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3G1 Bioengineering > Exam qs > Flashcards

Exam qs Flashcards

1
Q

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

A

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

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2
Q

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

A

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)

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3
Q

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

A

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.

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4
Q

What’s cDNA

A

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

mRNA that has been reverse transcribed into DNA

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5
Q

What enzyme is essential to making cDNAs

A

Reverse transcriptase

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6
Q

What is a stop codon

A

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

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7
Q

Are catabolism and anabolism linked?

A

Yes, by high energy intermediates such as ATP

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8
Q

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

A

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

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9
Q

What is ADP

A

When you remove a phosphate from ATP you get ADP

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10
Q

What are the variable regions on an antibody

A

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

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11
Q

What binds the different parts of an antibody together

A

Disulfide Bridges

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12
Q

Ways the structure of an antibody aids its function.

A

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

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13
Q

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

A

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

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14
Q

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

A

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

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15
Q

What is dynamic programming

A

An algorithmic technique used for sequence alignment

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16
Q

What’s the flux control coefficient

A

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
Q

What is regulation of metabolic pathways and why is it needed

A

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
Q

What is allosteric regulation

A

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

19
Q

Two types of metabolic regulation

A

Mass action and Allosteric

Mass action - regulated by the chain speed as a whole

Allosteric - signal is sent back

20
Q

Factors that can reduce the yield in a metabolic pathway

A

Side products being formed

Allosteric regulation that inhibits previous steps

21
Q

What is the elasticity coefficient

A

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
Q

Methods to increase the yield in a metabolic pathway

A

Optimisation and modulation of pathways

Enzyme engineering

Synthetic protein scaffold

23
Q

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

A

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
Q

Examples of proteins that recognise specific DNA sequences

A

Restriction enzymes
RNA polymerase
DNA recombinase

25
Q

What does NADH do in metabolism

A

Carries electrons from one reaction to another

26
Q

What group does ATP carry in its high energy linkage

A

Phosphate

27
Q

What does yeast do in aerobic conditions

A

Enters TCA cycle

28
Q

What does yeast produce in anaerobic conditions

A

Ethanol and/or lactate

29
Q

What is an operon

A

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

30
Q

What enzyme transcribes the information in an operon

A

RNA polymerase

31
Q

2 steps in protein synthesis

A

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
Q

Where does RNA polymerase on the operon

A

The promoter - sequence of DNA where RNA polymerase can bind

33
Q

What does RNA polymerase make

A

mRNA which can be used to make a protein

34
Q

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

A

A Repressor - stops mRNA being made therefore no proteins

35
Q

What is the purpose of the lac operon

A

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
Q

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

A

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
Q

What is the RBS on an operon

A

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
Q

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

A

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

Inefficiency/incompatibility of genetic elements from different organisms

39
Q

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

A

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

3G1 Bioengineering (3 decks)

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