Biochem principles Flashcards
what is the strongest and weakest bonds
covalent –> hydrophobic interactions
when does REDOX and OILRIG mean
redox: when one thing is reduced another is oxidised.
OILRIG: oxidation is loss (of H), reduction is gain (of H)
what is the first law of thermodynamic
energy is neither created or destroyed
what is the 2nd law of thermodynamics
when energy is converted from one form to another some of it’s ability to do work is lost
what is free energy
a systems ability to ‘do work)
what is the equation for free energy
∆ = ∆H -T∆S
what is entropy
the amount of disorder within a system,
what is an exergonic reaction
free energy of the products is less than the reactants and so has a -ive value and can occur spontaneously
what is an endergonic reaction
when the total free energy of the products is more than the reactants and ∆G is +ive, this requires energy to proceed
if A + B –> C + D, what is the ∆G equation
∆G = ∆G + RTln([C][D]/[A][B])
what is the bodies preferred pH
pH 7
what does coupling of processes do to a endergonic reaction
coupling with a very -ive ∆G reaction to make an overall -∆G system
if ∆G is close to 0 what does this mean
can be easily reversed
what are the 4 types of amino acids
hydrophobic, polar, basic, acidic
what is at the N-terminal and is it +ive or -Ive
NH2, amino group, +ive
what is at the C-terminal ana is it +ive or -ive
COOH, -ive
what is an amino acid with no overall net charger
zwitterions
what is the difference between a acid and base
acids donate protons (H), and bases accept them
what is the pH equation
pH = -log10[H+]
what is the buffer equation
buffer = pka - log10[acid/base]
what is primary structure of an amino acid
chain amino acids are synthesised to
what is the secondary structure of amino acids
hydrogen bonds creating 3D structure: alpha helix beta sheets parallel or antiparallel
what is the tertiary structure for proteins
3D shape plus additional chains
what is the quaternary structure proteins
additional of subunits
what do chaperone proteins do
quicken protein folding
what can denature proteins
heat, extreme pH, detergents, reducing agents
what structure is triple helix
collagen
what is the central dogma
total DNA in genoma –> RNA –> protein
where does transcription occur
nucleus
where does transcription occur
nucleus
where does translation occur
cytoplasm
what is a nucleoside
base and sugar
what is a nucleotide
base and sugar and phosphate
what connects at the 5’ end
phosphate
what connects at the 3’ end
hydroxyl
what direction does polymerase move in and what is required for synthesis
5’–>3’ and a primer
what joins okazaki fragments on the lagging strand
ligase
what unwinds DNA
helicase
apart from synthesis DNA, what can polymerase do
remove incorrect DNA
what are the differences between DNA and RNA
RNA has U not T, ribose not deoxyribose and is single stranded .
what are the 3 types of RNA and what do they do
mRNA carries DNA replica to ribosome, tRNA carries amino acid to protein rRNA ribosomes
what are promotors
specific nucleotide sequence to help initiate polymerase binding
what is transcription elongation
transcription bubble moves along with polymerase, unwinding and rewinding
what process removes introns and where does it take place
RNA splicing, nucleus
what are degenerate amino acids
have multiple codons
in initiation of translation what is required
GTP hydrolysation
what site does a-tRNA originally bind to
A
where does it move to when binding to other amino acids
P
where does it leave from
E
what does elongation factor (EF) do
brings a-tRNA to A site
what enzyme catalysed peptide bonds between P and A amino acids
peptidyl transferase
where are free ribosomes found
cytosol, nucleus, mitochondria
where are bound ribosomes found
rough ER, golgi and membrane
what can happen to amino acid chain after translation
post-translational modifications
can enzymes change equilibrium
no but they change the rate it can be reached
what do enzymes do to activation energy
lower it
how do they do this
bind to transition state, stabilise it and provide alternative pathways
what are cofactors
metal ions that assist enzymes
what are coenzymes
organic molecules that assist enzymes
what is an enzyme with a cofactor called
holoenzyme
what is an enzyme without a cofactor called
apoenzyme
what is an induced fit
when a substrate bind to active site it causes a conformational change making it fit better
what are zymogens
inactive precursors of enzymes, irreversible reactions
what is an isoenzyme
enzymes that catalyse same reaction but have different structures
which enzymes phosphorylate
kinases
what is vmax
max rate of reaction with unlimited substrate
what is km
conc of substrate that gives 1/2 vmax
in: E + S ES–> E + P. which reaction is K1, K2 and K-1
E + S –> ES = k1
E + S E + P = k2
how do you calculate km or michalis constant
(k-1 + k2)/ k1
what does a low km mean
low amount of substrate needed (high affinity)
in a lineweaver burk plot, what shows Km and Vmax
y intercept = vmax
x intercept = Km
do enzymes change vmax
no only km
in competitive inhibition (orthosteric) of an enzyme, what happens to km and Vmax
Km increases and Vmax stays the same
in non-competitive (allosteric) inhibition of an enzyme, what happens to km and Vmax
km stays the same and Vmax changes - binds to secondary binding site
in orthosteric inhibition what does the curve look like, does it follow M-M rules
hyberbola, yes
in allosteric inhibition what does the curve look like
sigmoid. no
feedback control is what type of inhibition
allosteric
