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Growth and Development > DNA and RNA synthesis > Flashcards

DNA and RNA synthesis Flashcards

1
Q

What is personalised medicine?

A
  • Move away from ‘one size fits all’ approach to treatment and care of pxs with particular condition
  • we are all unique, health being determined by differences, lifestyles & environment
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2
Q

100,000 Genomes Project

A

100,000 Genomes Project aims to bring benefits of personalised medicine to NHS
-Aim to complete by end of 2017 from 70,000 pxs
By combining and analysing info about genome, patterns identified to help determine individual risk of developing disease; detect illness earlier; determine most effective interventions to help improve health
-e.g. medicines, lifestyle choices, simple changes in diet

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3
Q

Protein synthesis

A

DNA –> transcription –> mRNA –> translation –> protein
Transcriptoin in nucleus
Translation in cytoplasm

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4
Q

Genome is fixed, cells are dynamic

A

Genome: static, every cell in our body has copy of same genome
Cell: dynamic, responds to external conditions.
-most cells follow cell cycle of division
-cells differentiate during development

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5
Q

How much of genome is translated into proteins?

A

3%

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6
Q

What are pseudogenes?

A

Section of chromosome that is an imperfect copy of functional gene
-Related to real genes and contain biological and evolutionary histories within their sequences

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7
Q

How much of genome is transcribed but not translated?

A

25% of the genome

Not associated with protein-coding genes

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8
Q

How many non-functional pseudogenes in the genome?

A

~20,000

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9
Q

ENCODE project

A

Encyclopaedia of DNA Elements project

  • systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification
  • assigned biochemical functions for 80% of genome
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10
Q

Differences between mRNA and DNA

A

mRNA is shorter than DNA (contains info to make one single polypeptide chain i.e. one protein)
DNA = 2 strands in double helix, mRNA = 1 strand
DNA = adenine, guanine, cytosine, thymine
RNA = adenine, guanine, cytosine, uracil
Ribose (RNA): OH gp on 2’ C
Deoxyribose (DNA): H hp on 2’ C

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11
Q

How do thymine and uracil bind to adenine?

A

Via H-bonds

Very similar

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12
Q

What is transcription?

A

Process whereby information in a gene in a DNA strand is transferred to an RNA molecule

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13
Q

Coding and template strand

A

Genetic info carried on coding strand, other one template.

-the strand that serves as coding template for one gene may be non-coding for other genes in same chromosome

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14
Q

mRNA sequence complimentary/ identical to which DNA strand

A

Complimentary to template strand

Identical to coding strand (except from T-U)

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15
Q

How to find start of gene on coding strand of DNA

A

RNA polymerase binds to promoter sequences

-one or more short sequences upstream of start of each gene i.e. slightly closer to 5’ end

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16
Q

RNA polymerase

A
  • synthesis of RNA requires DNA-dependent RNA polymerase
  • does not require primer but does need DNA template
  • 3 found in eukaryotes : I, II and III
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17
Q

RNA polymerase I

A

Nucleolar region of nucleus, transcribes large ribosomal RNA

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18
Q

RNA polymerase II (view pic on Word)

A

mRNA precursors

  • composed of several subunits
  • requires several accessory proteins (transcription factors)
  • all added to complex in defined order to initiate & carry out transcription
  • TFIID recognises TATA box and ensures correct site is used
  • enzyme wraps around both strands and is big enough to enclose promoter and beginning of gene
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19
Q

RNA polymerase III

A

Small RNAs (tRNA), 5S ribosomal RNA and other small DNA sequences

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20
Q

What do most RNA polymerase II genes have?

A

TATA box 25 - 35 bases upstream of initiation site

-affect transcription rate and determines location of start site

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21
Q

Promoters

A

Basal promoter contains TATA box and found in all protein-coding genes

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22
Q

What differs from gene to gene

A

Structure and associated binding factors

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23
Q

Enhancers

A

DNA sequences which can control efficiency and rate of transcription
-regulate expression of genes in specific cell type and control timing of gene expression (effects can be powerful)

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24
Q

What type of elements are promoters and enhancers?

A

‘Cis’ acting elements

-on same molecule of DNA as the gene they regulate

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25
Q

Strong or weak promoters and enhancers

A

According to effects on transcription rates and thus gene expression
-changes in promoter strength, deleterious effects on cell–> disease

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26
Q

Tumour promoting viruses and promoters

A

Transform healthy cells by inserting strong promoters near growth-stimulating genes
-translocations in some cancer cells place genes that should be ‘turned off’ in proximity of strong promoters and enhancers

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27
Q

Where is promoter necessary to start transcription located?

A

Usually on 5’ side of gene to be transcribed

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28
Q

Where can enhancers affect transcription from?

A

From afar
5’ or 3’ transcription start site
In introns or exons
Non-coding strand

29
Q

Are enhancers and promoters always close together?

A

Can be 1000s of nucleotides away from promoters, brought into close proximity by looping of DNA
-looping due to interactions between proteins bound to enhancers and those bound to promoter

30
Q

Protein facilitating/ ihibiting looping

A

Facilitating: activators
Inhibiting: repressors

31
Q

Enhancers and TF

A

Enhancers contain binding site sequences for transcription factors and enhance/ upregulate transcription
-active enhancers bound by activating TF and brought into proximity of target promoters by looping

32
Q

Basal transcription factors

A

TF bind to promoter and enhancer sequences and recruit RNA polymerase. Basal TF required at every promoter site for RNA polymerase interaction (TFIID)

33
Q

Are TF cis or trans

A

TFs are ‘trans’ acting factors as encoded by different gene to that being regulated

34
Q

What happens once polymerase is attached

A

Unwinds double helix over short length and splits them apart

-bubble of about 10 bases

35
Q

What bond does RNA polymerase catalyse?

A

Sugar-phosphate bond between 3’ -OH of ribose and 5’ PO4

36
Q

What does order of bases in DNA template strand determine?

A

Order of bases in transcript

37
Q

Where are nucleotides added to?

A

The 3’ -OH of growing chain

38
Q

What happens when polymerase moves down DNA?

A

DNA zips back up - bubbles moves along chain and growing RNA tail detaches from template

39
Q

How is RNA a 3D structure if it is only single stranded?

A

Base-pair interactions between complementary sequences found elsewhere on same molecules allow RNA molecule to fold.
Determined by sequence of nucleotides
-folding similar to way polypeptide chain folds in protein

40
Q

What functions does folding ability of RNA give?

A

Some RNA molecules have structural and catalytic functions

41
Q

Termination of pol I genes

A

By a termination factor

Leads to hair pin loop which causes RNA polymerase to pause and release transcript

42
Q

Termination sequence pol III genes

A

Includes a polyuracil stretch

Causes RNA pol to pause and release transcript

43
Q

Transcription of pol II genes

A

Can continue for 100s or 1000s of nucleotides beyond end of coding sequence

44
Q

Mature pol II mRNAs

A

Polyadenylated at 3’ end = poly(A) tail

AAAAAAAAAAAA

45
Q

Polyadenylation and termination

A

Same concensus sequence
Sequence AAUAAA found near polyadenylation site of eukaryotic mRNAs
-required for accurate and efficient cleavage and polyadenylation of premRNAs in vivo

46
Q

DNA to mRNA as RNA pol moves down gene

A
  1. CAP on 5’ end to stabilise mRNA (essential for transport of RNA out of nucleus)
  2. Alternative splicing
  3. Poly(A) tail on 3’ end - cleavage at AAUAAA (stop codon) by endonuclease then multiple adenosine (up to 250) added
    - needed for release of polymerase from DNA template
47
Q

Capping pre-mRNA

A

Takes place during transition from transcription initiation to elongation, when pre-mRNA only 20-40 nucleotides long

  • protects from degradation
  • serves as assembly point for proteins needed to recruit small subunit of ribosome to begin translation
48
Q

Alternative splicing

A

Several variants of same protein produced by one gene

Mutations at splice sites can result in aberrant or truncated proteins that do not function properly

49
Q

Alternative splicing - transciptome and proteome diversity

A
  • alternative selection of splice sites within a pre-mRNA
  • leads to production of different mRNA isoforms of gene
  • alters compositiong and function of encoded protein
  • plasticity allows for disease development - cancer
50
Q

What is a spliceosome and how is it formed

A

Exons defined by short, degenerate classical splice site sequences at intron/ exon borders
Components of basal splicing machinery bind to classical splice-site sequences and promote assebly of multi-component splicing complex - spliceosome

51
Q

Spliceosome function

A
  1. Recognition of intron/ exon boundaries

2. Catalysis of cut and paste reactions which remove non-coding introns and stitch flanking exons back together

52
Q

Spliceosome types

A

Two types

  • major: removes 99.5% of introns
  • minor: removes remaining 0.5%
53
Q

What do spliceosomes contain

A

Proteins (over 300 different proteins associated with human spliceosome) and RNAs

54
Q

Spliceosome and disease

A
  • mutations altering splice site or spliceosome proteins
  • mis-splicing = rapid degeneration of mRNA
  • mis-regulation of spicing factor levels = cancer
55
Q

Types of RNA

A
  1. mRNA
  2. rRNA
  3. tRNA
  4. Non-coding RNA (ncRNA)
  5. Small nuclear RNA (snRNA)
  6. Small nucleolar RNA (snoRNA)
  7. Micro RNA (miRNA)
56
Q

mRNA specificity

A

Specific for only certain types of cells, encoding proteins needed by ‘specialised’ cells e.g. mRNA for haemoglobin in precursors of RBCs

57
Q

mRNA size and variety

A

Wide range of sizes reflecting size of polypeptide

Many common to most cells, ‘housekeeping’ proteins needed by all cells e.g. enzymes of glycolysis

58
Q

Types of rRNA in eukaryotes

A

4 kinds
18S - 1 of these along with other proteins make the small subunit of the ribosome
28S, 5.8S & 5S - one each of these, along with 45 other proteins used to make the large subunit of the ribosome

59
Q

What is rRNA?

A

Builds ribosomes, the machinery for synthesising proteins by translating mRNA

60
Q

What does S stand for in types of rRNA?

A

Svedberg unit

Sedimentation rate, related to mass and shape

61
Q

How many types of tRNA in a typical eukaryotic cell?

A

32

Each kind carries, at 3’ end, one of 20 amino acids i.e. most amino acids have more than one tRNA

62
Q

What is non-coding RNA

A

Around 2% of genome corresponds to protein-coding sequences remainder - ‘junk’ sequence
-previously pathologic alterations due to aberration of gene sequence or altered promoter activity

63
Q

How much of genome is actively transcribed?

A

90%, this part is more complex

64
Q

What can ncRNA do

A

Can modify protein levels by mechanisms independent of transcription
Plays major roles in cellular physiology, development, metabolism and is implicated in disease process

65
Q

What is snRNA

A

Small nuclear RNA
Transcription of genes for mRNA, rRNA and tRNA produces large precursor molecules or primary transcripts
Must be processed in nucleus to allow export to cytosol of functional molecules
Some processing steps mediated by snRNAs
Several snRNAs are part of spilceosome

66
Q

snoRNA

A

Small nucleolar RNA
Participate in making ribosomes by helping cut large precursor of 28S, 18S and 5.8S
Modify many nucleotides in rRNA, tRNA and snRNA e.g. can add methyl groups to ribose
Implicated in alternative splicing of pre-mRNA
Template for synthesis of telomeres

67
Q

How are snoRNAs made in vertebrates?

A

Made from introns removed during RNA processing

68
Q

miRNA

A

Micro RNA
Tiny RNA molecules regulate gene function post-transcriptionally
Very small, 18-25 nucleotides
Bind to mRNA and cause degradation - inhibits protein synthesis
Regulation of developmentally timed events
Exhibit tissue-specific and/ or developmental stage-specific expression
Cancer & tooth development

69
Q

How many protein-coding genes are under control of miRNAs?

A

More than 1/3

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