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Flashcards in Exam qs Deck (39):
1

What needs to be added to single stranded dna dissolved in water to allow synthesis of complimentary strand

Buffer (to get correct pH for enzyme)
Complimentary dna primer
dNTPs
DNA polymerase

2

Mutations that could stop a trait being observed when cloned by PCR

Insertions/deletions
Introduction of a stop codon
Synonymous substitution of a base for another (don’t alter amino acid sequences- silent mutation)
Non synonymous codon changes (result in a biological change)

3

How Illumina gets around ambiguity that arises when reading dna with sequence variations

Where as Sanger aggregates the different fragments, leading to ambiguity when reading at the site of a sequence variation, Illumina reads the sequence of a single molecule at each sequencing reaction.

4

What’s cDNA

Complimentary DNA: DNA synthesised from a single stranded RNA (eg messenger RNA mRNA)

mRNA that has been reverse transcribed into DNA

5

What enzyme is essential to making cDNAs

Reverse transcriptase

6

What is a stop codon

A sequence of DNA that is needed to stop translation or making of proteins by stringing amino acids together.

7

Are catabolism and anabolism linked?

Yes, by high energy intermediates such as ATP

8

Equations for the complete catabolism of glucose by yeast in the absence of oxygen

Yeast in absence of oxygen means 100% alcoholic fermentation —> glycolysis (glucose to pyruvate) and pyruvate to ethanol

Overall equation:

Glucose + 2 ADP + 2 P -> 2 Ethanol + 2CO2 + 2 ATP

9

What is ADP

When you remove a phosphate from ATP you get ADP

10

What are the variable regions on an antibody

The ends of both the heavy and light chains that determine the antigen specificity of the antibody

11

What binds the different parts of an antibody together

Disulfide Bridges

12

Ways the structure of an antibody aids its function.

Two recognition sites aids the formation of antibody- antigen complexes

Disulfide Bridges keep the four peptide chains in a robust structure

Light and heavy combination allows more diversity

Variable regions allow for high antigen specificity


13

What’s humanising an antibody and how can it be achieved

Needed to prevent the human immune system of an antibody having a negative reaction

By: substituting the rodent complimentary determining/variable regions into a human antibody

Engineering recombinant mice that have human antibody genes

14

How to avoid designing primers that are likely to suffer from “self-priming”

Avoid designing a pair of primers that match each other well, especially ones that are G/C strong. Can be done by shortening the primers to remove the self priming bases

15

What is dynamic programming

An algorithmic technique used for sequence alignment

16

What’s the flux control coefficient

The degree of control that each enzyme exerts on a metabolic pathway flux

The percentage change in the pathway flux when a 1% change in the activity of a pathway enzyme is achieved

17

What is regulation of metabolic pathways and why is it needed

Regulation of an enzyme in a pathway is how it’s activity is increased and decreased in response to signals

Needed to react to changing external conditions to maintain a constant set of internal conditions, homeostasis

18

What is allosteric regulation

The regulation of an enzyme by binding an effect or molecule at a site other than the enzyme’s active site

19

Two types of metabolic regulation

Mass action and Allosteric

Mass action - regulated by the chain speed as a whole

Allosteric - signal is sent back

20

Factors that can reduce the yield in a metabolic pathway

Side products being formed

Allosteric regulation that inhibits previous steps

21

What is the elasticity coefficient

A local property indicating how responsive the rate of a reaction is to a fractional change in one of its substrates/products or effectors.

22

Methods to increase the yield in a metabolic pathway

Optimisation and modulation of pathways

Enzyme engineering

Synthetic protein scaffold

23

Ways to calculate the yield of a new pathway/effect of a modification without running experiments

Flux balance analysis (FBA)/ Metabolic Flux analysis (MFA) using knowledge of the stoichiometry of the system.

This will give optimal solution so may not be exact to real life.

24

Examples of proteins that recognise specific DNA sequences

Restriction enzymes
RNA polymerase
DNA recombinase

25

What does NADH do in metabolism

Carries electrons from one reaction to another

26

What group does ATP carry in its high energy linkage

Phosphate

27

What does yeast do in aerobic conditions

Enters TCA cycle

28

What does yeast produce in anaerobic conditions

Ethanol and/or lactate

29

What is an operon

A functioning unit of DNA containing a cluster of genes under the control of a single promoter

30

What enzyme transcribes the information in an operon

RNA polymerase

31

2 steps in protein synthesis

Transcription and translation

Transcription is where DNA is unwound and RNA polymerase creates a complimentary a single strand of mRNA (remember RNA has U instead of T nucleotides)

Translation is where the mRNA is sent to cytoplasm where it binds with ribosomes, the site of protein synthesis.

32

Where does RNA polymerase on the operon

The promoter - sequence of DNA where RNA polymerase can bind

33

What does RNA polymerase make

mRNA which can be used to make a protein

34

What can bind at the operator position on the operon to stop RNA polymerase transcribing the gene

A Repressor - stops mRNA being made therefore no proteins

35

What is the purpose of the lac operon

Lac Z,Y,A are the genes in the lac operon and encode for enzymes that break down lactose into sugars so that it can be metabolised by bacteria

36

What does the lac I gene do in the context of the lac operon

The Lac I gene has its own promoter and encodes for the repressor for the lac operon, in the situation where lactose isn’t present so the enzymes needed to break it down aren’t necessary

37

What is the RBS on an operon

The ribosome binding site is a sequence of nucleotides upstream of the start codon of an mRNA transcript that recruits the ribosome during the initiation of protein translation.

38

Factors that can contribute to the failure of a gene to express

Weak promoter: inefficient transcription.
Weak RBS: inefficient translation.

Inefficiency/incompatibility of genetic elements from different organisms

39

Simple way to increase gene expression of a particular gene of an operon

If you want to produce twice as much of something, have the gene twice on the operon!