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Year 1 - Principles (DP) > Biochemistry > Flashcards

Biochemistry Flashcards

0
Q

Is Carbon reduced or oxidised as

  1. Hydrogen is added
  2. Chlorine is added?
A
  1. Reduced

2. Oxidised

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1
Q

What is acylation?

A

Addition of COR

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2
Q

Rank the following in increasing States of carbon oxidation:

  • Aldehyde
  • Alkane
  • Carbon dioxide
  • Carboxylic acid
  • Alcohol
A

Alkane < Alcohol < Aldehyde < Carboxylic acid < Carbon dioxide

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3
Q

What is the first law of thermodynamics?

A

Energy is neither created nor destroyed

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4
Q

What is the second law of thermodynamics?

A

When energy is converted from one form to another some is unavailable to do work

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5
Q

What is the definition of entropy?

A

Free energy tends towards an unstable state after multiple transformations

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6
Q

Equation for DeltaG

A 
DeltaG = DeltaH - (T x DeltaS) or 
DeltaG = (energy of products) - (energy of reactants)
Where:
G - Free energy
H - Enthalpy
T - Temperature in K
S - Entropy
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7
Q

Is DeltaG negative or positive in an

  1. Exergonic reaction
  2. Endergonic reaction
A

Exergonic - Negative (spontaneous reactions)

Endergonic - Positive

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8
Q

Why does coupling of reactions occur?

A

It allows reactions with a positive DeltaG to proceed as highly favourable reactions when coupled with a highly negative DeltaG reaction

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9
Q

Why is the breakdown of ATP highly favourable?

A

DeltaG = -30kJ/mol

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10
Q

What is catabolism?

A

Breakdown of molecules - releasing energy

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11
Q

What is anabolism?

A

Synthesis of complex molecules - using energy

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12
Q

What shape is the water molecule?

A

Bent dipole

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13
Q

What are micelles?

A

Arrangement of amphipathic molecules in water

Hydrophilic head out and hydrophobic tail in

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14
Q

What is the only amino acid without a D or L isomer?

A

Glycine

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15
Q

What enzyme catalyses peptide bond formation?

A

Peptidyl transferase

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16
Q

What direction do peptides run in?

A

From N-terminal residue to C-terminal residue

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17
Q

What is the Henderson-Hasselbalch equation?

A

pH = pKa + log([A-]/[HA])
ie
pH = pKa + log([base]/[acid])

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18
Q

What is the primary structure of a protein?

A

Amino acid sequence

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19
Q

What is the secondary structure of a protein?

A

Conformation of polypeptide backbone

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20
Q

What bond(s) are present in the secondary structure?

A

Hydrogen bonds

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21
Q

What are the types of secondary protein structure?

A

Alpha-helix - one right handed, rod-like chain
Beta-sheets - two directions (parallel and anti-parallel) and turns between strands (glycine and proline)
Collagen triple helix - three left handed chains - Tropocollagen

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22
Q

What effect does proline have on an alpha-helix?

A

Breaks it as it puts in a left handed 90 degree turn

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23
Q

What is the repeated sequence in all strands of collagen?

A

X-Y-Gly
Where:
X - any amino acid
Y - proline or hydroxyproline

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24
What holds the chains together in collagen?
Inter-chain H bonds involving hydroxyproline and hydroxylysine Also inter-chain covalent bonds
25
What is the tertiary structure of a protein?
Arrangement of the atoms in three-dimensional space
26
What are the two types of tertiary structure/protein?
Fibrous | Globular
27
What are some examples of fibrous proteins?
Keratin | Collagen
28
What are some examples of globular proteins?
Myoglobin | Haemolytic
29
What forces are present in the tertiary protein structure?
``` Disulphide bonds Electrostatic interactions Hydrophobic interactions Hydrogen bonds Metal ion complexes ```
30
What can cause protein desaturation?
Heat - increase in vibrations pH extremes - interrupts electrostatic interactions Detergents/Urea/Guanidine hydrochloride - disrupt hydrophobics Thiol agents/Reducing agents - reduce and disrupt disulphide bonds
31
What is a haem group an example of?
A prosthetic group
32
What is the quaternary structure of a protein?
A protein with more than one subunit eg haemolytic
33
What is allosteric regulation in haemoglobin?
Binding of one oxygen molecule changes affinity for other subunits
34
What direction do nucleic acids run in?
5 prime to 3 prime
35
What is DNA replication catalysed by?
DNA polymerase
36
How is DNA replication described?
It is semi-conservative
37
What enzyme unwinds DNA?
Helicase
38
How is the lagging strand replicated?
As Okazaki fragments
39
What are the three classes of RNA?
Ribosomal Transfer Messenger
40
How many nucleotides comprises an anticodon?
Three
41
What are the steps of transcription?
``` RNA polymerase binding DNA chain separation Transcription initiation Elongation Termination ```
42
How does transcription terminate?
Stem-loop created Stretch of uracils forms Enzyme cleaves the finished RNA
43
How are the ends of mRNA processed?
Addition of a poly-A tail | Addition of five prime cap
44
Codons and anticodons consist of three nucleotides; the genetic code is based therefore on...
...triplets
45
How can the genetic code be described? (3 terms)
Degenerate (many AAs have more than one codon) Unambiguous Nearly universal
46
What are the start and stop codons?
Start - AUG (methionine) | Stop - UAA, UAG, UGA
47
What are the three tRNA binding sites on ribosomes called?
E - Exit (tRNA leaves) P - Peptidyl (holds growing peptide) A - Aminoacyl (Binds tRNA - site of bond formation)
48
What is the special initiator tRNA anticodon triplet?
UAC (matches start codon AUG)
49
What is the process of translation?
Initiator tRNA amino acid moves to P site Next aminoacyl-tRNA binds to A site Peptidyl transferase catalyses peptide bond formation between amino acids at P and A sites Ribosome moved along mRNA by one triplet Empty tRNA moves to E site tRNA with growing peptide moves from A to P site Repeat
50
What are the types of mutation?
``` Point Missense Nonsense Silent Frameshift ```
51
What happens to a finished protein?
Targeting Modification Degradation
52
What is an apoenzyme?
An enzyme without a cofactor
53
What is an enzyme with a cofactor called?
A holoenzyme
54
What are the models of enzyme function?
Lock-and-key | Induced fit
55
What are zymogens?
Inactive precursors of enzymes
56
What is the equation for glycolysis?
Glucose + 2ADP + 2Pi + 2NAD+ ---> 2Pyruvate + 2ATP + 2H2O + 2NADH + 2H+
57
Describe glycolysis
``` First section - Three reactions - Phosphorylation of glucose - Uses two ATP per glucose - Forms fructose-1,6-bisphosphate (6 carbon sugar with 2 phosphates) Second section - One reaction - Splits fructose bisphosphate into two triose-phosphates Third section - Generates energy - Triose-phosphates converted to pyruvate - For each, 2ADP + 2Pi ---> 2ATP - Produces 4 ATP - Net gain of 2 ATP - Electrons transferred to NAD+ ```
58
What are the regulators of glycolysis and how do they regulate it?
ATP - if in high amounts it is inhibited Citric acid - an intermediate; large amounts inhibits cycle Hydrogen ions - buildup leads to acidification and so inhibits cycle AMP - high amount means cell is low in energy so promotes cycle Fructose - promotes cycle
59
What are the important enzymes in the glycolysis?
Hexokinase - first reaction Phosphofructokinase - third reaction Pyruvate kinase - ninth (final) reaction
60
What is the name of the cycle through which Pyruvate is catabolised?
Citric acid/Krebs/Tricarboxylic acid cycle
61
Describe the TCA cycle
- Acetyl Co-A (C2) condensed with Oxaloacetate (C4) -> citric acid (C6) - C6 -> C5 -> C4 releasing CO2 - Four oxidations (three make NADH, one makes FADH) - One round generates (two CO2, three NADH, one FADH)
62
What is a transcription factor?
A protein other than RNA polymerase that is involved in transcription
63
How many ADP molecules are phosphorylated to ATP during glycolysis?
4 | Net gain of 2
64
What molecules do ribosomes consist of?
RNA and proteins
65
What subunits are the nicotinic ACh receptors made of?
Alpha 3 and Beta 4
66
What protein is activated in Burkitts lymphoma?
c-myc

Year 1 - Principles (DP) (5 decks)

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