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3G1 Bioengineering > Deck 2 > Flashcards

Flashcards in Deck 2 Deck (25):
1

What’s a catabolic process

The break down of complex organic compounds into simpler building blocks

Likely to generate energy

2

What’re anabolic processes

The synthesis of cell constituents from simple building blocks

Likely to utilise energy

3

What’s an endergonic metabolic process

One which requires the absorption of energy, as it’s energy unfavourable due to products having greater free energy

4

What’s an exergonic metabolic process

One which releases energy as it is energy favourable

5

Example of a compound used as high energy intermediates

ATP

6

Purpose of high energy intermediates in metabolic processes

They allow endergonic reactions to be indirectly coupled to exergonic (energy favourable) actions via a small numb of intermediate compounds. This balances the core enters requirements of the cell.

Without them the endo and exergonic reactions would have to be directly coupled which would be much more complex.

7

What is the Michaelis constant Km

The substrate concentration at which the reaction rate is half of Vmax, the maximum reaction rate achieved by the system.

Therefore, a substrate with a lower Km will outcompete one with a higher Km.

8

What is upregulation

The process of increasing the response to a stimulus

9

What is the concentration control coefficient

How sensitive the concentration of a metabolite (substance formed in/necessary for metabolism) is to a fractional relative change in a parameter eg activity of an enzyme

10

How to find control coefficient

Cause a perturbation in activity of the enzyme (small upregulate/downregulate) and observe the response in the concentration/flux.

11

Ways to increase the activity of a particular reaction pathway

Upregulate the activity of realer enzymes

Use molecular scaffolds to keep certain reactants/enzymes close together.

12

Pros and cons of using microbes to produce biofuels

Easy to culture
Easy genetic engineering

Often lack appropriate metabolic pathways
Need fuel source

13

Pros and cons of using plants to create biofuels

Can photosynthesise
Good farming knowledge

Use up arable land, drives up food costs

14

What’s the point of dna sequencing

To find the sequence of nucleotides that in a piece of DNA

15

Steps in Sanger sequencing

DNA sample to be sequenced is combined with a primer, DNA polymerase and free nucleotides (dATP, dTTP, dGTP, dCTP), then into 4 separate flasks the chain terminating versions of each nucleotide eg ddATP (dideoxy nucleotide) is added to each different it in much lower conc than that normal nucleotides. The subpopulations in each different flask is coloured to label which base is causing the termination.

Mixture is then heated to denature and separate the two strands.

Then cooled so the primer can attach to the single stranded template.

Temp is raised again so that the polymerase can add nucleotides to the chain starting from the primer. This happens until it adds a dideoxy nucleotide instead of a normal one, terminating the chain

Cycle repeated a number of times, so that it can be guaranteed that a dideoxy nucleotide will have been incorporated at every single position on the target dna.

Gel elctrophoresis is then used to separate the different sized fragments

16

How long of a chain can Sanger sequencing read

400-900 base pairs

17

What are the three parts to a deoxyribonucleotide

A nitrogenous base
A deoxyribose sugar
One phosphate group

18

How long of a chain can illuminate sequencing read

100-150 base pairs

19

Steps of illumina sequencing

Sample prep - pure dna gets chopped into smaller pieces and given adapters/indices/regions complimentary to the flow cell oligonucleotides

Clustering generation - the mix is run through the flow cell and the fragments join to the “lawn” of oligonucleotides at the complementary sites. Polymerase synthesises the template strand, and then the original is denatured and washed away.
Bridge amplification: The strand then folds over and creates a bridge to the 2nd type of oligonucleotide. Polymerase then makes it a double stranded bridge and then is denatured to create two single stranded copies. Repeated many times to result in clonal amplification of all fragments.
Reverse strands are then cleaved and washed off. 3’ ends are blocked to stop unwanted priming

Sequencing - fluorescently tagged nucleotides then are added to the chain, and when each is added the chain is excited by a light source which causes a characteristic fluorescent signal to be emitted. (Sequencing by synthesis)

Data analysis is then used together the many millions of individual reads

20

Sanger vs Illumina
Sequencing

Sanger better for small number of samples and longer reads

Illumina when you need a large number of reads (10^6-9) to provide good coverage of a genome

21

How to read genome that is millions of base pairs long with sequencing that only reads hundreds

Overlap between reads is used

22

Gene structure of prokaryote vs eukaryotes

Prokaryote: circular gene structure, high gene density, no introns (non coding sequences), organised into operons.

Eukaryotes: multiple linear chromosomes, regulatory regions are more complex and are more spaced out with introns, no operons

23

What’s the structure of an antibody

A Y shaped molecule made of four components, 2 light and 2 heavy chains. The light chains lie at the top of the Y at the ends of the heavy chains, and create an antigen binding site here.

24

How are antibodies used in the immune system

The antibodies are specific to a given antigen so can be used to locate foreign objects in the body. They then destroy these targets.

25

If you design an antibody in another animal but it is then rejected by the human immune system, how could you get around this?

The foreign antibodies may trigger an immune response in the human patient due to the non human component of the antibody. Can ‘humanise’ the antibody , replacing regions of the antibody with human antibody regions while preserving the antigen regions of the animal antibody.