Intro to biochemistry Flashcards
what determines the reactivity of an atom?
the number of electrons
unfilled outer orbital shells = reactive
filled outer orbital shells = stable
what is a covalent bond?
sharing of electron pairs
what is an ionic bond?
attraction of opposite charges
what is a hydrogen bond?
sharing of H atom
what is a hydrophobic interaction?
interaction of non-polar substances in the presence of polar substances
what is a van der walls interaction?
interaction of electrons of non polar substances
what is the order of bond energies?
covalent ionic hydrogen hydrophobic interactions van der walls interaction
can different atoms make different numbers of covalent bonds?
yes H = 1 O = 2 S = 2 N = 3 C = 4 P = 5
how many covalent bonds can carbon make? what shape does this make?
4
tetrahedral
what is electronegativity? what has the highest?
attractive force that an atomic nucleus exerts on electrons
oxygen
what is involved in acylation?
addition of an acyl group
-C-R
II
O
what is carboxylation?
addition of a carboxyl group
end of a carboxylic acid
what is esterification?
OH group replaced by an O-alkyl group
condensation vs hydrolysis?
condensation = two compounds joined by water being removed hydrolysis = break up compound by adding water
what happens during a redox reaction?
electrons transferred from one molecule to another
as one molecule is oxidised another is reduced
AH + B <> A + BH
what are the oxidation states of carbon?
alkane (fats) > alcohol (carbohydrates) > aldehyde > carboxylic acid > carbon dioxide (final product of catabolism)
name 5 functions of biomolecules in the body
info storage (DNA)
structure (teeth, bones etc)
energy generation (glycolysis, krebs etc)
energy currency/storage (ATP)
recognition/communication/specificity (receptors, hromones, enzymes etc)
name 3 disaccharides
lactose
maltose
sucrose
what is on the end of a disaccharide?
free anomeric carbon (reducing end)
HOH
bonding partners and energy in a reaction never change, true or false?
false
matter and energy are neither created nor destroyed
eg. protons and electrons transferred from propane to oxygen to form water
every energy transformation is 100% efficient, true or false?
false
no energy transformation is 100% efficient (2nd law of thermodynamics)
what will happen to a system if energy is not applied?
it will be randomly arranged or disordered
it takes order to impose order on a system
ΔG = ΔGo’ + RTln([C][D]/[A][B]) for A + B > C + D?
determines free energy
R = universal gas constant (8.3JK-1mol-1)
T = temp in kelvin
ΔGo’ = free energy change under standard conditions
unit = kJ/mol
what are the biochemical standard conditions?
T = 298K
1 atm pressure
1 M (1 mol/l) conc of reactants
pH 7
how is ΔG related to the point of equilibrium?
further towards point of equilibrium = more free energy released
ΔG near zero = readily reversible reaction
what is Keq?
equilibrium constant
for reaction A + B > C + D, Keq = [C] [D] / [A] [B]
what will increasing [A] [B] relative to [C] [D] do to ΔG?
[C] [D] / [A] [B] becomes smaller than 1
the ln of a number smaller than 1 is negative
ΔG becomes negative
name 2 cellular processes that are unfavourable, how is this overcome?
transport against a gradient
synthesis of large molecules
overcome by coupling to highly favourable processes
give an example of coupling
ADP + Pi > ATP + H2O (ΔG = +55)
PEP + H2O > pyruvate + Pi (ΔG = -78)
Joined together to form
PEP + ADP > pyruvate + ATP (ΔG = -23)
ATP + H2O > ADP + Pi = very favourable, true or false?
true
ΔG = -30
ADP is less stable than ATP, true or false?
false
ADP is more stable due to the strain the closely packed electric charges put on ATP
what bonds gold ATP phosphates together?
phosphoanhydride bonds (high energy bonds)
why is ATP constantly regenerated?
cells don't store large amounts of it active cells (eg. muscle cells) use a lot of it
how is ATP regenerated?
using creatine phosphate or using 2 ADP <> ATP + AMP
components of metabolism?
catabolism = breaking things, releasing energy anabolism = making things, using energy
example of a catabolic pathway?
glycolysis
glucose broken down to form 2 ATP
example of an anabolic pathway?
gluconeogenesis
making new glucose from non carbohydrate compunds
costs energy
what reactions are useful as control points?
those with large -ve ΔG values
water is a bent polar molecule, what does this mean?
polar = electrons shared unequally bent = forms a dipole
what substances dissolve in water?
ionic and polar (hydrophilic)
what is a hydrogen bond?
covalent bond between hydrogen and a more electronegative atom (eg. oxygen) creates polarized bond
the hydrogen ca interact with unshared electrons from another electronegative atom
what is the charge on the hydrogen in a hydrogen bond?
hydrogen has partial +ve charge
what is the shape of a hydrogen bond?
tend to be linear
what are hydrocarbons?
compounds consisting of carbon and hydrogen
very non-polar and hydrophobic
excluded by water (don’t mix)
how do water molecules interact with each other?
power attraction between them
prefer to interact with themselves rather than non-polar molecules
what is the hydrophobic effect?
oil and water don’t mix
what are amphipathic molecules?
hydrophilic and hydrophobic
hydrophilic head and hydrophobic tail
form micelles in water
example of an amphipathic molecule?
sodium palminate (fatty acid)
what types of lipids are present in the cell membrane?
structural (lipid bilayer)
precursors of signalling molecules (DAG, IP3)
all amino acids contain an alpha-carbon bonded to what?
amino group (NH2) carboxy group (COOH) hydrogen side chain (R)
what are D and L forms of amino acids?
stereoisomers
non-superimposable mirror images
what are the 4 types of amino acid, what determines this?
non-polar, hydrophobic polar, uncharged acidic basic determined by side chain
how is a peptide bond formed?
two amino acids joined together via removal of water molecule forming the CO-NH bond
what is the direction of a peptide chain?
always N terminal to C terminal
name 3 characteristics of a peptide bond
partial double bond character
planar
strong and rigid (important for protein folding)
what is an acid/base and what determines the strength\?
acid = donates a proton
base = accepts a proton
strength of an acid depends on how readily it donates a proton
how is the strength of an acid measured?
dissociation constant Ka
Ka = [H+] [A-] / [HA]
HA = acid
A- = conjugate base
what is pH and how is it calculated?
amount of protons in a solution
pH = -log10[H+]
pKa = -log10[Ka]
what effect does the log have on pH change?
1 unit pH change implies a tenfold change on proton conc
what is log?
log of X to base n is the number of times n has to multiplied by itself to result in X
e.g log(10)1000 = 3
what is the Henderson hasselbach equation?
connects Ka of a weak acid with the pH of a solution containing this acid
pH = pKa + log[A-]/[HA]
lets you calculate the properties of buffer solutions
at what value do buffers tend to resist a change of pH on addition of moderate amounts of acid or base
at their pKa value
what do titration curves show?
plots pH as a function of base added to an acid
close to pKa the pH remains the same in response to addition of base
what is a zwitterion?
amino acid without a charged side chain in neutral solution
have no net charge
contain 2 titratable groups and therefore 2 pKa values
what is the isoelectric pH?
pH at which a molecule has no net charge
what would a titration curve of a zwitterion (e.g alanine) look like?
sigmoidal with 2 horizontal parts ( pKa values)
how can proteins act as buffers? give an example
ends of proteins and several amino acid side chains can be ionised
e.g haemoglobin in blood
polypeptides rotate around the angles between what?
alpha carbon and amino group
alpha carbon and carboxyl group
what is secondary structure and what are the 3 types?
hydrogen bonded 3D arrangement of a polypeptide chain (backbone)
alpha helix
beta strand/sheet
triple helix
describe alpha helix
one polypeptide chain in (usually right handed) coil
CO group of one amino acid forms hydrogen bond with NH group of another amino acid 4 residues away
what breaks an alpha helix?
proline residues
describe beta sheets?
polypeptide backbone extended (can involve more than 1)
can be parallel or antiparralel
turns between strands (glycine and proline)
what is a beta pleated sheet?
repeated zig zag structure
can different 2ndary structures occur in same protein?
yes
e.g - phosphoglycerate kinase
describe collagen triple helix
3 left handed helical chans twisted around each other forming a right handed superhelix
repeated sequence of X-Y-Gly in all strands (X = amino acid, Y = proline or hydroxyproline)
H bonds between chains, covalent bonds inside chains
where are triple helixes most found? Give an example
most common protein in vertebrates
component of bone and connective tissue
E.g - tropocollagen
what is the importance of collagen?
give strength of connective tissue
can cause scurvy or bleeding gums if lacking
what does tertiary structure of proteins give?
fibrous or globular proteins
arrangement of atoms of polypeptide in space
what is the difference between fibrous and globular proteins?
fibrous = chains organised in parallel along single axis, long strong fibres (e.g keratin in hair, collagen of connective tissue) globular = proteins folded to more or less spherical shape, soluble (myoglobin, haemoglobin)
what forces stabilise tertiary structures?
covalent disulphide bonds salt bridges hydrophobic interactions H bonds (backbone/side chains) complex formation with metal ions
how are disulphide bridges formed?
CH2-SH–SH-CH2
becomes (with loss of 2H)
CH2-S-S-CH2
give an example of an electrostatic interaction in proteins
salt bridges
give an example of hydrophobic interaction in proteins
amino acids with hydrophobic side chains tend to cluster in the centre of globular proteins
what would happen if a mutation in a given protein changes a glutamic acid to a valine?
functional change
glutamic acid = -ve charge, can form ionic bonds or hydrogen bonds with water or other amino acid side chains
valine = hydrophobic, interacts with other hydrophobic amino acids
how does sickle cell anaemia arise?
single nucleotide sequence change in coding region of beta chain of haemoglobin A changing glutamic acid to valine
what does sickle cell anaemia result in?
altered protein meaning haemoglobin polymerises under low O2 conditions resulting in rigid, sickle shaped cells that can block blood flow in capillaries
how do proteins fold?
primary structure contains info for 3D shape
can fold spontaneously but this is slow and can fold incorrectly or associate with other proteins before properly folded
Can be aided by chaperones
what diseases can result from problems in protein folding?
mad cow disease (infection)
Creutzfeld-jacob disease
presence of disease causing prion protein PrPSc
what physical things can denature a protein by disrupting its structure?
heat
extreme pH
detergents, urea, guanidine hydrochloride (disrupt hydrophobic interactions)
thiol agents, reducing agents (disrupt disulphide bond)
structure of myoglobin?
globular protein with haem group which contains iron ion (Fe2+ - prosthetic group)
haem binds O2 (1 O2 per myoglobin)
stores O2 in muscle
structure of haemoglobin?
4 subunits (2 alpha and 2 beta chains)
each contains a haem
can bind 4 O2
transports O2 in blood
how does binding of one O2 affect the haemoglobin molecule?
binding of one O2 changes affinity of the other subunits for O2
