Biochemistry Flashcards
condensation
water removed
hydrolysis
water added
Oxidation
loss of electrons
reduction
gain of electrons
protein
chain of amino acid
peptide
chains of amino acids smaller than protein
lipids
fatty acids
soluble in inorganic substances but insouble in water
eg cholesterol
nucleic acid
composed of nucleotides
carbohydrates
composed of carbon, hydrogen and oxygen
efficiency of converting energy
energy cannot be created, only change form
converting energy from one source to another is not 100% efficient,and each time it occurs some of the energy becomes unusable
e.g. eventually there will be no usable energy
enthalpy
heat H
entropy
disorder S
change in free energy
ΔG° = ΔH° - TΔS°
temp in kelvin
ΔG° = energy of the products- energy of the reactants
free energy
the internal energy of a system minus the amount of energy that cannot be used to perform work.
exergonic reactions
ΔG° = -ve
the energy of the products is less than the energy of the reactants
can occur spontaneously
endergonic reactions
ΔG° = +ve
energy of the products is higher than the energy of the reactants
cannot occur spontaneously
what drives endergonic reactions
coupling to a exergonic reaction
many reactions coupled to ATP
ATP is highly unstable so produces energy by breaking 1 phosphate bond, stored as ADP
metabolism
all anabolic and catabolic reactions
catabolism
breaking down larger molecules to produce smaller ones
there are some energy consuming stages but net gain
exergonic and oxidative
anabolism
producing larger molecules from smaller molecules requiring ATP
endergonic and reductive
what is the ΔG of control reactions
large -ve ΔG° as the reaction will be mostly irreverisble as would require so much energy
water
polar, forms a dipole, ionic substances dissolve in water
non-polar substances are insoluble in water
amphiphilic
polar and non-polar
hydrophobic
water hating
hydrophilic
water loving
amino acids
form proteins
NH2, COO, H and side chain
amino group, carboxyl and H
categories of amino acid
acidic, basic, polar and non-polar
direction of amino acids
N terminus (amino group) to the C terminus (carboxyl terminus)
strength of peptides bond and the importance
strong, important for folding
acids
donate a proton( H+)
strength of an acid depends on how readily it donates the H+ e.g. strong acids will readily donate the H+ in water and fully ionise
Bases
Proton acceptors
pH
the concentration of H+ ions
buffer
solution to control the pH of a reaction mixture
resist pH change
proteins as buffers
proteins contain amino acid groups and carboxyl groups so are able to act as buffer
a change in pH can cause ionisation of proteins resulting in a change in protein structure and function
primary protein
sequence of amino acids
secondary protein
polypeptide backbone
tertiary protein
3D structure
quaternary protein
spatial arrangement of polypeptide chains with multiple subunits
Polypeptide rotation
polypeptides can rotate around the alpha carbon and the carboxyl group and they can rotate around the alpha carbon and the amino group.
bonds in secondary proteins
hydrogen bonds
3 types of secondary structure
1) alpha helix
2) beta pleated sheat
3) collagen triple helix
alpha helix
the H in the NH2 forms a bond with the O from C
B pleated sheet
zig zag
parallel B sheet
both strands start and end same place
e.g. both N-C or both C-N
antiparallel B sheet
the strands start and finish in different places eg one is C-N and the other is N-C
collagen triple helix
component of bone and connective tissue
bonds in primary protein structure
peptide
tertiary proteins
fibrous and globular proteins
bonds stabilising tertiary structure
ionic bonds
hydrophobic bonds
convalent disulphide bonds
hydrogen
quaternary
proteins with more than 1 polypeptide chain
transcription
RNA polymerase is used to transfer DNA to RNA
translation
ribosomes translate the mRNA/RNA to an amino acid sequence
nucleoside
base and sugar
nucleotide
nucleoside and phosphate
bonds between bases
AT is a double bond
CG is a triple bond
DNA polymerase
synthesise DNA from deoxyribonucleotides
enzyme for DNA replication
3’
has a free phosphate
5’
has a free deoxyribose
differences between DNA and RNA
RNA is single stranded while DNA is double stranded.
RNA has a sugar called ribose while DNA has a sugar called deoxyribose.
RNA has the base uracil while DNA has the base thymine.
Replication
many sites of origin of DNA replication
nucleotides can only be added to the 3’ end
leading strand is continuous
lagging strand is added in short segments and joineed together by DNA ligase
DNA ligase
joins together the okazaki fragments of the lagging strand
chromosomes
carry DNA
one from mum and one from dad
23 pairs of chromosomes in each human cells
rRNA
ribosomal ribonucleic acid
combines with proteins to form ribosomes where protein synthesis takes place
types of rna
ribosonal rna
messenger RNA
transfer RNA
mRNA
transfers a copy of the genetic code from the nucleus to ribosomes for protein synthesis
tRNA
translates nucleotides to amino acids
steps of transcription
RNA polymerase binds DNA sequence separates Transcription is initiated Elongation: addition of further nucleotides Termination: release of finished RNA
Types of mutation
silent missense nonsense chromosomal frameshift point
point mutation
change in a single base
missense mutation
change in amino acid sequence and can change proteins function
nonsense mutation
creates anew termination codon
silent mutation
no chance on amino acid sequence
frameshift mutation
insertion or deletion
chromosomal mutation
large sections of the genome affected
what happens to the finished protein
Tareted to location
modified
unwanted proteins are degraded
factors
initiation, termination and elongation all require factors
post translational modifications
glycosylation
disulphide bonds
cleavage
Enzymes affect on equilibrum position
do not affect the equillibrum of reactions
specificity
enzymes are v specific and stabilise the transition state
how do enzymes reduce the actiation energy
provide an alternative pathway
cofactors
assist enzymes
metal ions
coenzymes
aid enzymes
organic molecules
prosthetic group
tightly bought coenzymes
haloenzymes
enzymes with cofactor
apoenzyme
enzyme without cofactor
isoenzymes
catalyse same reaction but different properties and structure
phosphorylation
can activate or deactivate a protein
irreversible convalent modifiation
activate of enzymes
eg digestive enzymes
Vmax
Maximum velocity of a reaction ie inifinite substrate
the reaction velocity never reaches V max
Km
substrate concentration that gives half of V max
orthosteric inhibition
inhibitor binds at active site and blocks substrate acess
allosteric inhibition
inhibitor binds at a site other than the active site and changes conformation
irreversible inhibition
non-competitive, cannot be reversed, usually involves the formation or breakage of a convalent bond
competitive inhibition on graph
Km varies but Vmax does not change
non-competitive inhibition on graph
Km stays the same but Vmax changes
allosteric enzymes
contain multiple subunits. binding of a substrate to one subunit causes a conformational change which causes a conformational change in the other subunits increasing their affinity for the substrate
increasing substrate conc in allosteric enzymes
sigmoid curve
what does a sigmoid curve show
cooperative behaviour
what controls allosteric enzymes
allosteric inhibitors and allosteric activators
glucose fermented
lactate
glucose oxidised
pyruvate
ribose
glucose stored
glycogen
glucose transporters
GLUT1: brain GLUT2: liver GLUT3:brain GLUT4: muscles GLUT5: gut
where does glycolysis take place?
cyptoplasm
hexokinase
regulates how much glucose is converted to glucose pyruvate
phosphofructokinase
rate of flow
pyruvate kinase
how much pyruvate leaves
names of the control enzymes in glycolysis
hexokinase
phosphofructokinase
pyruvate kinase
glycolysis activators
amp
fructose-2,6- biphosphate
glycolysis inhibitors
ATP, citrate and H+
where does the citric acid cycle take place
mitochondria
orthosteric enzymes
bind to the active site
isoenzymes
same function different structure
kinases
phosphorylate
zymogens
an inactive substance which is converted into an enzyme when activated by another enzyme
