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Biochemistry Flashcards

1
Q

What is the function of an enzyme?
What is its effect on the equilibrium position?

A

Enzymes are biological catalysts. They:
- Speed up the rate at which a reaction reaches equilibrium
- Lower the activation energy
- Stabilise the transition state

They don’t, however, have any effect on the equilibrium position.

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2
Q

What are enzymes without a coenzyme called?

A

Apoenzymes.

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3
Q

What are enzymes with a coenzyme called?

A

Haloenzymes

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4
Q

What are enzymes with a cofactor called?

A

Metalloenzymes

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5
Q

What is a cofactor?

A

Cofactors = Usually metal ions (form coordination centre)

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6
Q

What is a coenzyme?

A

Coenzymes = Organic molecules (change charge or structure during reaction)

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7
Q

What is an active site? What does it contain?

A

Active site = Where substrate binds an enzyme, contains essential amino acids

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8
Q

What is the lock & key model?

A

Lock & Key model = Active site of unbound enzyme is complementary to the shape of the substrate

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9
Q

What is the induced fit model?

A

Induced fit model = Binding of a substrate induces a conformational change in the enzyme. Results in a complementary fit.

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10
Q

What carries out phosphorylation reactions?

A

Protein kinases

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11
Q

What carries out dephosphorylation?

A

Phosphatase enzymes

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12
Q

What is the Vmax of a reaction?

A

Vmax = maximal rate of reaction at unlimited substrate concentration

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13
Q

What is Km?

A

Km = Michaelis constant = 50% Vmax

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14
Q

Lineweaver Burk plots are used instead of hyperboles (michaelis menten) because it is easier to read Vmax and Km. How can the Vmax and Km be read off of a Linweaver Burk plot?

A
  • Vmax is the intersection of the straight line with the Y axis
  • Km is the line’s intersection with the X axis
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15
Q

What are the 2 main types of enzyme inhibition?

A
  • Competitive inhibitors
  • Non-competitive inhibitors
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16
Q

Where do competitive inhibitors bind?
What is the effect of competitive inhibitors on Vmax?
What is the effect of competitive inhibitors on Km?

A
  • Binds to active site
  • Vmax remains the same
  • Km varies
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17
Q

Where do non competitive inhibitors bind?
What is the effect of non competitive inhibitors on Vmax?
What is the effect of non competitive inhibitors on Km?

A
  • Binds to site other than active site
  • Vmax varies
  • Km stays the same
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18
Q

Enzymes can undergo allosteric control. What relationship is then seen between the reaction velocity and substrate concentration?

A

A sigmoidal relationship is formed

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19
Q

Where is cholesterol present?
What does cholesterol form a component of?
Cholesterol is a precursor molecule for?

A
  • Cholesterol is present in cell membranes
  • It is a component of myelin sheath
  • It is the precursor molecule for:
    • Steroid hormones
    • Vitamin D
    • Bile acids
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20
Q

Where are triglycerides present?
What is a use of triglycerides?

A

Triglycerides:
- Present in all cell membranes (lipid bilayer)
- Highly concentrated energy stores

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21
Q

What are isozymes?

A

These are isoforms of enzymes. They:
- Catalyse the same reaction
- Have different properties and structures

They are synthesised at different stages in development, in different tissues and in different cellular locations.

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22
Q

What 2 physical conditions can affect the activity of an enzyme?

A

Temperature & pH

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23
Q

What is a nucleoside?

A

Nucleoside = Base + sugar

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24
Q

What is a nucleotide?

A

Nucleotide = Nucleoside + Phosphate

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25
What are the 2 purines?
Adenine & Guanine
26
What are the 3 pyrimidines?
Uracil, Thymine & Cytosine
27
In the sugar-phosphate backbone, what bond forms between the 3’ OH group and the 5’ triphopshate?
A phosphodiester bond
28
What are the 2 base pairings?
A=T C=G
29
What is the basic DNA structure?
DNA forms an anti-parallel double helix: - One strand 5’ to 3’, other strand 3’ to 5’
30
What direction does DNA replication always take place in?
Always in a 5’-3’ direction
31
What is required to start replication?
A DNA primer
32
What are 2 properties of DNA replication?
It is a semi conservative process. And takes places bidirectionally, starting at several points in the genome.
33
There are 4 main enzymes involved in DNA replication. These can be seen below: - DNA Polymerase - Primase - Helicase - Ligase What are the functions of each of these enzymes?
DNA Polymerase = Catalyse DNA Replication in 5’-3’ direction Primase = Catalyses primer synthesis Helicase = Unwinds DNA double helix Ligase = Joins Okazaki fragments
34
Directionality of Leading strand vs Lagging strand
Leading strand has a free 3’ end, only one RNA primer required. Lagging strand has to be replicated in short, Okazaki fragments
35
Steps involved in DNA Replication
1. DNA primer required 2. Helix unwound by Helicase 3. Replication fork with leading and lagging strand 4. Leading synthesised in 5’ to 3’ direction. Catalysed by DNA polymerase. 5. Lagging is synthesised in Okazaki fragments which are then joined by DNA Ligase.
36
What are the 3 main classes of RNA?
3 main classes: - rRNA (ribosomal) - tRNA (transfer) - mRNA (messenger)
37
What is the function of rRNA?
rRNA combines with proteins to form ribosomes where protein synthesis takes place.
38
What is the function of tRNA?
tRNA carries amino acids to be incorporated into protein. Anticodons consists of 3 nucleotides.
39
What is the function of mRNA?
mRNA carries genetic information for protein synthesis.
40
How many types of RNA Polymerases can be found in: A) Prokaryotic cells B) Eukaryotic cells
A) Prokaryotic cells have 1 type B) Eukaryotic cells have 3 types: - Pol I, II, III - Pol II synthesises all mRNA
41
Where does RNA Polymerase bind on DNA? What is required for this binding?
RNA Polymerase binding: - Detects initiation sites on DNA (promoters) - Requires transcription factors
42
What are the 3 stages involved in transcription?
- Initiation - Elongation - Termination
43
What is involved in the initiation stage of transcription?
- Selection of first nucleotide of growing RNA - Required additional general transcription factors
44
What is involved in the elongation stage of transcription?
- Addition of further nucleotides to RNA chain - RNA synthesised in 5’ to 3’ direction
45
What is involved in the termination stage of transcription?
Release of finished RNA
46
What is TFIID?
TFIID = General transcription factor required for all Pol II transcribed genes.
47
What are exons vs introns?
Exons are coding regions and introns are non coding regions.
48
What is removed from the mRNA strand before translation into the protein?
Introns are removed by splicing.
49
How many amino acids are there? Therefore, how many possible codons are there?
- 20 amino acids - 64 possible combinations
50
What are the main components for translation of mature mRNA into proteins?
Amino acids, tRNAs, aminoacyl-tRNA synthetases, protein factors, ATP/GTP, ribosomes and mRNA
51
What is the start codon?
AUG is the start codon
52
What are the 3 stages of translation?
- Initiation - Elongation - Termination
53
What provides the energy for initiation of translation?
GTP provides energy
54
What is involved in the initiation of translation?
- Ribosomal subunit binds to 5’ end of mRNA, moves along until start codon found. - Initiator tRNA pairs to start codon - Large subunit joins assembly and initiator tRNA is located in the P site
55
What is involved in the elongation stage of translation?
- Elongation factors brings aminoacyl-tRNA to A site - Second elongation factor regenerates the first to pick up next aminoacyl-tRNA
56
What enzymes catalyses peptide bond formation between amino acids in P and A sites?
Peptidyl transferase
57
What is involved in the termination stage of translation?
- Occurs when the A site of ribosome encounters a stop codon (UAA, UAG, UGA) - Finished protein cleaves off tRNA
58
What are the 3 tRNA binding sites on the ribosome?
Exit, Peptidyl, Aminoacyl
59
Post/co-translational refers to the method in which the proteins are translocated. What is the difference between these 2 methods?
Free ribosomes in cytosol proteins for - cytosol, nucleus, mitochondria = Post translational Bound ribosomes on rough ER - plasma membrane, ER, Golgi, Secretion = Co translational
60
The genetic code is known as degenerate and unambiguous. What do these terms mean?
Degenerate = many amino acids have more than 1 codon Unambiguous = each codon codes only for 1 amino acid
61
What are the 5 different categories of single gene mutations?
1. Point = Single based change 2. Missense = Change in amino acid sequence 3. Nonsense = New stop codon 4. Silent = No effect due to degeneracy of genetic code 5. Frameshift = Affects amino acid sequence there after
62
What are the 4 types of chromosomal mutations?
1. Deletions 2. Duplications 3. Inversions 4. Translocations
63
What are the primary, secondary, tertiary and quaternary structures of a protein?
Primary structure: - Amino acids sequence Secondary structure: - H bonds - a helix & b sheets Tertiary structure: - 3D structure, R group interactions, prosthetic groups - Ionic bonds, Hydrophobic bonds, covalent bonds, disulphide bridges, LDFs Quaternary structure: - Multiple subunits e.g haemoglobin
64
What are catabolic vs anabolic reactions?
Catabolism: - Breakdown, release energy - Exergonic & oxidative Anabolism: - Synthesis, use energy - Endergonic & reductive
65
What is the 1st law of thermodynamics? What is the 2nd law of thermodynamics?
1st law = Energy is neither created nor destroyed (just converted into different forms) 2nd law = Energy transformation is never 100% efficient, proportion of energy becomes unstable
66
What is enthalpy? What is entropy?
Enthalpy = Heat content Entropy = Disorder
67
At equilibrium /\G is equal to?
/\G = 0 The reaction is readily reversible.
68
What is the /\G of a exergonic reaction? Can an exergonic reaction occur spontaneously?
Negative /\G Yes, it can occur spontaneously
69
What is the /\G of an endergonic reaction? Can an endergonic reaction occur spontaneously?
Positive /\G No, it cannot occur spontaneously
70
What are the standard conditions in the body?
T = 298K 1 atm 1M reactants pH = 7
71
What does reaction coupling involve? What is an example of this?
Cellular processes that are unfavourable can take place, driven by coupling to highly favourable processes. ATP breakdown is coupled with the highly exergonic reaction to regenerate ATP.
72
What are bases vs acids?
Base = Proton acceptor Acid = Proton donor
73
What does the strength of an acid depend on? What is it measured by?
Depends on how readily it donates a proton to a base. Measured by the acid dissociation constant Ka: - Ka = [H+][A-]/[HA] - pKa = -log10[Ka] Larger Ka, smaller pKa = Stronger acid Smaller Ka, larger pKa = Weaker acid
74
What is pH?
pH is the measurement of the number of protons in a solution.
75
What are buffers?
A buffer is a solution that can resist small changes in pH.

Foundations (Year 1) (12 decks)

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