution
377
Q

What 3 things should we know about enzyme kinetics?

A
  1. Enzymes are catalysts
  2. Enzymes are specific
  3. Enzymes control well-defined chemical reactions.
378
Q

Give 2 functions of enzymes

A

Their catalytic behaviour can be used to diagnose disease.

They can be used in the lab to investigate and develop a wide variety of diagnostic kits and therapeutic drugs.

379
Q

What is V used to denote?

A

Moles of substrate converted to product per second.

380
Q

How do you abbreviate the concentration of substrate in moles?

A

[S]

381
Q

What is Vmax?

A

Vmax is the point where increasing the concentration of substrate has no futher effect on the rate of reaction.

382
Q

What is Km?

A

The substrate concentration that achieves the rate of reaction for the enzyme which is half of the maximum rate.

383
Q

What relationship does the michaelis-menten model explain?

A

The relationship between Vmax and Km

384
Q

What makes the enzyme substrate complex (ES) inherently unstable?

A

The activation energy barrier.

385
Q

How are Vk and Km measured?

A
  • Measure initial reaction velocit, V0, at a known substrate concentration.
  • Repeat at increasing substrate concentrations.
  • Initial reaction rates V0 are plotted as functions of the substrate concentration [S]
  • At infinite substrate concentration the initial reaction rate approaches a maximal rate, Vmax.
  • the michaelis constant Km is equivalent to the substrate concentration where the initial reaction rate is half-maximal.
386
Q

Why is it not straightfoward to determine Vmax and Km from a graph of V0 against [S]?

A

The kinetics are not linear- reaction velocity never quite reaches true Vmax.

387
Q

On a lineweaver-burk plot how do we tell V max?

A

Intersection of the straight line with the Y axis.

388
Q

On a lineweaver-burk plot how do you determine Km?

A

Intersection of the straight line with the X axis.

389
Q

Km is [S] at _____ Vmax

A

0.5

390
Q

What does a low Km mean?

A

That an enzyme only needs a little substrate to work at half-maximal velocity.

391
Q

What does a high Km mean?

A

A high Km means that an enzyme needs a lot of substrate to work at half-maximal velocity.

392
Q

Does Km tell you anything about Vmax?

A

No

393
Q

Is it possible for enzymes to display the same Vmax and have different Km?

A

Yes

394
Q

Why is the low Km of hexokinase in RBCs beneficial?

A

Low Km maintains energy production in red blood cells by glycolysis even if glucose levels fall dramatically.

395
Q

Why is the high Km of glucokinase in the liver and pancreas beneficial?

A

Enables glucose sensing and homeostasis. Its abundance in the liver is regulated by insulin. Excess blood glucose is metabolisd.

MODY=loss of glucokinase activity

396
Q

Name the 2 types of reversible inhibition?

A

Competitive and non-competitive

397
Q

What is the one type of irreversible inhibition?

A

Non-competitive

398
Q

Describe reversible, competitive inhibition

A

Inhibitor binds to the active (catalytic) site and blocks substrate access.

orthosteric inhibition- at the same site.

399
Q

What is orthosteric inhibition?

A

When inhibition happens at the same site.

400
Q

Describe reversible, non-competitive inhibition

A

When the inhibitor binds to a site other than the catalytic centre; inhibits enzyme by changing its conformation.

allosteric inhibition- at different sites.

401
Q

What is allosteric inhibition?

A

Inhibition at different sites to the active site.

402
Q

Describe irreversible, non-competitive inhibition

A

Inhibition cannot be reversed. Usually involves formation or breakage covalent bonds in the enzyme complex.

403
Q

What happens to the Vmax and Km in competitive inhibition?

A

Vmax does not change

Km varies

404
Q

Describe how methanol poisoning is an example of competitive inhibition in the clinic?

A
  • methanol is substrate for alcohol dehydrogenase (ADH)
  • causes severe tissue damage & blindness by conversion to formaldehyde. Also drives metabolic acidosis.
  • ADH Km for ethanol is 20 x greater than methanol
  • treat patient with 40% ethanol in combination with dialysis and ventilation
405
Q

How does non-competitive inhibition effect the Vmax and Km?

A

The Vmax varies but Km remains the same.

If the Vmax looks higher (i.e. the intercept is higher on the Y axis), It is actually lower as it is the reciprocal.

406
Q

What is feedback inhibition?

A

Inhibition of rate limiting enzyme by end product.

407
Q

What type of control is feedback inhibition?

A

Allosteric

408
Q

Do allosteric enzymes follow Michaelis menten kinetics?

A

No

409
Q

Describe the curve produced by allosteric enzymes and the enzymes themselves?

A
  • increasing substrate concentration results in sigmoidal curve, instead of hyperbola.
  • shows co-operative behaviour
  • allosteric factors modulate enzyme kinetic behaviour
  • can be controlled by allosteric inhibitors and allosteric activators
410
Q

Give one example of allosteric regulation which shows positive co-operativity.

A

Binding of oxygen to haemoglobin.

411
Q

How is the positive co-operativity of oxygen binding to haemoglobin controlled?

A
  • H+
  • Carbon dioxide
  • 2,3 biphosphoglycerate (a side product of glycolysis)
412
Q

Explain why Vmax and Km cannot be accurately measured from a hyperbolic plot of V/[S]

A

The kinetics are not linear- reaction never quite reaches the true Vmax.

413
Q

True or false:- In a lineweaver-burk plot enzymes with high Km values will tend towards the zero intercept on the x-axis

A

True

414
Q

True or false:- Vmax varies with non-competitive inhibition but Km remains unaltered

A

True

415
Q

True or False:- A plot of V/[S] will always produce a hyperbolic relationship

A

False

416
Q

True or False:- Low Km enzymes in a multi-step pathway control the rate of substrate movement along its length.

A

Principles (10 decks)

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