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Principles: Biochemistry > Introduction > Flashcards

Introduction Flashcards

1
Q

What determines the reactivity of an atom

A

The number of electrons in the outer shell

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2
Q

What are covalent bond

A

shared pair of electrons

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3
Q

What are ionic bonds

A

attraction of opposite charges

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4
Q

what is a hydrogen bond

A

sharing of H atom

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5
Q

Define electronegativity

A

attractive force that an atomic nucleus exerts on electrons

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6
Q

What is phosphorylation/dephosphorylation

A

addition/removal of a phosphate group

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7
Q

what Is acetylation

A

addition of double bonded oxygen

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8
Q

what is carboxylation

A

addition of COOH group using CO2

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9
Q

What is esterification

A

reaction between alcohol and carboxylic acid to form ester and water

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10
Q

What is condensation reaction

A

removal of water

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11
Q

what is hydrolysis

A

addition of water

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12
Q

What is a redox reaction

A

one molecule is oxidised (looses electrons) and other is reduced (gains electrons)

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13
Q

What is a reducing agent

A

electron donor, undergoes oxidation

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14
Q

What Is an oxidising agent

A

electron acceptor, undergoes reduction

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15
Q

What are the oxidation states of carbon

A

alkane (in fats) > alcohol (in carbohydrates) > aldehyde > carboxylic acid > carbon dioxide

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16
Q

what is the final product of catabolism

A

carbon dioxide

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17
Q

List some functional groups

A 
Methyl - CH3
Methylene - CH2
Amino/amine group - NH3/NH2
Carboxyl - COOH
Ester
Carbonyl/aldehydes -
Phosphates
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18
Q

Function of biomolecules

A

Information storage - DNA
Structural - teeth/bones/cartilage
Energy generation - glycolysis/citric acid cycle, electron transport chain
Energy currency/storage - ATP
Recognition/communication/specificity - receptors/hormones/enzymes

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19
Q

Examples of carbohydrates

A

Monosaccharides - glucose
Disaccharides - lactose/sucrose/maltose
Polysaccharides - cellulose/glycogen

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20
Q

What is thermodynamics

A

Biophysical discipline deals with question if a process is energetically favourable or not

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21
Q

What is the first law of thermodynamics

A

energy is neither created no destroyed - when converted to a different form the total energy before and after is the same

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22
Q

What is the second law of thermodynamics

A

when energy is converted to a different form some of that energy becomes unavailable to work - no energy transformation is 100% efficient

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23
Q

What changes occur when a reaction takes place

A

change in:
enthalpy (heat content): H
entropy (randomness/disorder): S
Energy required to impose order on a system, if energy is not applied to system it is randomly arranged/disordered

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24
Q

What is Gibbs free energy

A

free energy change
delta G = delta H - TdeltaS
delta G = energy of products - energy of reactants

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25
Q

What is an exergonic reaction

A

reaction in which the total free energy of products is less than the total free energy of reactants
so free energy one is negative
can occur spontaneously

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26
Q

Why are exergonic reaction useful in the body

A

when generating body heat

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27
Q

What is an endergonic reaction

A

Reaction in which the total free energy of the products is more than the total free energy of the reactants
free energy change is positive
cannot spontaneously occur, need energy input

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28
Q

How can we determine delta G for the reaction:

A + B = C + D

A

delta G = change in free energy under standard conditions + RTln([C][D]/[A][B])
R - universal gas constant (8.3 kJ/moll)
T - absolute temp (in degrees Kelvin)
Units- kJ/moll

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29
Q

What is standard conditions for a chemist

A

T - 298K
1 atmospheric pressure
1 M (1 moll/l) conc. reactants

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30
Q

What is standard conditions for a biochemist

A

T = 298 K

1 atmospheric pressure 1 M (1 mol/l) concentration of reactants (except H ions as pH7, pH1 would be too acidic)

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31
Q

What does it mean if delta G is zero (or near)

A

reaction is readily reversible

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32
Q

what happens the further towards completion of the point of equilibrium

A

the more free energy is released

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33
Q

what reactions are favourable

A

those with a negative delta G, ie. reaction going from high energy reactant to low energy products are favourable

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34
Q

What do reactions with a positive delta G depend on in order to occur

A

the initial concentration of reactants
if [A][B] are increased then [C][D] is smaller than 1
the ln of a number smaller than 1 is negative

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35
Q

What cellular processes are unfavourable (have a positive delta G)

A

transport against a gradient

synthesis of large molecules

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36
Q

how do unfavourable cellular processes occur

A

they are driven by coupling to highly favourable processes
eg.using ATP as energy currency
ATP + H2O > ADP + Pi + H
this has a very negative delta G (-30 kJ/moll)

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37
Q

Describe the structure of AtP

A

1 sugar
base attached to sugar
3 phosphate groups attached to sugar

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38
Q

Why is ATP less stable that ADP

A

negative changes close together in ATP put a strain on molecule (electrostatic repulsion) on the molecule that makes it less stable than ADP
Strain partially released by phosphate removal
Anhydride bonds between phosphates release high energy

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39
Q

why is ATP constantly regenerated

A

as cells do not store large amounts < 10mM

active muscle cells have high ATP regenerations

40
Q

How is ATP regenerated

A

using creatine phosphate (standard free energy of hydrolysis -43 kJ/mol)
using 2 ADP ATP + AMP

41
Q

Define metabolism

A

all reactions taking place in the body

metabolism = anabolism + catabolism

42
Q

Define catabolism

A

breaking down complex molecules into smaller ones and releasing energy
however there is energy consuming steps in some pathways

43
Q

Define anabolism

A

synthesising complex molecules from smaller ones, energy, energy consuming

44
Q

Give an example of a catabolic pathway

A 
Glycolysis
initial glucose breakdown for ATP generation
early steps - uses 2 ATP
later steps generate 4 ATP
Net gain of 2 ATP per glucose molecule
45
Q

Give an example of an anabolic pathway

A

Gluconeogenesis - making of new glucose from non-carbohydrate precursors eg. pyruvate
Costs energy - can come from fat metabolism
not the reverse of glycolysis

46
Q

What reactions are useful as control points in metabolic pathways

A

ones with large negative delta G values (not ones with delta G = 0)
flux through these points is controlled by altering the activity of the enzyme involved

47
Q

What is special about water

A 
It is polar (electrons not equally shard, depend on atom electronegative)
Bent molecule (forms dipole, tetrahedral shape)
48
Q

Solvent properties of vater

A

ionic and polar substances disolve
ion-dipole interaction
dipole-dipole interaction

49
Q

Define hydrogen bond

A

hydrogen interacts with unshared electors from another electronegative atom
hydrogen has a partial positive charge

50
Q

list the bonding strength from strongest to weakest

A

covalent > ionic> hydrogen

51
Q

Define hydrophobic effect

A

non-polar substances are insoluble in water- hydrophobic, powerful attraction between water molecules, don’t interact with non-polar molecules only each other
eg. hydrocarbons
oil and water don’t mix

52
Q

What are amphipathic/amphiphilic molecules

A

both hydrophobic and hydrophilic
polar head at one end (eg. choline group, carboxylic acid group)
non-polar hydrophilic tail at other end (eg. hydrocarbon) doesn’t interact with water

53
Q

what do amphipathic molecules form in water

A

micelles
head - in contact with water
tail - sequestered from water
form globules, tails on inside, heads on inside

54
Q

example of amphipathic molecule

A

sodium palmitate

55
Q

What are proteins and polypeptides in the body made from

A

20 different types of different L-amino acids

(L and D refers to stereochemistry of amino acids) one exception

56
Q

Whta do all amino acids contain

A 
a-carbon bonded to:
an amino group (NH2)
carboxyl grop (COOH)
Hydrogen group (H)
a side chain (R)
57
Q

What are stereoisomers

A

non-superimposable mirror images

D and L forms

58
Q

4 types of amino acids

A

basic amino acids
acidic amino acids
polar amino acids
non-polar amino acids

59
Q

How are peptide bonds formed

A

reaction between 2 amino acids, removal of a water molecule, formation of CO-NH peptide bond

60
Q

Peptides have a direction what does this mean

A

N-terminal is at the beginning of the peptide chain, c-terminal is at the end

61
Q

Describe petide bonds

A

resonance structures
partial double bond character
planar bonds

62
Q

Why are petite bonds strong and rigid

A

important for protein folding

63
Q

What are acids

A

molecules which can donate a proton - hydrogen ion

strength of acid depends ion how readily it donates

64
Q

what is the acid dissociation constant

A

measures the strength of an acid on how readily it dissociates to donate a proton (hydrogen ion)
Ka = [H]{A]/[HA]

65
Q

what is a base

A

proton acceptor

66
Q

what is pH

A

measurement of the amount of protons in a solution

pH = -log10[H+)

67
Q

an equation that measures acid strength

A

pKa = -log10[Ka]

use ln to work out base pH

68
Q

what is the Henderson-hasselbalchequation and why is it used

A

connects the Ka of a weak acid with pH of a solution containing the acid
pH = pKa + log[A]/[HA}
used to calculate properties of puffer solution, depending on the conc of acid and conjugate base

69
Q

what is a buffer solution

A

used to control the pH of a reaction mixture
when the conc. of acid = conc of conjugate base
[HA] = [A]
[A]/[HA] = 1
log [A]/[HA] = 0
pH = pKa

70
Q

what happens to buffers at their pKa

A

buffers tend to resits a change of pH on addition of moderate amounts of acid/base

71
Q

what do amino acids without charged side groups exist as

A

zwitterions in neutral solution
no net charge
contain 2 titratable groups

72
Q

define isoelectric pH

A

pH at which a molecule has no net charge

73
Q

Why do uncharged amino acids have 2 pKa values

A

they have two titratable groups

74
Q

Why can proteins act as buffers

A

the ends can be ionised, several of the amino acid side chains can be ionised, the ones that are uncharged

75
Q

What buffer exists in blood

A

haemoglobin

76
Q

What affect does a change in pH cause on a protein

A

change in pH = change in ionisation therefore changes in protein structure & function

77
Q

what are the hierarchy of protein structure

A

primary - sequence of amino acid residues
secondary - localised conformation of polypeptide backbone
tertiary - 3D structure of entire polypeptide including side chains
quaternary - spatial arrangement of polypeptide chains in a protein with multiple subunits

78
Q

What can polypeptides rotate around

A

the angles between the a-carbon and amino group and the a carbon and the carboxyl group

79
Q

What is the secondary structure

A 
hydrogen bonded 
3D 
polypeptide chain
localised
only backbone
80
Q

3 types

A

a helices
b strands and sheets
triple helix

81
Q

describe the secondary structure a helix

A

rod like
one polypeptide chain
mostly right handed
CO group of one amino acid forms hydrogen bond with NH group of another 4 residues away
proline residues break a helices as it has no amine hydrogen to donate

82
Q

Describe B sheets

A

Type 1:
polypeptide backbone almost completely extended
can be >1 chain parallel/antiparallel
turns between strand - glycerine and proline
Type 2:
repeated zigzag structure, pleated sheet

83
Q

Describe the collagen triple helix

A 
in bone/connective tissue
most abundant protein in vertebrae
water-insulble fibres
3 left handed helical chains twisted around each other = right handed superhelix
Tropcollagen
inter chain H bonds
covalent inter/intra-molecular bonds
repeating sequence X-Y-Gly
X - any amino acid
Y - proline/hydroxyproline
contains hydroxylysine
84
Q

Use of collagen

A

gives strength to connective tissue
weakened collagen - bleeding gums
covalent cross liking increases with age

85
Q

Describe the tertiary structure

A

arrangement of all atoms of a polypeptide in space
consists of local regions with distinct secondary structure
fibrous protein
globular protein

86
Q

Describe fibrous protein as a secondary structure

A

contains polypeptide chains organised approximately parallel along a single axis - consisting of long fibres.sheets, strong, water insoluble
eg. keratin of hair
collagen of connective tissue eg cartilage, bones, teeth, blood vessels

87
Q

Describe globular proteins as tertiary structures

A 
proteins folded in spherical shape
water soluble and salt solutions
polar side chains on outside
non-polar chains inside
eg. myoglobin, haemoglobin
88
Q

give examples of forces that establish tertiary structures

A 
covalent disulphide bonds
salt bridges
hydrophobic interactions
hydrogen bonds (backbone/side chain) 
complex formation with metal ions
89
Q

hydrophobic interactions in proteins

A

water from H bonds with other water
weaker - water and hydrocarbons
weaker - hydrocarbon to hydrocarbon (van der waals)
strong organising influence - the hydrophobic effect
amino acids with hydrophobic side chains cluster at centre of globular proteins

90
Q

Give an example of how a mutation can cause the production of a different protein

A

single nucleotide sequence change
results in altered protein
under low oxygen, haemoglobin polymerises
can block blood flow in capillaries = sick cell anaemia

91
Q

what are chaperones

A

specialised proteins that can aid folding of polypeptide chain into protein

92
Q

what can happen since polypeptide folding is slow and erroneous

A

protein may begin to fold incorrectly before completely synthesised
may associate with other proteins before folding properly
eg. alzheimers, parkinsons, CJD

93
Q

What is denaturation

A

disrupts protein structure
eg.
by heat
extremes of pH
detergents - urea, disrupts hydrophobic interactions
thiol agents - reducing agent of disulphide bonds

94
Q

Describe myoglobin

A

globular protein containing a haem group (prosthetic group)

haem binds oxygen for storage in muscle

95
Q

describe the quaternary structure

A

more than 1 polypeptide chain
eg. haemoglobin (4 subunits - 2 a and 2 b chains, all with ahem group for oxygen binding)
binding of oxygen changes affinity of other subunits

Principles: Biochemistry (6 decks)

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