Biochemistry Flashcards
van der Waals Interactions
interactions of electrons of non polar substances
what is electronegativity?
the attractive force that an atomic nucleus exerts on electrons within a bond
what is acylation?
the addition of an acyl group -C(O)-R
what is a carboxyl group
COOH
esterification
carboxyl group and alcohol group makes an ester link plus water
what happens during redox reactions
electrons are transferred from one molecule to another
what are the four major classes of biomolecules?
peptides and proteins (consist of amino acids), lipids (triglycerides, phospholipids, steroids), nucleic acids (DNA, RNA) and carbohydrates
different types of carbohydrates
mono, di and polysaccharides
different types of lipids
triglycerides, phospholipids and steroids
what is a nucleoside?
base + sugar
what is a nucleotide?
base + sugar (nucleoside) + phosphate group
what is a phosphodiester bond formed between?
a free 3’ OH group and a 5’ triphosphate (nucleotide)
what enzyme adds the next deoxyribonucleotide to the -OH group at the 3’ end of the growing strand?
DNA polymerase
what happens to the pyrophosphate ion when the nucleotide attaches to the growing strand?
it is broken apart, releasing energy to drive the reaction
what end are nucleotides added to?
only added to a free 3’end
what is the bond called that links the DNA chain together? They are between 3’ OH group and 5’ triphosphate
phosphodiester
what bonding to base pairs take part in?
hydrogen bonding from one strand to the other
when does DNA have to be replicated?
before cell division
why does DNA have to be replicated?
to ensure the daughter cells have a full complement of the genome
what catalyses DNA replication?
DNA polymerase
what does DNA need to start replication?
an RNA primer
what is the name of the strand that has to add nucleotides in fragments?
the lagging strand
what are the fragments of nucleotides called that are added to the lagging strand?
OKAZAKI fragments
what enzyme unwinds DNA?
helicase
the enzyme that synthesises a complementary DNA strand
DNA polymerase
what synthesises an RNA primer?
primase
what does rRNA do?
combines with proteins to form ribosomes where protein synthesis takes place
tRNA does what?
carries the amino acids to be incorporated into the protein
mRNA does what?
carrier the genetic information for protein synthesis
how many types of RNA polymerase do prokaryotic cells have?
one type of RNA polymerase
what does Pol 2 RNA polymerase synthesise?
all mRNA
where is the TATA box present?
about 25 nucleotides before the transcriptional start (-25)
what recognises the TATA box?
TATA box binding protein (TBP)
What does the TBP do?
It introduces kink into DNA
what does the TBP provide?
a landing platform for further transcription factors and for RNA polymerase
what does the initiation of transcription require?
additional general transcription factors
what direction is the RNA chain synthesised in?
5’ to 3’ direction
what is the new RNA sequence identical to?
the coding strand (but uracil instead of T)
what structure does RNA make?
stem-loop structure followed by a stretch of Us
what type of specific transcription factors are required?
DNA-binding domain and transcriptional activation domain
what are enhancers and how do they specifically regulate transcription?
an enhancer is a short (50–1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur. They are specific transcription factors
what happens to the primary mRNA once it has been spliced?
a 5’ G cap and a poly(A) tail is added
do tRNA molecules have codons or anticodons?
anticodons
what do the anticodons on tRNA do?
form base pairs with the codons on mRNA
the genetic code is generate- meaning?
many amino acids have more than one codon
the genetic code is unambiguous meaning?
each codons codes for only one amino acid or a stop
what 7 components are needed for translation?
- amino acids
- tRNA
- aminoacyl-tRNA synthetases
- a specific set of protein factors for the initiation of protein synthesis, the elongation of polypeptide chain and translocation and termination
- ATP and GTP as energy sources
- ribosomes
- mRNA
what are aminoacyl-tRNA synthetases?
they bind amino acids to their corresponding tRNA molecule and are highly specific. There is at least one for every amino acid
how many rRNA molecules are in ribosomes?
four
what are the three tRNA binding sites on ribosomes?
Exit, peptidyl and aminoacyl
what does initiation require?
initiation factors?
what provides energy for initiation?
hydrolysed GTP
what brings the next aminocyl-tRNA to the A site (aminoacyl site)?
an elongation factor
when does termination occur?
when the A site of the ribosome encounters a stop codon
what are the three stop codons?
UAA, UAG or UGA
what binds to a stop codon?
a release factor
point mutation
change in a single base in DNA (there are different types of point mutations)
missense mutation
one base is changed which produces a different amino acid sequence which can alter proteins function
nonsense mutation
base change creates a stop codon. shortens length of amino acid chain
silent mutation
base change which doesn’t alter the amino acid
frameshift mutation
addition or deletion of a single base which changes the reading frame of translation into protein
four types of chromosomal mutations
deletions, duplications, inversions and translocations
what is targeting?
moving a protein to its final cellular destination
what three things happen to the finished protein?
targeting, modifications and degradation
bound ribosomes on the rough endoplasmic reticulum make proteins destined for… (4)
- plasma membrane
- ER
- Golgi apparatus
- secretion
how are proteins that are made on the rough endoplasmic reticulum translocated?
they are translocated co-translationally
post-translational modification: glycosylation
addition and processing of carbohydrates in the ER and the Golgi
post-translational modification in the ER
formation of disulphide bond and folding of multisubunit proteins
what model is used to explain the relationship between Vmax and Km?
The Michaelis-Menten model
how are Vmax and Km measured?
measure the initial reaction velocity, V0, at a known substrate concentration and repeat at increasing substrate concentration
what is the Michaelis Constant (Km) equivalent to?
The substrate concentration where the initial reaction rate is half of the Vmax
What graph enables accurate determination of Vmax and Km?
The Lineweaver-Burk plot
instead of V against [S], you plot…
1/V over 1/[S]
where can you read the V max on a Lineweaver Burk plot?
intersection of the straight line on the y axis
where can you read the Km on a Lineweaver Burk plot?
on the intersection with the X axis
what is the Vmax
the maximum rate of reaction at unlimited substrate concentration (point at which the line crosses the Y axis)
what is the Km?
substrate concentration that gives half Vmax also known as Michaelis Constant (point at which the line crosses the X axis)
what does a low Km mean?
an enzyme only needs a little substrate to work at half-maximal velocity
what does a high Km mean?
an enzyme needs a lot of substrate to work at half-maximal velocity
what is glucokinase?
a gene that helps the body to recognise how high the blood glucose level is in the body
opposite to allosteric inhibition
orthosteric inhibition. the inhibitor binds to the same active site
effects of competitive inhibition of Vmax and Km?
Vmax does not change but the Km does
effects of non- competitive inhibition of Vmax and Km?
Vmax does change but the Km does not
common mechanism of allosteric control ?
feedback inhibition
what are allosteric enzymes?
enzymes that change their conformational ensemble upon binding of an effector
what is an allosteric site?
places on the enzyme where any enzyme regulator can bind
what can control allosteric enzymes?
allosteric inhibitors and allosteric activators
how do enzymes reduce the activation energy>?
provide alternative pathways
what are cofactors?
molecules that enzymes depend on for catalytic activity. Metal ions (zinc, iron, copper) and they stabilise transition states. In the centre
what are coenzymes?
molecules that enzymes depend on for catalytic activity and are usually organic molecules.
what are tightly bound coenzymes called?
prosthetic groups
where are many coenzymes deprived from?
vitamins
What are coenzymes involved in?
redox reactions and group transfer processes (ATP transfers phosphate groups)
what are the amino acids on an active sites essential for?
for catalytic activity and highly specific interactions
what is an isoform?
any of two or more functionally similar proteins that have a similar but not an identical amino acid sequence
what are isozymes?
isoforms of enzymes. Enzymes with different properties, structure and sequence but are able to catalyse the same reaction
how can enzymes have covalent modification?
side groups of serine, threonine and tyrosine can form phosphate esters
how can enzymes be activated or deactivated?
phosphorylation or dephosphorylation
what carries out phosphorylation?
protein kinases
what carries out dephosphorylation?
protein phosphatase
what are zymogens?
inactive precursors of an enzyme that are irreversibly transformed into active enzymes by cleavage of a covalent bond
examples of zymogens?
digestive enzymes, blood-clotting enzymes, clot-dissolving enzymes
what is an enzyme without a cofactor called?
apoenzyme
what is an enzyme with a cofactor called?
holoenzyme
how can you create a holoenzyme?
apoenzyme + cofactor
difference between anabolism and catabolism
- in anabolism, the complexity increases but in catabolism the complex is broken down into more simple molecules
- anabolism requires energy and catabolism yields energy
anabolism is e……gonic and ……
endogonic and reductive
catabolism is e…….gonic and …….
exogonic and oxidative
examples of oxidised precursors in metabolism
CO2 and H2O
basic structure of glycogen
A glucose chain
examples of cells that only use glucose as an energy source
erythrocytes, retina, renal medulla (in the kidney), all cancer cells, brain
basic structure of disaccharides
a double sugar formed with two monosaccharides or simple sugars
how is glucose transported into cells?
via Na+/glucose symporters and via passive facilitated diffusion glucose transporters
what are the three ‘control point’ enzymes?
hexokinase (substrate entry), phosphofructokinase (rate of flow) and pyruvate kinase (product exit)
what are two activators that will increase glycolysis if energy is needed?
AMP and fructose 2,6-biphosphate
what are two inhibitors that will inhibit the act of phosphofructokinase?
ATP, Citrate and H+ ions
effect of too much ATP on glycolysis?
glycolysis will show down
what is citrate?
a citric acid cycle intermediate
effect of H ion inhibition on phosphofructokinase?
slows down glycolysis if too much lactic acid is being produced
another name for the ATP/AMP ratio?
the energy charge
what is the Warburg effect?
the up-regulation of anaerobic glycolysis in cancer cells to produce lactate
3 drugs that can target glycolysis and treat cancer?
2-deoxy-glucose, 3-bromopyruvate and dichloroacetate
what shape will the graph of allosteric controlling enzymes have? (regulation of haemoglobin)
Sigmoid
what shape will the graph of myoglobin show?
Hyperbolic (Michaelis menten regulation)
where is cholesterol present and what is it a precursor of?
present in: cell membranes, component of myelin sheath
Precursor for: steroid hormones, vitamin D and bile acids
what does the leading strand of DNA replication always have?
A free 3’ end (where nucleotides are added)
what are the types of eukaryotic RNA polymerase?
Pol 1, 2, 3
what is FF2D?
a general transcription factor required for all Pol 2 transcribed genes
what is the start codon in translation?
AUG
five steps of transcription
- RNA polymerase binding
- DNA chain separation
- Transcription initiation
- Elongation
- Termination
four steps of translation
- Initiation
- Elongation
- Peptidyl transferase catalyses peptide bond formation between amino acids in P and A sites
- Termination
what triggers the termination of translation?
When the A site of the ribosome encounters a stop codon (UAA, UAG, UGA)
what does the description ‘degenerate’ mean in relation to the genetic code?
many amino acids have more than one codon
what does unambiguous mean in relation to the genetic code?
each codon only codes for one amino acid
what is the initial pathway fr the conversion of glucose to pyruvate?
glycolysis
what is the net gain of ATP for one glucose molecule in glycolysis?
4 ATP
what enzymes phosphorylates glucose in glycolysis to glucose-6-phosphate?
hexokinase
role of phosphofructokinase in glycolysis?
it phosphorylates fructose-6-phosphate to fructose-1,6-biphosphate
what is the key enzyme in the control of glycolysis?
Phosphofuctokinase
negative modulators of phosphofructokinase?
ATP, citrate, H+
decrease glycolysis when energy is abundant
positive modulators of phosphofructokinase?
AMP, fructose, 2,6-biphosphate
increase glycolysis when energy is required
fate of pyruvate in anaerobic conditions
alcoholic fermentation, lactic acid formation
describe the structure of mitochondria
has an inner membrane (proteins), an outer membrane and a central matrix which contains enzymes of the TCA cycle AND CRISTAE folds
what is used to ferment pyruvate to lactic acid?
NADH
where does the oxidative metabolism of pyruvate occur?
in the mitochondria
describe the Krebs cycle?
2-carbon unit from acetyl CoA (from pyruvate) combines with a 4-carbon unit to form a 6 carbon unit
6C is decarboxylated twice so 2x CO2 are released, recreating a 4 carbon unit
total products of two cycles of the Krebs cycle|?
from 2 acetyl-coA
4 CO2
2 ATP
2 FADH2
6 NADH + H+
what is the one enzyme of the TCA cycle not located in the central matrix of the mitochondrion ?
succinate dehydrogenase (it’s in the inner mitochondrial membrane)
what is phosphoryl transfer potential?
free energy change for ATP hydrolysis
what is the electron transfer potential?
aka the redox potential of a compound
How readily a substance donates electrons
what does a negative redox potential mean?
the reduced form of X has lower affinity for electrons than hydrogen
what does a positive redox potential mean?
the reduced form of X has a higher affinity for electrons than hydrogen
how does the transfer of electrons move through the respiratory chain?
coupled to H+ transport from mitochondrial matrix to inter membrane space
The flow of H+ back into the matrix, following the concentration gradient, phosphorylates ADP to ATP
what inhibits oxidative phosphorylation?
cyanide, azide and CO inhibit the transfer of electrons to O2 so no proton gradient is formed, no ATP synthesised
in oxidative phosphorylation, what is used to reduce O2 and H20?
Electrons from NADH and FADH2
Total ATP yield
- Glycolysis – 2 ATP
- TCA cycle (2 GTP) – 2ATP
- Glycolysis, PDH, TCA (10 NADH + H+) - 25 ATP
- TCA (2 FADH2) – 3 ATP
- 1 glucose molecule yields 30-32 ATP molecules
