Biochem Flashcards
(138 cards)
1
Q
Name basic biochemical bonds
A
covalent ionic h-bonding hydrophobic interactions van der waals
2
Q
what is electronegativity
A
attraction of nucleus for electrons, greater the electronegativity the closer atoms van pull electrons to it
3
Q
Monosaccharide and example
A
6 carbon structure with oxygen binding it into a ring shape
cannot by hydrolysed to a simpler sugar
eg glucose
4
Q
Disaccharides and examples
A
2 monosaccharides connected by a bond
formed by condensation
safe to consume and transport
fructose, sucrose, lactose and maltose
5
Q
polysaccharides and examples
A
many monosaccharides connected by a bond
Eg glycogen and cellulose
6
Q
First and second law of thermodynamics
A
1- Energy cannot be created or destroys
2-when energy is converted from one form to another it is not 100% efficient and some is unable to do work
7
Q
What is entropy
A
a measure of disorder in a system
8
Q
what is an exergonic reaction
A
favorable reactions where free energy is negative
total free energy of products is less than that of reactants
can occur spontaneously
9
Q
what is an endergonic reaction
A
free energy of product is greater than that of reactants
unfavorable reactions where free energy is positive
10
Q
Define anabolism
A
Synthesizing complex molecules out of smaller ones - energy consuming
11
Q
Define catabolism
A
Breaking large complex molecules into smaller ones to release energy.
Some exceptions involve energy consuming steps
12
Q
What is coupling
A
an unfavorable reaction is put together with a favorable reaction to utilise the energy to drive it
13
Q
Give an example of coupling
A
ATP - provides energy by its dephosphorylation
3 phosphate groups, the negative charges on the phosphates put electrostatic repulsion on the molecule. It splits to become ADP + Pi to partially relieve the strain and as a result releases energy.
14
Q
what is ΔGo’
A
the change in free energy under standard conditions
15
Q
what are standard conditions
A
298K, 1atm pressure, pH7 and 1M concn reactants except H ion
16
Q
Describe the polarity of water
A
it is polar
can form H- bonds with other molecules
17
Q
define the hydrophobic effect
A
Where water interacts with the water molecules and not other non polar molecules to form a 2 layer system
18
Q
What branches do amino acids have
A
Carboxyl group
hydrogen group
side chain
amino group
19
Q
Non polar amino acids
A
hydrophobic side chain
20
Q
Polar amino acids
A
polar but uncharged side chain
capable of molecular bonding
21
Q
Acidic amino acids
A
acid functional group on side chain
can be used as buffer
22
Q
Basic amino acids
A
amine functional group on side chain
also useful as buffer
23
Q
what is the c terminal
A
carboxyl group
front/joinable end
24
Q
what is the n terminal
A
amino group
rear direction of travel
25
How is pKa calculated
pKa = -log10[Ka]
26
what is pH
measure of amount of protons in a solution
27
henderson hasselbalch equation
pH=pKa+log10[A−]/[HA]
28
When can an acid or base act as a buffer
when close to its pKa value as pH can remain slightly constant
29
what is a zwitterion
no net charge but can be cationic or anionic depending on whether carboxyl group is reduced or amine group is oxidised
30
when does a zwitterion have no net charge
at its isoelectric point
31
Primary proteins
Sequence of amino acids in a linear line joined by s polypeptide bond
32
true/false - peptide bonds have rotation
false - they display a partial double bond character and rotate between alpha carbon and amino group as well as alpha carbon to carboxyl group
33
types of structures in secondary proteins and the bonding
Hydrogen bonding
Alpha helix
Beta I and II sheet
Collagen triple helix
34
Alpha helix
-CO group forms bond with -NH of amino acid 4 residues away
forms a helical shape
broken by proline
35
Beta sheets
Parallel or antiparallel
glycine and proline turn sheet
Beta II is a zigzag
36
Collagen triple helix
found in bone and connective tissue
superhelix formed by 3 helical chains
covalent inter and intra molecular bonds
repeats X - Y (proline/hydroxyproline) - Gly
37
What is a fibrous protein
large sheets or fibres
mechanical strength
water insoluble
38
what is a globular protein
folded spherically
| hydrophobic parts not exposed and so often water soluble
39
What is tertiary structure and give examples
Arrangement of atoms of polypeptide in space
Disulphide bonds
salt bridges
hydrophobic interactions
H-bonds
Formation with metal ions to form prosthetic
40
What is quaternary structure
Proteins containing more than one polypeptide chain
| Haemoglobin
41
DNA runs _____
Antiparallel
42
Name the bases and their nucleosides
```
Adenine - Adenosine
Thymine - thymidine
Uracil - uridine
Cytosine - cytidine
Guanine - guanosine
```
43
what is a nucleoside and how does it differ from a nucleotide
A nucleoside is a base and sugar, whereas a nucleotide is a nucleoside with a phosphate group
44
How many H-bonds do adenine and thymine form
2
45
How many H-bonds do cytosine and guanine form
3
46
True/false - DNA can only be added to free 3' end
true
47
True/false - DNA is read 3' to 5'
false - it is read 5' to 3'
48
Example of how an analogue can act as a drug
retrovir acts as an analogue of thymine to be incorporated into viral DNA and terminates chain elongation due to it lacking OH group on 3' end
49
DNA replication is ____
semi conservative
50
Where does DNA replication occur and what unwinds it
Replication bubble, Helicase
51
What catalyses replication
DNA polymerase
52
can DNA polymerase begin replication on its own?
No. it requires an RNA primer formed by primase
53
What are okazaki fragments
short fragments of DNA made by replication forks enlargement on lagging strand. these must be joined together by DNA polymerase
54
Types of RNA
mRNA, tRNA, rRNA
55
What is a stem loop
local stretches of intramoleculear base pairing on RNA
56
What are the stages of transcription
```
Binding of RNA polymerase
Chain separation
Transcription initiation
Elongation
Termination
```
57
what enzyme unwinds DNA
helicase
58
what direction does elongation occur in
5' to 3'
59
how is mRNA terminated
Step loop structure, followed by stretch of uracil
| this is cleaved to release mRNA
60
how does RNA polymerase bind
requires transcription factors on initiation sites, marked by promoters
61
What are promoters
DNA sequence marking site of a gene
62
Explain how TATA box helps to induce transcription
present 25 nucleotides prior to transcription
TPB binds to it and introduces kink to DNA to determine start of transcription and travel
direction
provides landing platform for Pol II an dother transcription factors
63
True/false - introns removed from mRNA prior to translation
true - called splicing
64
What happens to 3' and 5' end at end of transcription
5' end capped
| sequence of adenosine nucleotides added to 3' end
65
How is transcription regulated
DNA binding proteins, contain a binding domain and a transcription activation/repression domain
66
when do DNA binding proteins bind?
Presence of enhancer (promoter)
67
Can DNA be regulated by gene expression?
Yes. regulated by specific regulatory proteins to coordinate translation in response to specific stimuli
68
what is a reading frame and how many are there
3 reading frames, the reading frame is how genetic code is read in triplets
69
what does unambiguous mean
amino acids with once codon coding for them or a stop codon
70
what does degenerate mean
amino acids with several codons coding for them
71
How does initiation of transcription occur
initiation factors required. GTP hydrolysed to GDP
Small ribosomal unit binds to cap on mRNA
tRNA brings complementary anticodon to start of mRNA in P site, carrying methionine
72
Describe translation elongation
Elongation factor brings aminoacyl-tRNA to A site, the anticodon on the tRNA binds to the codon on the mRNA strand. The elongation factor then detaches from tRNA. A second elongation factor regenerates the first to collect the next tRNA. Peptidyl transferase catalyses the peptide bond formation between amino acids in the P and A sites
EF-2 (elongation factor) moves the ribosome along by one triplet. The now empty tRNA moves to E site to exit and reload with a new amino acid
A is now free for next aminoacyl-tRNA, and the tRNA with the growing peptide chain is located in the P region
This is repeated for as long as required
73
Transcription termination
'A' site encounters stop codon. no tRNA base pairs with it so release factor binds and cleaves from rRNA
74
what is protein degradation
discarding of unwanted or damaged proteins
75
what is targeting
transport of protein to final destination
76
free ribosome makes proteins for...
cytosol, nucleus or mitochondria
77
bound ribosomes makes proteins for....
cell membrane, golgi apparatus, ER and secretion
78
types of post translational modification
Glycosylation
Formation of disulphide bonds in ER
Proteolytic cleavage in ER, golgi apparatus or secretory vessels
79
what is the transition state
maximum of Activation energy and greatest free energy
80
Apoenzyme
enzyme without cofactor
81
Holoenzyme
Apoenzyme and a cofactor
82
What are cofactors
metal ions often with a coordination centre
| involve in redox
83
what are coenzymes
organically occurring molecules
many derived from vitamins
involved in redox
84
What is the lock and key model
active site is specific to substrate conformation and complementary
85
what is the induced fit model
active site not really complementary to substrate but upon binding, active site changes conformation and fits substrate complementary.
86
What are isozymes and example
isoforms of enzymes - catalyse same reaction but different structure and properties
can be used in clinical testing
eg lactate dehydrogenase
87
What is phosphorylation regulation
reversible covalent modification converting enzyme between active and inactive form
carried out by protein kinases
88
what is irreversible covalent modification
involved in enzyme activation.
| zymogens are irreversibly turned into active form by cleavage of a covalent bond
89
what is K1
forward rate constant for enzyme association with substrate
90
What is K-1
backwards rate constant for enzyme dissociation with substrate
91
What is K2
forward rate constant for enzyme conversion of substrate to product
92
What is Km
substrate concentration where initial rate of reaction is half maximal
93
What is Vmax
maximum velocity of a reaction
94
What is the michaelis menten equation
V=Vmax[S]/Km+[S]
95
How can Vmax and Km be accurately determined
lineweaver burk plot
96
What does a low Km suggest
little substrate required to make enzyme work at half max rate. more effective at low substrate concentrations
97
What does a high Km suggest
higher concentration of substrate required to work at half maximal rate
98
Competitive reversible inhibition
binds to active site to block substrate access
Vmax remains constant but Km varies
if a great enough concentration of substrate was added inhibitor could be overcome
99
Non competitive reversible inhibition
binds to allosteric site and changes conformation of active site
alters Vmax but keeps Km constant
100
Irreversible inhibition
covalent bonds have been added or destroyed
101
True/fasle - allosteric enzymes follow michaelis menten kinetics
false - they do not
102
Anabolism is oxidation/reduction
reduction
103
Catabolism is oxidation/reduction
oxidation
104
what is the structure of glucose
6 carbon structure - 5 carbon ring with carbon branch
105
What are the stages of metabolism
Stage 1 - Eating
Stage 2 - Acetyl CoA production and glycolysis
Stage 3 - Acetyl CoA oxidation - electron csrriers fully reduced for ETC
Stage 4 - Electron transfer and oxidative phosphorylation
106
What are the uses of glucose
oxidation by aerobic glycolysis to yield pyruvate
fermentation by anaerobic glycolysis
oxidation by pentose phosphate pathway - ribose-5-phosphate
Can be stored
107
how is glucose transported into cells
Na/Glucose symporter
| Glucose transporters - passive GLUT 1-5
108
Action of GLUT 1
glucose binds to site extracellular and causes a conformational change to face binding site intracellular and release glucose
then changes conformation again to face outside
109
glucose is phosphorylated to produce _____ then further broken down to ______ and then _____
fructose-1,6-bisphosphate
2 triose phosphates
pyruvate
110
Steps of glycolysis
glucose trapped and destabilised
Destabilised intermediates split into 2, 3 carbon molecules
ATP generation
111
Glycolysis control points
First by hexoinase to ensure cell wants to break glucose down
Second prior to destabilisation by phosphofructokinase (flow rate regulator)
Last before pyruvate formation by pyruvate kinase - exit of products from glycolysis
112
Are glycolysis control points reversible
No!
113
How is phosphofructokinase regulated?
It regulates the conversion of fructose 6-phosphate to fructose-1,6-biphosphate by use of ATP
it is activated by AMP
inhibited by protons (lactic acid), ATP abundance and citrate
114
What happens in lack of oxygen?
NADH ferments pyruvate to lactate to free glycolysis
| can be regenerated
115
What is the ATP and NADH yield
Net gain of 2 ATP - 4 produced but 2 used
| 2NAD reduced to NAHD and 2 protons for ETC
116
What is the warburg effect
Cancer cells have a low Km so glucose can be metabolized quickly, allowing for rapid energy production and proliferation
due to their inefficient ATP production they have a high glucose demand to comtete with the patient and leave lactate and protons which act as toxins
117
True/false - nad and fad are unlimited
False - they must be regenerated and are produced by niacin
118
Where does the TCA occur?
mitochondrial matrix
119
how is pyruvate catalysed to Acetyl CoA for TCA?
PDC (pyruvate dehydrogenase complex decarboxylates pyruvate to Acetyl CoA in an irreversible reaction
120
Roughly explain the TCA
Acetyl CoA added to 4 carbon oxaloacetate to form citrate
citrate is decarboxylated twice to yield 2 molecules carbon dioxide
One GTP is formed
There are 4 oxidation reactions to yield 3 NADH+3protons and one FADH
Oxaloacetate is regenerated
121
True/false - only glucose is converted to acetyl CoA
False - carbohydrates, proteins and fats are all broken down to Acetyl-CoA
122
What are the net yields from the TCA
10 NADH and 10 protons
2 FADH
4 ATP from glycolysis and 1 from each TCA, 2 lost during glycolysis so net gain 4
123
What are the different control points in the TCA
High ATP, NADH and Acetyl CoA suggests abundance of energy and so negatively feeds back on cycle
High NAD and ADP suggest lack of energy so favour cycle
124
What are electrons from NADH and FADH used to do?
Reduce oxygen and hydrogen
125
What does the energy from electrons allow for
protons to be pumped from mitochondrial matrix to intermembrane space
126
what does the glycerol-3-phosphate and malate-asparate shuttle do and how does it work?
allows for indirect crossing of 2 NADH that were formed in cytoplasm
NADH from cytoplasm generates malate from oxaloaceteate. these transport malate to the extracellular matrix where mitochondrial NAD is converted to NADH and malate reverts to oxaloacetate
127
What is the chemosmotic hypothesis
coupling of respiration to ATP syntheis, consisting of 2 parts:
Electron transport - where electrons flow from NADH and FADH to oxygen via respiratory chain - while pumping protons out of matrix
ATP synthesis - electrochemical gradient of protons across inner mitochondrial membrane harnesses energy that can be used to make ATP
128
What are the complexes of the resp chain
Complex I - NADH electrons
Complex II - FADH electrons
electrons handed to carriers that are increasingly more oxidative
transferred to oxygen, forming water
129
Where does the F1 subinit of ATP synthase lie
protruding into the matrix
130
Where does the F0 subunit of ATP synthase lie
In the inner membrane
131
How does ATP synthase synthesise ATP
Flow of protons turn rotor and conformational change forces ADP and Pi together
132
How does cyanide, carbon monoxide and azide inhibit ATP synthesis
inhibit transfer of electrons to oxygen so no protein gradient formed
133
What is the P/O ratio
meaure of coupling of ATP synthesis to electron transport
134
What is the overall respiration ATP yield
30-32 ATP
135
What factors influence ATP yield
depends on P/O ratio
| depends on what shuttle is used for transporting cytoplasmic NADH
136
2 functions cholesterol
maintains structure and fluidity cell membrane
| cell signalling
137
what is the endogenous cycle
fat binds to VLDL, leave liver and LPL snips to IDL/LDL to transport cholesterol to cells
138
what is the exogenous cycle
fat from portal circulation enter liver and LPL snips fat from chylomicrons
