Introduction Flashcards
1
Q
What determines the reactivity of an atom
A
The number of electrons in the outer shell
2
Q
What are covalent bond
A
shared pair of electrons
3
Q
What are ionic bonds
A
attraction of opposite charges
4
Q
what is a hydrogen bond
A
sharing of H atom
5
Q
Define electronegativity
A
attractive force that an atomic nucleus exerts on electrons
6
Q
What is phosphorylation/dephosphorylation
A
addition/removal of a phosphate group
7
Q
what Is acetylation
A
addition of double bonded oxygen
8
Q
what is carboxylation
A
addition of COOH group using CO2
9
Q
What is esterification
A
reaction between alcohol and carboxylic acid to form ester and water
10
Q
What is condensation reaction
A
removal of water
11
Q
what is hydrolysis
A
addition of water
12
Q
What is a redox reaction
A
one molecule is oxidised (looses electrons) and other is reduced (gains electrons)
13
Q
What is a reducing agent
A
electron donor, undergoes oxidation
14
Q
What Is an oxidising agent
A
electron acceptor, undergoes reduction
15
Q
What are the oxidation states of carbon
A
alkane (in fats) > alcohol (in carbohydrates) > aldehyde > carboxylic acid > carbon dioxide
16
Q
what is the final product of catabolism
A
carbon dioxide
17
Q
List some functional groups
A
Methyl - CH3 Methylene - CH2 Amino/amine group - NH3/NH2 Carboxyl - COOH Ester Carbonyl/aldehydes - Phosphates
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
19
Q
Examples of carbohydrates
A
Monosaccharides - glucose
Disaccharides - lactose/sucrose/maltose
Polysaccharides - cellulose/glycogen
20
Q
What is thermodynamics
A
Biophysical discipline deals with question if a process is energetically favourable or not
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
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
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
24
Q
What is Gibbs free energy
A
free energy change
delta G = delta H - TdeltaS
delta G = energy of products - energy of reactants
25
What is an exergonic reaction
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
26
Why are exergonic reaction useful in the body
when generating body heat
27
What is an endergonic reaction
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
28
How can we determine delta G for the reaction:
| A + B = C + D
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
29
What is standard conditions for a chemist
T - 298K
1 atmospheric pressure
1 M (1 moll/l) conc. reactants
30
What is standard conditions for a biochemist
T = 298 K
| 1 atmospheric pressure 1 M (1 mol/l) concentration of reactants (except H ions as pH7, pH1 would be too acidic)
31
What does it mean if delta G is zero (or near)
reaction is readily reversible
32
what happens the further towards completion of the point of equilibrium
the more free energy is released
33
what reactions are favourable
those with a negative delta G, ie. reaction going from high energy reactant to low energy products are favourable
34
What do reactions with a positive delta G depend on in order to occur
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
35
What cellular processes are unfavourable (have a positive delta G)
transport against a gradient
| synthesis of large molecules
36
how do unfavourable cellular processes occur
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)
37
Describe the structure of AtP
1 sugar
base attached to sugar
3 phosphate groups attached to sugar
38
Why is ATP less stable that ADP
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
39
why is ATP constantly regenerated
as cells do not store large amounts < 10mM
| active muscle cells have high ATP regenerations
40
How is ATP regenerated
using creatine phosphate (standard free energy of hydrolysis -43 kJ/mol)
using 2 ADP ATP + AMP
41
Define metabolism
all reactions taking place in the body
| metabolism = anabolism + catabolism
42
Define catabolism
breaking down complex molecules into smaller ones and releasing energy
however there is energy consuming steps in some pathways
43
Define anabolism
synthesising complex molecules from smaller ones, energy, energy consuming
44
Give an example of a catabolic pathway
```
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
Give an example of an anabolic pathway
Gluconeogenesis - making of new glucose from non-carbohydrate precursors eg. pyruvate
Costs energy - can come from fat metabolism
not the reverse of glycolysis
46
What reactions are useful as control points in metabolic pathways
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
What is special about water
```
It is polar (electrons not equally shard, depend on atom electronegative)
Bent molecule (forms dipole, tetrahedral shape)
```
48
Solvent properties of vater
ionic and polar substances disolve
ion-dipole interaction
dipole-dipole interaction
49
Define hydrogen bond
hydrogen interacts with unshared electors from another electronegative atom
hydrogen has a partial positive charge
50
list the bonding strength from strongest to weakest
covalent > ionic> hydrogen
51
Define hydrophobic effect
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
What are amphipathic/amphiphilic molecules
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
what do amphipathic molecules form in water
micelles
head - in contact with water
tail - sequestered from water
form globules, tails on inside, heads on inside
54
example of amphipathic molecule
sodium palmitate
55
What are proteins and polypeptides in the body made from
20 different types of different L-amino acids
| (L and D refers to stereochemistry of amino acids) one exception
56
Whta do all amino acids contain
```
a-carbon bonded to:
an amino group (NH2)
carboxyl grop (COOH)
Hydrogen group (H)
a side chain (R)
```
57
What are stereoisomers
non-superimposable mirror images
| D and L forms
58
4 types of amino acids
basic amino acids
acidic amino acids
polar amino acids
non-polar amino acids
59
How are peptide bonds formed
reaction between 2 amino acids, removal of a water molecule, formation of CO-NH peptide bond
60
Peptides have a direction what does this mean
N-terminal is at the beginning of the peptide chain, c-terminal is at the end
61
Describe petide bonds
resonance structures
partial double bond character
planar bonds
62
Why are petite bonds strong and rigid
important for protein folding
63
What are acids
molecules which can donate a proton - hydrogen ion
| strength of acid depends ion how readily it donates
64
what is the acid dissociation constant
measures the strength of an acid on how readily it dissociates to donate a proton (hydrogen ion)
Ka = [H]{A]/[HA]
65
what is a base
proton acceptor
66
what is pH
measurement of the amount of protons in a solution
| pH = -log10[H+)
67
an equation that measures acid strength
pKa = -log10[Ka]
| use ln to work out base pH
68
what is the Henderson-hasselbalchequation and why is it used
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
what is a buffer solution
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
what happens to buffers at their pKa
buffers tend to resits a change of pH on addition of moderate amounts of acid/base
71
what do amino acids without charged side groups exist as
zwitterions in neutral solution
no net charge
contain 2 titratable groups
72
define isoelectric pH
pH at which a molecule has no net charge
73
Why do uncharged amino acids have 2 pKa values
they have two titratable groups
74
Why can proteins act as buffers
the ends can be ionised, several of the amino acid side chains can be ionised, the ones that are uncharged
75
What buffer exists in blood
haemoglobin
76
What affect does a change in pH cause on a protein
change in pH = change in ionisation therefore changes in protein structure & function
77
what are the hierarchy of protein structure
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
What can polypeptides rotate around
the angles between the a-carbon and amino group and the a carbon and the carboxyl group
79
What is the secondary structure
```
hydrogen bonded
3D
polypeptide chain
localised
only backbone
```
80
3 types
a helices
b strands and sheets
triple helix
81
describe the secondary structure a helix
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
Describe B sheets
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
Describe the collagen triple helix
```
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
Use of collagen
gives strength to connective tissue
weakened collagen - bleeding gums
covalent cross liking increases with age
85
Describe the tertiary structure
arrangement of all atoms of a polypeptide in space
consists of local regions with distinct secondary structure
fibrous protein
globular protein
86
Describe fibrous protein as a secondary structure
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
Describe globular proteins as tertiary structures
```
proteins folded in spherical shape
water soluble and salt solutions
polar side chains on outside
non-polar chains inside
eg. myoglobin, haemoglobin
```
88
give examples of forces that establish tertiary structures
```
covalent disulphide bonds
salt bridges
hydrophobic interactions
hydrogen bonds (backbone/side chain)
complex formation with metal ions
```
89
hydrophobic interactions in proteins
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
Give an example of how a mutation can cause the production of a different protein
single nucleotide sequence change
results in altered protein
under low oxygen, haemoglobin polymerises
can block blood flow in capillaries = sick cell anaemia
91
what are chaperones
specialised proteins that can aid folding of polypeptide chain into protein
92
what can happen since polypeptide folding is slow and erroneous
protein may begin to fold incorrectly before completely synthesised
may associate with other proteins before folding properly
eg. alzheimers, parkinsons, CJD
93
What is denaturation
disrupts protein structure
eg.
by heat
extremes of pH
detergents - urea, disrupts hydrophobic interactions
thiol agents - reducing agent of disulphide bonds
94
Describe myoglobin
globular protein containing a haem group (prosthetic group)
| haem binds oxygen for storage in muscle
95
describe the quaternary structure
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
