Introduction Flashcards
What determines the reactivity of an atom
The number of electrons in the outer shell
What are covalent bond
shared pair of electrons
What are ionic bonds
attraction of opposite charges
what is a hydrogen bond
sharing of H atom
Define electronegativity
attractive force that an atomic nucleus exerts on electrons
What is phosphorylation/dephosphorylation
addition/removal of a phosphate group
what Is acetylation
addition of double bonded oxygen
what is carboxylation
addition of COOH group using CO2
What is esterification
reaction between alcohol and carboxylic acid to form ester and water
What is condensation reaction
removal of water
what is hydrolysis
addition of water
What is a redox reaction
one molecule is oxidised (looses electrons) and other is reduced (gains electrons)
What is a reducing agent
electron donor, undergoes oxidation
What Is an oxidising agent
electron acceptor, undergoes reduction
What are the oxidation states of carbon
alkane (in fats) > alcohol (in carbohydrates) > aldehyde > carboxylic acid > carbon dioxide
what is the final product of catabolism
carbon dioxide
List some functional groups
Methyl - CH3 Methylene - CH2 Amino/amine group - NH3/NH2 Carboxyl - COOH Ester Carbonyl/aldehydes - Phosphates
Function of biomolecules
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
Examples of carbohydrates
Monosaccharides - glucose
Disaccharides - lactose/sucrose/maltose
Polysaccharides - cellulose/glycogen
What is thermodynamics
Biophysical discipline deals with question if a process is energetically favourable or not
What is the first law of thermodynamics
energy is neither created no destroyed - when converted to a different form the total energy before and after is the same
What is the second law of thermodynamics
when energy is converted to a different form some of that energy becomes unavailable to work - no energy transformation is 100% efficient
What changes occur when a reaction takes place
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
What is Gibbs free energy
free energy change
delta G = delta H - TdeltaS
delta G = energy of products - energy of reactants
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
Why are exergonic reaction useful in the body
when generating body heat
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
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
What is standard conditions for a chemist
T - 298K
1 atmospheric pressure
1 M (1 moll/l) conc. reactants
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)
What does it mean if delta G is zero (or near)
reaction is readily reversible
what happens the further towards completion of the point of equilibrium
the more free energy is released
what reactions are favourable
those with a negative delta G, ie. reaction going from high energy reactant to low energy products are favourable
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
What cellular processes are unfavourable (have a positive delta G)
transport against a gradient
synthesis of large molecules
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)
Describe the structure of AtP
1 sugar
base attached to sugar
3 phosphate groups attached to sugar
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
why is ATP constantly regenerated
as cells do not store large amounts < 10mM
active muscle cells have high ATP regenerations
How is ATP regenerated
using creatine phosphate (standard free energy of hydrolysis -43 kJ/mol)
using 2 ADP ATP + AMP
Define metabolism
all reactions taking place in the body
metabolism = anabolism + catabolism
Define catabolism
breaking down complex molecules into smaller ones and releasing energy
however there is energy consuming steps in some pathways
Define anabolism
synthesising complex molecules from smaller ones, energy, energy consuming
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
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
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
What is special about water
It is polar (electrons not equally shard, depend on atom electronegative) Bent molecule (forms dipole, tetrahedral shape)
Solvent properties of vater
ionic and polar substances disolve
ion-dipole interaction
dipole-dipole interaction
Define hydrogen bond
hydrogen interacts with unshared electors from another electronegative atom
hydrogen has a partial positive charge
list the bonding strength from strongest to weakest
covalent > ionic> hydrogen
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
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
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
example of amphipathic molecule
sodium palmitate
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
Whta do all amino acids contain
a-carbon bonded to: an amino group (NH2) carboxyl grop (COOH) Hydrogen group (H) a side chain (R)
What are stereoisomers
non-superimposable mirror images
D and L forms
4 types of amino acids
basic amino acids
acidic amino acids
polar amino acids
non-polar amino acids
How are peptide bonds formed
reaction between 2 amino acids, removal of a water molecule, formation of CO-NH peptide bond
Peptides have a direction what does this mean
N-terminal is at the beginning of the peptide chain, c-terminal is at the end
Describe petide bonds
resonance structures
partial double bond character
planar bonds
Why are petite bonds strong and rigid
important for protein folding
What are acids
molecules which can donate a proton - hydrogen ion
strength of acid depends ion how readily it donates
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]
what is a base
proton acceptor
what is pH
measurement of the amount of protons in a solution
pH = -log10[H+)
an equation that measures acid strength
pKa = -log10[Ka]
use ln to work out base pH
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
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
what happens to buffers at their pKa
buffers tend to resits a change of pH on addition of moderate amounts of acid/base
what do amino acids without charged side groups exist as
zwitterions in neutral solution
no net charge
contain 2 titratable groups
define isoelectric pH
pH at which a molecule has no net charge
Why do uncharged amino acids have 2 pKa values
they have two titratable groups
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
What buffer exists in blood
haemoglobin
What affect does a change in pH cause on a protein
change in pH = change in ionisation therefore changes in protein structure & function
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
What can polypeptides rotate around
the angles between the a-carbon and amino group and the a carbon and the carboxyl group
What is the secondary structure
hydrogen bonded 3D polypeptide chain localised only backbone
3 types
a helices
b strands and sheets
triple helix
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
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
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
Use of collagen
gives strength to connective tissue
weakened collagen - bleeding gums
covalent cross liking increases with age
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
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
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
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
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
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
what are chaperones
specialised proteins that can aid folding of polypeptide chain into protein
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
What is denaturation
disrupts protein structure
eg.
by heat
extremes of pH
detergents - urea, disrupts hydrophobic interactions
thiol agents - reducing agent of disulphide bonds
Describe myoglobin
globular protein containing a haem group (prosthetic group)
haem binds oxygen for storage in muscle
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
