Biochemistry Flashcards
1
Q
van der Waals Interactions
A
interactions of electrons of non polar substances
2
Q
what is electronegativity?
A
the attractive force that an atomic nucleus exerts on electrons within a bond
3
Q
what is acylation?
A
the addition of an acyl group -C(O)-R
4
Q
what is a carboxyl group
A
COOH
5
Q
esterification
A
carboxyl group and alcohol group makes an ester link plus water
6
Q
what happens during redox reactions
A
electrons are transferred from one molecule to another
7
Q
what are the four major classes of biomolecules?
A
peptides and proteins (consist of amino acids), lipids (triglycerides, phospholipids, steroids), nucleic acids (DNA, RNA) and carbohydrates
8
Q
different types of carbohydrates
A
mono, di and polysaccharides
9
Q
different types of lipids
A
triglycerides, phospholipids and steroids
10
Q
what is a nucleoside?
A
base + sugar
11
Q
what is a nucleotide?
A
base + sugar (nucleoside) + phosphate group
12
Q
what is a phosphodiester bond formed between?
A
a free 3’ OH group and a 5’ triphosphate (nucleotide)
13
Q
what enzyme adds the next deoxyribonucleotide to the -OH group at the 3’ end of the growing strand?
A
DNA polymerase
14
Q
what happens to the pyrophosphate ion when the nucleotide attaches to the growing strand?
A
it is broken apart, releasing energy to drive the reaction
15
Q
what end are nucleotides added to?
A
only added to a free 3’end
16
Q
what is the bond called that links the DNA chain together? They are between 3’ OH group and 5’ triphosphate
A
phosphodiester
17
Q
what bonding to base pairs take part in?
A
hydrogen bonding from one strand to the other
18
Q
when does DNA have to be replicated?
A
before cell division
19
Q
why does DNA have to be replicated?
A
to ensure the daughter cells have a full complement of the genome
20
Q
what catalyses DNA replication?
A
DNA polymerase
21
Q
what does DNA need to start replication?
A
an RNA primer
22
Q
what is the name of the strand that has to add nucleotides in fragments?
A
the lagging strand
23
Q
what are the fragments of nucleotides called that are added to the lagging strand?
A
OKAZAKI fragments
24
Q
what enzyme unwinds DNA?
A
helicase
25
the enzyme that synthesises a complementary DNA strand
DNA polymerase
26
what synthesises an RNA primer?
primase
27
what does rRNA do?
combines with proteins to form ribosomes where protein synthesis takes place
28
tRNA does what?
carries the amino acids to be incorporated into the protein
29
mRNA does what?
carrier the genetic information for protein synthesis
30
how many types of RNA polymerase do prokaryotic cells have?
one type of RNA polymerase
31
what does Pol 2 RNA polymerase synthesise?
all mRNA
32
where is the TATA box present?
about 25 nucleotides before the transcriptional start (-25)
33
what recognises the TATA box?
TATA box binding protein (TBP)
34
What does the TBP do?
It introduces kink into DNA
35
what does the TBP provide?
a landing platform for further transcription factors and for RNA polymerase
36
what does the initiation of transcription require?
additional general transcription factors
37
what direction is the RNA chain synthesised in?
5' to 3' direction
38
what is the new RNA sequence identical to?
the coding strand (but uracil instead of T)
39
what structure does RNA make?
stem-loop structure followed by a stretch of Us
40
what type of specific transcription factors are required?
DNA-binding domain and transcriptional activation domain
41
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
42
what happens to the primary mRNA once it has been spliced?
a 5' G cap and a poly(A) tail is added
43
do tRNA molecules have codons or anticodons?
anticodons
44
what do the anticodons on tRNA do?
form base pairs with the codons on mRNA
45
the genetic code is generate- meaning?
many amino acids have more than one codon
46
the genetic code is unambiguous meaning?
each codons codes for only one amino acid or a stop
47
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
48
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
49
how many rRNA molecules are in ribosomes?
four
50
what are the three tRNA binding sites on ribosomes?
Exit, peptidyl and aminoacyl
51
what does initiation require?
initiation factors?
52
what provides energy for initiation?
hydrolysed GTP
53
what brings the next aminocyl-tRNA to the A site (aminoacyl site)?
an elongation factor
54
when does termination occur?
when the A site of the ribosome encounters a stop codon
55
what are the three stop codons?
UAA, UAG or UGA
56
what binds to a stop codon?
a release factor
57
point mutation
change in a single base in DNA (there are different types of point mutations)
58
missense mutation
one base is changed which produces a different amino acid sequence which can alter proteins function
59
nonsense mutation
base change creates a stop codon. shortens length of amino acid chain
60
silent mutation
base change which doesn't alter the amino acid
61
frameshift mutation
addition or deletion of a single base which changes the reading frame of translation into protein
62
four types of chromosomal mutations
deletions, duplications, inversions and translocations
63
what is targeting?
moving a protein to its final cellular destination
64
what three things happen to the finished protein?
targeting, modifications and degradation
65
bound ribosomes on the rough endoplasmic reticulum make proteins destined for... (4)
- plasma membrane
- ER
- Golgi apparatus
- secretion
66
how are proteins that are made on the rough endoplasmic reticulum translocated?
they are translocated co-translationally
67
post-translational modification: glycosylation
addition and processing of carbohydrates in the ER and the Golgi
68
post-translational modification in the ER
formation of disulphide bond and folding of multisubunit proteins
69
what model is used to explain the relationship between Vmax and Km?
The Michaelis-Menten model
70
how are Vmax and Km measured?
measure the initial reaction velocity, V0, at a known substrate concentration and repeat at increasing substrate concentration
71
what is the Michaelis Constant (Km) equivalent to?
The substrate concentration where the initial reaction rate is half of the Vmax
72
What graph enables accurate determination of Vmax and Km?
The Lineweaver-Burk plot
73
instead of V against [S], you plot...
1/V over 1/[S]
74
where can you read the V max on a Lineweaver Burk plot?
intersection of the straight line on the y axis
75
where can you read the Km on a Lineweaver Burk plot?
on the intersection with the X axis
76
what is the Vmax
the maximum rate of reaction at unlimited substrate concentration (point at which the line crosses the Y axis)
77
what is the Km?
substrate concentration that gives half Vmax also known as Michaelis Constant (point at which the line crosses the X axis)
78
what does a low Km mean?
an enzyme only needs a little substrate to work at half-maximal velocity
79
what does a high Km mean?
an enzyme needs a lot of substrate to work at half-maximal velocity
80
what is glucokinase?
a gene that helps the body to recognise how high the blood glucose level is in the body
81
opposite to allosteric inhibition
orthosteric inhibition. the inhibitor binds to the same active site
82
effects of competitive inhibition of Vmax and Km?
Vmax does not change but the Km does
83
effects of non- competitive inhibition of Vmax and Km?
Vmax does change but the Km does not
84
common mechanism of allosteric control ?
feedback inhibition
85
what are allosteric enzymes?
enzymes that change their conformational ensemble upon binding of an effector
86
what is an allosteric site?
places on the enzyme where any enzyme regulator can bind
87
what can control allosteric enzymes?
allosteric inhibitors and allosteric activators
88
how do enzymes reduce the activation energy>?
provide alternative pathways
89
what are cofactors?
molecules that enzymes depend on for catalytic activity. Metal ions (zinc, iron, copper) and they stabilise transition states. In the centre
90
what are coenzymes?
molecules that enzymes depend on for catalytic activity and are usually organic molecules.
91
what are tightly bound coenzymes called?
prosthetic groups
92
where are many coenzymes deprived from?
vitamins
93
What are coenzymes involved in?
redox reactions and group transfer processes (ATP transfers phosphate groups)
94
what are the amino acids on an active sites essential for?
for catalytic activity and highly specific interactions
95
what is an isoform?
any of two or more functionally similar proteins that have a similar but not an identical amino acid sequence
96
what are isozymes?
isoforms of enzymes. Enzymes with different properties, structure and sequence but are able to catalyse the same reaction
97
how can enzymes have covalent modification?
side groups of serine, threonine and tyrosine can form phosphate esters
98
how can enzymes be activated or deactivated?
phosphorylation or dephosphorylation
99
what carries out phosphorylation?
protein kinases
100
what carries out dephosphorylation?
protein phosphatase
101
what are zymogens?
inactive precursors of an enzyme that are irreversibly transformed into active enzymes by cleavage of a covalent bond
102
examples of zymogens?
digestive enzymes, blood-clotting enzymes, clot-dissolving enzymes
103
what is an enzyme without a cofactor called?
apoenzyme
104
what is an enzyme with a cofactor called?
holoenzyme
105
how can you create a holoenzyme?
apoenzyme + cofactor
106
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
107
anabolism is e......gonic and ......
endogonic and reductive
108
catabolism is e.......gonic and .......
exogonic and oxidative
109
examples of oxidised precursors in metabolism
CO2 and H2O
110
basic structure of glycogen
A glucose chain
111
examples of cells that only use glucose as an energy source
erythrocytes, retina, renal medulla (in the kidney), all cancer cells, brain
112
basic structure of disaccharides
a double sugar formed with two monosaccharides or simple sugars
113
how is glucose transported into cells?
via Na+/glucose symporters and via passive facilitated diffusion glucose transporters
114
what are the three 'control point' enzymes?
hexokinase (substrate entry), phosphofructokinase (rate of flow) and pyruvate kinase (product exit)
115
what are two activators that will increase glycolysis if energy is needed?
AMP and fructose 2,6-biphosphate
116
what are two inhibitors that will inhibit the act of phosphofructokinase?
ATP, Citrate and H+ ions
117
effect of too much ATP on glycolysis?
glycolysis will show down
118
what is citrate?
a citric acid cycle intermediate
119
effect of H ion inhibition on phosphofructokinase?
slows down glycolysis if too much lactic acid is being produced
120
another name for the ATP/AMP ratio?
the energy charge
121
what is the Warburg effect?
the up-regulation of anaerobic glycolysis in cancer cells to produce lactate
122
3 drugs that can target glycolysis and treat cancer?
2-deoxy-glucose, 3-bromopyruvate and dichloroacetate
123
what shape will the graph of allosteric controlling enzymes have? (regulation of haemoglobin)
Sigmoid
124
what shape will the graph of myoglobin show?
Hyperbolic (Michaelis menten regulation)
125
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
126
what does the leading strand of DNA replication always have?
A free 3' end (where nucleotides are added)
127
what are the types of eukaryotic RNA polymerase?
Pol 1, 2, 3
128
what is FF2D?
a general transcription factor required for all Pol 2 transcribed genes
129
what is the start codon in translation?
AUG
130
five steps of transcription
1. RNA polymerase binding
2. DNA chain separation
3. Transcription initiation
4. Elongation
5. Termination
131
four steps of translation
1. Initiation
2. Elongation
3. Peptidyl transferase catalyses peptide bond formation between amino acids in P and A sites
4. Termination
132
what triggers the termination of translation?
When the A site of the ribosome encounters a stop codon (UAA, UAG, UGA)
133
what does the description 'degenerate' mean in relation to the genetic code?
many amino acids have more than one codon
134
what does unambiguous mean in relation to the genetic code?
each codon only codes for one amino acid
135
what is the initial pathway fr the conversion of glucose to pyruvate?
glycolysis
136
what is the net gain of ATP for one glucose molecule in glycolysis?
4 ATP
137
what enzymes phosphorylates glucose in glycolysis to glucose-6-phosphate?
hexokinase
138
role of phosphofructokinase in glycolysis?
it phosphorylates fructose-6-phosphate to fructose-1,6-biphosphate
139
what is the key enzyme in the control of glycolysis?
Phosphofuctokinase
140
negative modulators of phosphofructokinase?
ATP, citrate, H+
| decrease glycolysis when energy is abundant
141
positive modulators of phosphofructokinase?
AMP, fructose, 2,6-biphosphate
| increase glycolysis when energy is required
142
fate of pyruvate in anaerobic conditions
alcoholic fermentation, lactic acid formation
143
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
144
what is used to ferment pyruvate to lactic acid?
NADH
145
where does the oxidative metabolism of pyruvate occur?
in the mitochondria
146
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
147
total products of two cycles of the Krebs cycle|?
| from 2 acetyl-coA
4 CO2
2 ATP
2 FADH2
6 NADH + H+
148
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)
149
what is phosphoryl transfer potential?
free energy change for ATP hydrolysis
150
what is the electron transfer potential?
aka the redox potential of a compound
| How readily a substance donates electrons
151
what does a negative redox potential mean?
the reduced form of X has lower affinity for electrons than hydrogen
152
what does a positive redox potential mean?
the reduced form of X has a higher affinity for electrons than hydrogen
153
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
154
what inhibits oxidative phosphorylation?
cyanide, azide and CO inhibit the transfer of electrons to O2 so no proton gradient is formed, no ATP synthesised
155
in oxidative phosphorylation, what is used to reduce O2 and H20?
Electrons from NADH and FADH2
156
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
