Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Molecular and Cellular Biology > functional genomics 2 > Flashcards

functional genomics 2 Flashcards

1
Q

what is genomics?

A

The study of genes and their functions.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is the genome

A

The genome is the entire DNA content that is
present within one cell of an organism

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What does functional genomics use?

A

uses genomic data to study gene and protein expression and function on a global (genome-wide) scale

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is the focus of study in functional genomics?

A

uses genomic data to study gene and protein expression and function on a global (genome-wide) scale

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is transcriptomics?

A

the whole complement of transcripts in a tissue, organ, or organ system.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is proteomics?

A

the whole complement of proteins in a tissue, organ, or organ system.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Function of large scale, high-throughout assays?

A

track many genes or proteins in parallel under different experimental or environmental conditions (e.g. withsamples from patients and healthy individuals)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Whats the genome wide approach?

A

“genome-wide” approach allows the function of different parts of the genome to be discovered by combining information from genes, transcripts and proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What techniques are used in genome wide approach?

A

Assays to measure changes insynaptic plasticity performed
alongside assays that quantifychanges in proteins involved in a range of pathways e.g.
MAP kinase signalling cascade

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Functional genomics integrates information from various molecular methodologies to …

A

…gain an understanding of how DNA sequence is translated into complex information in a cell
(DNA → RNA → Proteins → biological process)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

slide 6

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Proteins can be separated according to…

A

… their molecular weight

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

electrophoresis is usually conducted in…

A

… a vertical electrophoresis system.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

the matrix where proteins are separated according to their molecular weight is…

A

… polyacrylamide instead of agarose but the principle is the same.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

in gel electrophoresis, the smaller the molecule, the…

A

…faster they will migrate.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

DNA molecules are uniformly charged. What does this mean?

A

the sugar phosphate backbone is negatively charged regardless of DNA sequence.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

DNA molecules are uniformly charged, so…

A

… migration is solely due to molecular weight.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Protein molecules consist of …

A

different amino acids that may have different charges

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

charge of DNA molecules?

A

negative because of phosphates.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Why are the charge differences between amino acids important?

A

The charge differences between amino acids are important in determining protein structure and function but the presence of different amino acids means that proteins do not have uniform charge

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Proteins are denatured prior to…

A

electrophoresis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Proteins are denatured prior to electrophoresis by addition of …

A

…mercaptoethanol and SDS (sodium dodecyl sulphate)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Mercaptoethanol disrupts …

A

disulphide bridges between cysteine amino acid pairs by reducing the double bond - SDS binds all over the protein negating its charge

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

As SDS is negatively charged the presence of excess SDS molecules binding to protein results in …

A

…a uniform negative electric charge on protein molecules

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

MW = ?

A

= molecular weight marker

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Protein gels can be…

A

…blotted

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

the principle of blotting in protein gels is the same as…

A

… DNA and RNA gels.

28
Q

Describe the process of protein gel blotting.

A

Proteins and buffer are forced to migrate through filter paper but proteins are unable to travel through a membrane (PVDF – polyvinylidine fluoride)

This produces a duplicate of the gel on a membrane

29
Q

How is blotting accomplished in protein gels?

A

The difference is that this is accomplished by electroblotting rather than capillary action

30
Q

In the case of Southern and Northern blots we use ….

A

DNA probes to detect the presence of homologous sequences of nucleic acids

31
Q

How do we detect proteins?

A

Using antibodies.

32
Q

proteins can be bound by…

A

… antibodies

33
Q

The vertebrate immune system relies on antibodies to bind to …

A

… antigens

34
Q

The vertebrate immune system relies on antibodies to bind to antigens – these complexes are then recognised by…

A

…components of the immune system where they activate an immune response.

35
Q

If we can bind protein with antibodies and label antibodies (as we label a DNA probe) then…

A

… we have a means of detecting specific proteins in a Western blot.

36
Q

We can make use of the vertebrate immune system to …

A

… generate antibodies

37
Q

The first step in creating an antibody that specifically recognises our protein is to …

A

… express the protein (creating the antigen)

38
Q

Simple cloning techniques allow us to …

A

… insert a gene we want to express into a plasmid

39
Q

If it is downstream of a strong promoter recognised by E. coli then if we transform E. coli with the plasmid…

A

… the protein will be produced.

40
Q

The protein we want antibodies generated against is…

A

… purified and injected into an animal (usually a rat or rabbit)

41
Q

The animal then …

A

… makes antibodies specific to that protein as it recognises the protein as foreign – after several weeks blood is harvested and serum produced.

42
Q

slide 14

A
43
Q

By producing antibodies specific to our protein we have solved one problem …

A

… –we have something that will bind to our protein

44
Q

By producing antibodies specific to our protein we have solved one problem – we have something that will bind to our protein – but we still have another which is…

A

how do we detect binding?

45
Q

The answer lies in using antibodies from …

A

another animal that are raised to the first antibody (if we inject IgG from a rabbit into a goat, the goat will generate antibodies to rabbit IgG)…

46
Q

The answer lies in using antibodies from another animal that are raised to the first antibody (if we inject IgG from a rabbit into a goat, the goat will generate antibodies to rabbit IgG)

If we then collect those antibodies and covalently link another protein on to it that will give us a…

A

colour reaction then we can detect the first antibody.

47
Q

As with a northern blot, spatial expression of the protein can be…

A

… studied.

48
Q

Protein is extracted from…

A

…various tissues.

49
Q

how is protein extracted?

A

this is quite a simple procedure just relying on gently lysing the cells and collecting the protein extract

50
Q

The protein extracts are separated by…

A

…SDS-PAGE and then blotted.

51
Q

As with a northern blot, spatial expression of the protein can be studied

Protein is extracted from various tissues (this is quite a simple procedure just relying on gently lysing the cells and collecting the protein extract)

The protein extracts are separated by SDS-PAGE and blotted

The western blot is then probed with …

A

… primary antibodies and finally with secondary antibodies with an enzymatic tag.

52
Q

slide 15

A
53
Q

In ELISA assays, the same principle as western blotting can be used to …

A

… make detecting protein quantitative

54
Q

Antigen is bound to a surface and then primary antibodies, secondary antibodies, and finally substrate are

A

… added to detect antigen.

55
Q

The same drawbacks for Northern blotting occur with Western blotting and ELISA –

A

it does not say in which cells the protein is expressed and is a ‘rough estimate’ of what is actually going on.

56
Q

In the same way that the presence of RNA can be detected at the cellular level by the use of RNA in situ hybridisation we can examine…

A

… the cellular distribution of proteins

Sections can be taken of an organism and these can be probed with antibodies

57
Q

Proteins are targeted to specific parts of the cell and it is important in our investigation of gene function to find the …

A

… subcellular as well as the cellular location of a protein.

58
Q

slide 17

A
59
Q

The subcellular localisation of proteins can also be

A

analysed using electron microscopy

60
Q

Rather than relying on enzymatic reactions to detect antibody in this procedure

A

small gold particles (10nm) are attached to the secondary antibody and the presence of antibody is seen because gold is ‘opaque’ to the electron microscope

61
Q

The big problem with analysing sections using immunohistochemistry is that …

A

… the cells are dead – remember that the cell is a dynamic environment, proteins don’t just stay in the same place necessarily

62
Q

The big problem with analysing sections using immunohistochemistry is that the cells are dead – remember that the cell is a dynamic environment, proteins don’t just stay in the same place necessarily

In order to analyse what our proteins might be doing in the cell…

A

…we can make use of GFP

63
Q

Protein-GFP fusions can be constructed as for …

A

… promoter-fusions – as long as you can construct this then you can transfect into cells.

64
Q

go look at slide 19

A
65
Q

By re-engineering the GFP protein it has been possible to…

A

… produce proteins that emit light at different wavelengths – red RFP, yellow YFP and blue CFP

66
Q
A

Molecular and Cellular Biology (16 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions