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Biochemistry > Introduction to Biochemistry > Flashcards

Introduction to Biochemistry Flashcards

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1
Q

What is the mass and charge of a proton?

A

Each proton has a mass of 1 and a positive charge.

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2
Q

What is the mass and charge of a neutron?

A

Each neutron has a mass of 1 and no charge.

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3
Q

What is the mass and charge of an electron?

A

Each electron has negligible mass and a negative charge.

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4
Q

What does an element’s position in a periodic table show?

A

The number of protons in an element
The number of electrons in an element
The total mass of an element.

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5
Q

What does a full orbital mean?

A

Electrons occupying the same orbital are shown as pairs.

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6
Q

What does it mean for the reactivity of the atom if the outermost shell contains unfilled orbitals (unpaired electrons)?

A

The atom is reactive.

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7
Q

When all the orbital in the outermost shell are filled, what does this mean for the reactivity of the atom?

A

The atom is stable.

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8
Q

What does it mean if there are unpaired electrons in the outer orbital?

A

The electrons are available for bonding.

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9
Q

What is the basis of the interaction of a covalent bond?

A

Electrons are shared in covalent bonds.

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10
Q

What is the basis of the interaction of an ionic bond?

A

It is the attraction of opposite charges.

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11
Q

What is the basis of the interaction of a hydrogen bond?

A

Sharing a H atom.

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12
Q

What is the basis of the interaction of a hydrophobic interaction?

A

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

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13
Q

What is the basis of the interaction of a van der Waals interaction?

A

Interaction of electrons of nonpolar substances.

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14
Q

What is bond energy?

A

It is the amount of energy needed to separate two bonded or interacting atoms under physiological conditions.

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15
Q

Carbon compounds can form complex structures because of what?

A

Carbon can form covalent bonds with itself.
Carbon can form 4 covalent bonds which leads to tetrahedral form.
Carbon can also form bonds with hydrogen, Nitrogen and oxygen atoms, causing variability.

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16
Q

What is electronegativity?

A

The attractive force that an atomic nucleus exerts on electrons within a bond.

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17
Q

What is Phosphorylation?

A

It is the addition of phosphorous/

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18
Q

What is dephosphorylation?

A

It is the removal of phosphate.

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19
Q

What is acylation?

A

It is the addition of an acyl functional group.

It is relatively stable, useful for joining molecules together

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20
Q

What is carboxylation?

A

It is the addition of a carboxyl functional group.

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21
Q

What is esterification?

A

It is the combining of a carboxylic acid and alcohol to form an ester bond and water is released.

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22
Q

What is a condensation reaction?

A 
Water is removed.
Molecules polymerize (e.g. formation of glycogen)
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23
Q

What is a hydrolysis reaction?

A

Water is added. Molecules depolymerize (e.g. glycogenolysis to release glucose).

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24
Q

What are oxidation-reduction reactions also referred as?

A

Redox, where electrons are transferred from one molecule to another.

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25
Q

What is an oxidation reaction?

A

This is where there is a loss of electrons.

OILRIG

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26
Q

What is a reduction reaction?

A

This is where there is a gain of electrons.

OILRIG

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27
Q

What is a redox reaction?

A

This is where as one molecule is oxidised, another one is reduced.
The molecule being oxidised is also known as an electron donor or a reducing agent.
The molecule being reduced is also known as an electron acceptor or an oxidising agent.

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28
Q

What do charge imbalances help to form?

A

They help to form reactive groups on biological molecules.

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29
Q

What are 6 common arrangements of atoms in biological molecules?

A 
Methyl groups
Methylene groups
Amino groups and amides
Carboxyl groups and esters
Carbonyl groups and aldehydes
Phosphates
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30
Q

What are 5 functions of biomolecules and some examples?

A

Information storage
e.g. DNA, RNA
Sometimes info is stored as a charge…like a diode, e.g. NADH/NAD+

Structural e.g. teeth, bones, cartilage

Energy generation e.g. glycolysis, citric acid cycle, electron transport chain.

Energy currency/storage e.g. ATP

Recognition/communication/specificity e.g. receptors, hormones, enzymes

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31
Q

What are 5 functions of biomolecules and what are examples for each?

A
  1. Information storage
    - DNA, RNA
    - sometimes info stored as a charge … like a diode, e.g. NADH/NAD+
  2. Structural
    - teeth, bones, cartilage
  3. Energy Generation
    - glycolysis, citric acid cycle, electron transport chain
  4. Energy currency/storage
    - ATP
  5. Recognition/communication/specificity
    - receptors, hormones, enzymes
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32
Q

What are the 4 major classes of biomolecules and what does each class consist of?

A 
Peptides and proteins
 - Consist of amino acids
Lipids
 - triglycerides, phospholipids, steroids
Nucleic Acids
 - DNA, RNA
Carbohydrates
 - mono - ,di - , polysaccharides
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33
Q

What is an example of a monosaccharide?

A

Glucose

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34
Q

What is the structure of monosaccharides and what holds them together?

A

Monosaccharides have a ring like structure.

The oxygen between carbons 1 and 5 hold tis ring together.

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35
Q

What is an example of a disaccharide?

A

Sucrose

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36
Q

What is the structure of disaccharides?

A

Disaccharides have a two ring structure.

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37
Q

What are some properties of disaccharides?

A

The are soluble in water.
They are high energy molecules.
They allow the transport of high energy molecules.

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38
Q

What are two examples of polysaccharides?

A

Cellulose and glycogen

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39
Q

What are the roles of polysaccharides?

A

They are used in storage and the rapid conversion in energy.

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40
Q

How do we know that in chemical reactions, matter and energy are neither created and destroyed?

A

The number of H, C and O are the same on both sides.

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41
Q

In the equation
Propane + Oxygen Gas -> Carbon Dioxide + Water + Energy
What happens to the electrons and protons?

A

The electrons and protons are transferred from propane (the reducing agent) to oxygen (the oxidising agent) to form water.

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42
Q

What is thermodynamics?

A

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

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43
Q

What is 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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44
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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45
Q

What is entropy?

A

Free energy will tend towards an unstable state after multiple transformations.
(Entropy describes the way that energy is transferred from one body/chemical to another).

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46
Q

What is enthalpy?

A

Heat content (H). Therefore change in enthalpy is (ΔH).

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47
Q

What is entropy?

A

Randomness, disorder (S).
Change in entropy (ΔS).
A high level of order means that there is a nigh level of entropy. A low level of order and so a high level of disorder means that there is a low level of entropy.
It takes energy to impose order on a system. Unless energy is applied to a system, it will be randomly arranged or disordered.

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48
Q

How do you calculate Free Energy (ΔG)?

A

ΔG = ΔH - TΔS
Free energy change = (energy of the products) - (energy of the reactants)
(T is the temperature in K)

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49
Q

What are exergonic reactions?

A

Reactions in which the total free energy of the product(s) is less than the total free energy of the reactant(s).
Therefore the free energy change is negative.
The energy liberated in these reactions can be used to do work.

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50
Q

Can exergonic reactions occur spontaneously?

A

Yes

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51
Q

What are Endergonic reactions?

A

Reactions in which the total free energy of the product(s) is more than the total free energy of the reactant(s).
Therefore the free energy change is positive.
They need an input of energy to proceed.

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52
Q

Can endergonic reactions occur spontaneously?

A

No

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53
Q

How can we determine ΔG for a given reaction?

A

ΔG = ΔGo’ + RTln([C][D]/[A][B])

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54
Q

What is R?

A

R is the universal gas constant (8.3JK-1mol-1)

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55
Q

What is ln?

A

ln is the natural log.

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56
Q

What is T?

A

T is the absolute temperature (in degrees Kelvin)

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57
Q

What are the units for ΔG?

A

kJ/mol

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58
Q

What is ΔGo’?

A

It is the change in free energy under standard conditions.

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59
Q

What are the standard conditions for a physical chemist?

A

T = 298K
1 atmosphere pressure
1M (1mol/l) concentration of reactants
ΔGo

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60
Q

Why in the body is 1MH+ difficult to obtain?

A

pH = 0, which is extremely acidic, pH=7 is preferred.

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61
Q

What are standard conditions for biochemists?

A 
T=298K
1 atmosphere pressure
1 M (1 mol/l) concentration of reactants (except for H+)
pH=7
ΔGo’
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62
Q

How is ΔG related to the point of equilibrium?

A

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

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63
Q

What are ΔG values near zero characteristic of?

A

Readily reversible reactions

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64
Q

What happens when a system is at equilibrium?

A

The forwards and backwards reactions are balanced.
ΔG = 0 and therefore
ΔGo’ = -RTlnKeq
Keq = [C][D]/[A][B]
(substrate and product concentrations at equilibrium)

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65
Q

Why are reactions with a negative ΔGo’ favourable?

A

Reactions going from high energy reactants to low energy products.

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66
Q

What will increasing [A][B] relative to [C][D] do to ΔG?

A

[C][D]/[A][B] becomes smaller than 1.

The ln of a number smaller than 1 is negative.

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67
Q

For the reaction
Glucose-6-phosphate Glucose-1-phosphate,
Does the reaction have a positive or negative
positive ΔGo’?
What is the equation for when the reaction is at equilibrium?
What happens if G1P is removed?

A

It has a positive ΔGo’.
At equilibrium, [G1P]/[G6P] = 6mM / 94mM
If G1P is removed (e.g. by glycogen synthesis), so that [G1P]/[G6P] = 3mM/94mM , DG becomes negative:
ΔG = ΔGo’ + RTln([3]/[94])
= 6.9 kJ/mol + (-8.86 kJ/mol) = - 1.96 kJ/mol

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68
Q

What are 3 reasons that cellular processes are unfavourable?

A

Have to proceed in the direction of a positive ΔG.
Transport against a gradient.
Synthesis of large molecules.

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69
Q

What is the process by which unfavourable reactions can be coupled with highly favourable reaction to make the process more favurable?

A

PEP + H2O -  pyruvate + Pi
ΔG = -78 kJ/mol
ADP + Pi - ATP + H2O ΔG = +55 kJ/mol

PEP + ADP - pyruvate + ATP
ΔG = -23 kJ/mol

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70
Q

What is coupling?

A

THis is where an unfavourable reaction (positive ΔG) with a very favourable reaction e.g.
ATP + H2O - ADP + Pi + H+
has a very negative ΔGo’ (-30 kJ/mol).

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71
Q

What does the phrase ATP is used as universal energy currency mean?

A

It means that ATP is used for driving many different processes.

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72
Q

Why is ATP less stable than ADP?

A

The negative charges close together in ATP put a strain (electrostatic repulsion) on the molecule making it less stable tan ADP.

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73
Q

How can the strain on ATP be partially relieved?

A

The strain can be partially relieved by removing one or more phosphate groups.
(The phosphates are held together by hydrolysable oxygen).

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74
Q

What type of bonds are Anhydride bonds?

A

They are high energy bonds.

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75
Q

What is the limit of ATP for which cells can store?

A

They cannot store concentrations < 10mM.

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76
Q

What are 3 examples of why ATP is constantly regenerated?

A

Active muscle cells (for example) use it at a high rate.
Using creatine phosphate (standard free energy of hydrolysis = -43 kJ/mol).
Using 2 ADP ↔ ATP + AMP

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77
Q

What is the definition of metabolism?

A

All the reactions taking place in the body, divided into Catabolism and Anabolism.

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78
Q

What is the definition of catabolism?

A

The breaking down complex molecules into smaller ones and releasing energy.
(However there are energy-consuming steps in some catabolic pathways).

79
Q

What is the definition of anabolism?

A

The synthesizing complex molecules out of smaller ones in energy-consuming reactions.

80
Q

What is the role of glycolysis?

A

It is the initial breakdown of glucose for the generation of ATP.

81
Q

What is the role of glycolysis in the generation and use of ATP?

A

The early steps use 2 ATP molecules
The later steps generate 4 ATP molecules
This is a net gain of 2 ATP molecules per glucose molecule

82
Q

What is the definition of gluconeogenesis?

A

The making of new glucose from non-carbohydrate precursors e.g. pyruvate.
(This pathway is not simply the reverse of glycolysis).

83
Q

Why is Gluconeogenesis one basis for the Atkin’s diet?

A

It costs energy, which could for example come from fat metabolism.

84
Q

Are hydrogen bonds kept at an angle or are they straight?

A

They are straight.

85
Q

What type of reactions are not used as control points?

A

Reactions close to the equilibrium (ΔG close to 0).

86
Q

What type of reactions are useful control points?

A

Reactions with large negative ΔG values.

87
Q

How is flux through these points controlled?

A

Altering the activity of the enzyme involved.

88
Q

What is the result In the water molecules charge because the molecule is bent?

A

It forms a dipole where the charge differs from one end to the other.

89
Q

What is the shape of a water molecule?

A

It is a tetrahedral shape.

90
Q

How does water’s polarity affect the molecule?

A

Electrons are shared unequally. How they are shared depends on the electronegativity of atoms.

91
Q

What type of substances dissolve in water?

A

Ionic and Polar substances. These molecules are hydrophilic.

92
Q

What affects whether a molecule is polar or non-polar?

A

Whether a molecule is polar or non-polar, is based on electrostatic interactions.

93
Q

What are the two types of interactions found in solutions containing polar liquids?

A

Ion-dipole interactions

Dipole-dipole interactions

94
Q

What is the definition of an ion-dipole interaction?

A

It is an attractive force that results from the electrostatic reaction between an ion and a neutral molecule that contains a dipole.

95
Q

Where are ion-dipole interactions most commonly found?

A

They are most commonly found in solutions. Especially important for solutions of ionic compounds in polar liquids.

96
Q

What is the process by which an ion-dipole interaction occurs?

A

A positive ion attracts the partially negative end of a neutral polar molecule.
A negative ion attracts the partially positive end of a neutral polar molecule.
Ion-dipole attractions become stronger as either the charge on the ion increases, or as the magnitude of the dipole of the polar molecule increases.

97
Q

What is the process by which a hydrogen bond arises?

A

This is where a covalent bond arises between a hydrogen and a more electronegative atom (e.g. oxygen) creating a polarized bond.
(Hydrogen has a partial positive charge).
This hydrogen can interact with unshared electrons from another electronegative atom.
This interaction is a hydrogen bond.

98
Q

What is the strength of hydrogen bonds?

A

Individually they are much weaker than covalent bonds but can be strong collectively.
They are very important in water and biological structures.

99
Q

What is hydrogen bonding important in?

A

Water and biological structures.

100
Q

How do hydrogen bonds in biomolecules arise?

A

Hydrogen atoms are shared between two electronegative atoms.
Bonds tend to be linear.
One molecule is a hydrogen bond donor and one molecule is a hydrogen bond acceptor.

101
Q

What happens to non-polar substances in water?

A

Non-polar substances are insoluble in water as they are hydrophobic (Greek for “water-hating”).
There is a powerful attraction between water molecules and so they prefer to interact with themselves instead of non-polar molecules.

102
Q

What in particular are very non-polar and hydrophobic?

A

Hydrocarbons, compounds consisting only of carbon and hydrogen.

103
Q

Why does water tend to exclude hydrocarbons?

A

They are non-polar solids that do not dissolve.
They are non-polar liquids that form a two-layer system with water, e.g. Oil slick. Oil and water don’t mix and is often called the hydrophobic effect.

104
Q

Why are amphipathic molecules also called amphiphilic?

A

They have regions (domains) which are either hydrophilic or hydrophobic.

105
Q

What are examples of substances that have a polar (hydrophilic) “head” group (at one end)?

A

The choline group, carboxylic acid group.

They interact well with water.

106
Q

What is an example of a substance with a non-polar (hydrophobic) “tail” (at other end)?

A

Hydrocarbon

do not interact well with water

107
Q

Why do amphipathic molecules form micelles in water?

A

“head” groups in contact with water.

“tail” groups sequestered from the water.

108
Q

What are examples of amphipathic molecules?

A

Sodium palmitate
- Sodium salt pf palmitic acid
- a fatty acid
Micelle formation
- balls represent the hydrophilic “heads”
- Zigzag lines represent the hydrophobic “tails”

109
Q

What is a cell membrane?

A

It is a selective and controllable barrier to the outside world. It also aids in compartmentalization by isolating organelles.

110
Q

What do cell membranes contain?

A 
Lipids of various types
- structural (lipid bilayer)
- precursors of signalling molecules (e.g. diacylglycerol-DAG Inositol-3-phosphate-IP3)
Proteins of various types
- Confer selectivity
- Involved in recognition
- and more
To interact with the interior and exterior of the lipid bilayer, proteins must have amphiphilic properties.
111
Q

Proteins and polypeptides in humans are made up from how many different L-amino acids?

A

20 different amino acids

D and L refers to stereochemistry of amino acids

112
Q

All amino acids contain to an alpha-carbon bonded to what?

A

An amino group (-NH2)
A carboxyl group (-COOH)
A Hydrogen (-H)
A side chain (-R)

113
Q

What are D and L forms of amino acids to each other?

A

Stereoisomers. This means that they are non-superimposable mirror images.

114
Q

What are some defining characteristics of non-polar, hydrophobic amino acids?

A

They don’t dissolve in water.
They will interact with lipid or other non-polar structures.
They have non-polar functional groups.
There is no difference in charge between the amino and carboxy ends of the molecule.

115
Q

What are the names of the 8 amino acids present the non-polar, hydrophobic amino acid category?

A 
Leucine (Leu, L)
Proline (Pro, P)
Alanine (Ala, A)
Valine (VAL, V)
Methionne (Met, M)
Tryptophan (Trp, W)
Phenylalanine (Phe, F)
Isoleucine (Ile, I)
116
Q

What are some defining characteristics of polar, uncharged amino acids?

A

They are polar so will dissolve in water.
There is no charge difference between the amino and carboxy ends of the molecule but hydrogen bonding interaction with water is possible.
Varying solubility among members of this group contributes to the amphiphilic nature of some proteins.
Hydrogen bonding is useful for reversible protein binding.

117
Q

What are the names of the 7 amino acids present in the polar, uncharged amino acid category?

A 
Glycine (Gly, G)
Serine (Ser, S)
Asparagine (Asn, N)
Glutamine (Gln, Q)
Threonine (Thr, T)
Cysteine (Cys, C)
Tyrosine (Tyr, Y)
118
Q

What are the defining characteristics of acidic amino acids?

A

They are useful as buffers.

Useful for pH sensitive functions

119
Q

What are the names of the 2 amino acids present in the acidic amino acid category?

A 
Aspartic acid (Asp, D)
Glutamic Acid (Glu, E)
120
Q

Wat are the defining characteristics of basic amino acids?

A

They are useful as a buffer.

Useful for pH sensitive functions.

121
Q

What are the names of the 3 amino acids present in the basic amino acid category?

A

Lysine (Lys, K)
Arginine (Arg, R)
Histidine (His, H)

122
Q

What is peptide bond formation catalysed by?

A

It is catalysed by an enzyme called peptidyl transferase.

123
Q

What is the process of peptide bond formation?

A
  1. There are two amino acids
  2. There is a removal of a water molecule.
  3. A CO-NH or peptide bond is formed.
124
Q

Why are peptide bonds said to have partial double bond character?

A

The electrons from N and C contribute to bond strength though they are not part of the covalent bond structure itself.

125
Q

Why is it important that peptide bonds are strong and rigid?

A

It is important for folding proteins.

126
Q

What are so characteristic of peptide bonds?

A

Peptide bonds have partial double bond character.
Peptide bonds are planar.
Peptide bonds are strong and rigid.

127
Q

How does pH affect protein structure and function?

A

Acids are molecules which can donate a proton (Hydrogen ion, H+).
Bases are proton acceptors.
The strength of an acid depends on how readily it donates a proton to a base. This is measured by the acid dissociation constant Ka.

128
Q

What is the definition of pH?

A

It is the measurement of the amount of protons in a solution.

129
Q

How can you calculate pH?

A

pH = -log10[H+]
Logarithm to base 10 of the proton concentration.
Because of the logarithm, a change of one pH unit implies a tenfold change on proton concentration!

130
Q

How do you calculate acid strength?

A

pKa = -log10[Ka]

131
Q

What is log?

A

The logarithm of a number X to a base n is the number of times n has to be multiplied with itself to result in X.
This also works for other bases e.g. ln is loge

132
Q

Pure/Distilled water does not dissociate much:
[H2O] = 55.5 mol/l
[H+] = 10(-7) mol/l = 0.0000001 mol/l
But: at pH = 1 the proton concentration is 0.1 mol/l
A solution with a pH = 7 is?
A solution with a pH<7 is?
A solution with a pH>7 is?

A

A solution with a pH = 7 is neutral
A solution with a pH<7 is acidic
A solution with a pH>7 is alkali.

133
Q

The Henderson-Hasselbalch equation connects the Ka of a weak acid with the pH of a solution containing this acid. What does this equation look like?

A

pH = pKa+log [A-]=base
[HA]=acid
(A/HA) is what it’s supposed to be.

134
Q

What does the Henderson-Hasselbalch equation let us calculate?

A

It lets us calculate the properties of buffer solutions - depending on the concentrations of acid and conjugate base.

135
Q

How can the Henderson-Hasselbalch equation also be written?

A

pKa - pH = log [HA]

[A-]

136
Q

What is the definition of a buffer?

A

A buffer is a solution to control the pH of a reaction mixture.

137
Q

At what point is the concentration of acid equal to the concentration of conjugate base?

A

[HA] = [A-]
Therefore pH = pKa
(full working in notebook)

138
Q

What happens when buffers are at their pKa value?

A

They tend to resist a change of pH on addition of moderate amounts of acid or base.
THIS IS A KEY CHARACTERISTIC OF A BUFFER

139
Q

What are titration curves?

A

A titration curve is where you plot the pH as a function of a base added to an acid.
Close to pKa the pH remains relatively unchanged in response to the addition of a base.
THIS IS A KEY CHARATERISTIC OF A BUFFER

140
Q

How do amino acids without charged side groups exist in neutral solution.

A

They exist as zwitterions.

They have no net charge.

141
Q

Why do uncharged amino acids have 2 pKa groups?

A

They contain 2 titratable groups.

142
Q

What is the isoelectric pH, pI?

A

The pH at which a molecule has no net charge.

143
Q

How does the fact that uncharged amino acid have 2 titratable groups, and therefore 2 pKa values affect proteins?

A

THIS ENABLES PROTEINS TO ACT IN DIFFERENT WAYS AS pH VARIES. PROTEINS HAVE WODE AND VARIED FUNCTIONS.

144
Q

What are the acid-base properties of proteins?

A

The ends of proteins can be ionised.
Several of the amino acid side chains can be ionised.
Therefore proteins can act as buffers - haemoglobin in blood.
A change in pH can change ionisation of a protein, this can lead to changes in structure and thereby in function.

145
Q

What is the hierarchy of protein structure?

A

Primary structure - the sequence of amino acid residues
Secondary structure - the localised conformation (shape) of the polypeptide backbone
Tertiary structure - the three-dimensional structure of an entire polypeptide, including all its side chains.
Quaternary structure - the spatial arrangement of polypeptide chains in a protein with multiple subunits.

146
Q

What kind of structure are amino acids?

A

Planar structures

147
Q

Polypeptides can rotate around the angle between what?

A

The alpha carbon and the amino group.
The alpha carbon and the carboxyl group.
(Imagine a series of playing cards, linked at opposite corners).

148
Q

Hydrogen-bonded three-dimensional arrangements of a polypeptide chain are what?

A

Localised and only considers the backbone of the polypeptide.

149
Q

What are the three types of secondary structures in a polypeptide?

A

Alpha helix
Beta strands and sheets
Triple helix

150
Q

What is the role of the hydrogen bonds in a polypeptide chain?

A

To stabilize the helix structure.

151
Q

What can the helix of a polypeptide be viewed as?

A

The helix can be viewed as a stacked array of peptide planes hinged at the alpha carbon and approximately parallel to the helix.

152
Q

What is the structure of an alpha helix?

A

They are rod-like one polypeptide chains and are mostly right-handed.

153
Q

How are alpha helixes formed?

A

A -C-O group of one amino acid forms a hydrogen bond with the -N-H group of an amino acid four residues/amino acids away.

154
Q

Why does proline break amino acids?

A

Prolines are frequently found in the first, N-terminus turn of a helix where the loss of the H-bond to the immino nitrogen does not cause significant effects. Prolines in alpha helices after the first turn (4th residue) cause a kink in the helix. This kink is caused by proline being unable to complete the H-bonding chain of the helix and steric or rotamer effects that keep proline from adapting the preferred helical geometry. The kink is “away” from the proline residue, which is frequently on the hydrophilic side of the helix.

155
Q

In Beta sheets l what is happening to the polypeptide backbone and hydrogen bonds?

A

Polypeptide backbone is almost completely extended (not folded).
H bonds between C=O & N-H of neighbouring peptides. Amino side chains have a relativlely minor influence.

156
Q

Do Beta sheets l consist if one or more chains?

A

It can involve more than one chain.

157
Q

What are the two directions that are possible for beta sheets l to run in?

A

Parallel
Antiparallel
Beta sheets turn between strands (glycine and proline)

158
Q

What structure di Beat sheets ll have?

A

They have a repeated “zigzag” structure also called a beta pleated sheet.

159
Q

Can one protein contain more than one secondary structure.

A

Yes.

For example phosphoglycerate kinase contains both an alpha helix and parallel beta sheets.

160
Q

Where can you find collagen triple helix’s?

A

They are components of bone and connective tissue.

They are extremely strong - think of tendons

161
Q

Are collagen triple helix’s water soluble or water insoluble?

A

They are water insoluble fibres.

162
Q

How do collagen triple helix’s form a right-handed triple helix?

A

Threee left-handed helical chains twisted around each other form a right-handed supehelix.

163
Q

What is a superhelix also known as?

A

Tropocollagen.

164
Q

There is a repeating sequence of X-Y-Gly in all strands of collagen triple helix’s what do the X and Y stand for?

A
  • X=any amino acid
  • Y=proline or hydroxyltsine
  • also contains hyydroxylysine
165
Q

What kind of bonds are present between collagen triple helix?

A

There are inter-chain H-bonds (no intra-chain). These involve hydroxylysine and hydroxyproline.
There are also covalent inter- and intra- molecular bonds.

166
Q

Why s collagen relevant?

A

It influences the strength of connective tissue.

Weakened collagen results in bleeding gums.

167
Q

How do we know that covalent crosslinking increases with age?

A

Meat form older animals is tougher.

168
Q

Why does scurvy result in bleeding gums and skin discolouration?

A

Proline needs to be hydroxylated to form H bonds between collagen chains. This stabilises the tropocollagen structure.
The enzyme which hydroxylates proline requires ascorbic acid (Vitamin C).
Dietary deficiency of vitamin C results in reduction in hydroxyproline.
Results in weakened collagen.

169
Q

what are tertiary structures?

A

It is the arrangement of all atoms of a polypeptide in space.
Consists of local regions with distinct secondary structure.
E.g. fibrous proteins and globular proteins.

170
Q

Fibrous proteins contain polypeptide chains organized approximately parallel along a single axis. They …

A
  • 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.
171
Q

What are examples of the polypeptide chains organized approximately parallel along a single axis in fibrous proteins?

A
  • Keratin of hair and wool

- Collagen of connective tissue of animals including cartilage, bones, teeth, skin and blood vessels.

172
Q

Proteins which are folded to a more or less spherical shape …

A
  • they tend to be soluble in water and salt solutions
  • most of their polar sode chains are on the outside and interact with the aqueous environment by hydrogen bondig and ion-dipole interactions
  • most of their nonpolar sid chains are buried inside
  • nearly all have substantial sections of alpha-helix and beta-sheet
173
Q

What are examples of proteins that are folded to a more or less spherical shape?

A

Myoglobin

Haemoglobin

174
Q

what are the forces stabilising tertiary structures?

A 
Covalent disulphide bonds
Electrostatic interactions = salt bridges
Hydrophobic interactions
Hydrogen bonds
 - backbone
 - side chain
Complex formation with metal ions
175
Q

What are 3 defining characteristics of disulphide bonds?

A

Often act as reduction-oxidation (redox) centres
Reversible change in protein shape
Reversible function

176
Q

What are examples of electrostatic interactions in proteins?

A

Positive charges attract negative charges
Salt bridges
Repulsion between similar charges
Charged (polar) side groups are normally located on the outside of proteins - interact with water

177
Q

What bonds form between water molecules?

A

Water forms H-bonds with other water molecules - relatively strong water-water interactions.

178
Q

Between what molecules are there weaker attractions?

A

weaker attraction between water and hydrocarbon

Weaker attraction between hydrocarbon and hydrocarbon (van der Waals interactions)

179
Q

What influence does the hydrophobic effect have?

A

A strong organizing influence.

180
Q

What tends to cluster in the centre of globular proteins?

A

Amino acids with hydrophobic side-chains tend to cluster in the centre of globular proteins.
Amino acids with hydrophobic side-chains tend to be mainly in the hydrophobic part of the membrane in transmembrane proteins.

181
Q

What would you expect if a mutation in a given protein changes a glutamic acid into a valine?

A

Glutamic acid is negatively charged at physiological pH
- can form ionic bonds or hydrogen bonds with water or other amino acid side chains.
Valine is hydrophobic
- interacts with other hydrophobic amino acids.

182
Q

What can a change from glutamic acid to valine cause?

A

A change from glutamic acid to valine can potentially lead to significant functional changes.

183
Q

What is the cause and result of sickle cell anaemia?

A

Single nucleotide sequence change - in coding region of the beta chain of haemoglobin A results in sickle cell anaemia
Results in an altered protein
- Valine instead of glutamic acid
Under low O2 conditions, haemoglobin polymerises
- results in rigid, sickle shape cells
Can block blood flow in capillaries

184
Q

Where is the information needed for a protein’s 3D shape?

A

Th primary structure of a protein contains all the information needed for its three-dimensional shape.

185
Q

Do proteins fold spontaneously into their correct shape or is it organised?

A

Proteins may fold spontaneously into their correct shape.

186
Q

Is folding a quick process or a slow process?

A

It can be a slow and erroneous process.

  • Proteins may begin to fold incorrectly before it is completely synthesised
  • It may associate with other proteins before it is folded properly
  • e.g. Alzheimer’s, Parkinson’s, CJD
187
Q

What are the specialised proteins that sometimes aid in the folding process called?

A

Chaperones

188
Q

What is mad cow disease caused by?

A

Infection

189
Q

What is Creutzfeldt-Jacob disease caused by?

A

Caused by spontaneous or inherited mutations

190
Q

Prion proteins (proteinaceous infections agent) are normal components of the brain. What is the difference between the normal conformation and disease-causing form?

A
  • Normal conformation PrPc
  • disease-causing form PrPsc (from scrapie)
  • enriched in beta sheets
  • aggregates into multimeric complexes, resistant to degradation
    Spontaneous refolding of PrPc into PrPsc is extremely rare
    but; presence if PrPsc acts as a template for misforming of native prion proteins
191
Q

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

A

Denaturation

192
Q

What different factors cause denaturation?

A 
Heat
- increase in vibrations in a protein
Extremes in pH
- electrostatic interactions interrupted
Detergents, urea, guanidine hydrochloride
- disrupt hydrophobic interactions
Thiol agents, reducing agents
- reduce and thereby disrupt disulphide bonds
193
Q

What is the tertiary structure of myoglobin?

A 
It is a globular protein.
It contains a haem group
- which contains an iron ion Fe(ll)
- Prosthetic group
Haem group binds oxygen 
- one oxygen molecule per myoglobin protein
Stores oxygen in muscle
194
Q

What is the quaternary structure of haemoglobin?

A

Proteins which contain more than one polypeptide chain
- between 2 and more than a dozen subunits
- identical or different subunits
Haemoglobin
- 4 subunits
- 2 alpha and 2 beta 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

Biochemistry (1 decks)

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