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Baz: Semester 2 > Integrity: Maintaining the Genome & Maintaining the Cell > Flashcards

Integrity: Maintaining the Genome & Maintaining the Cell Flashcards

1
Q

Broadly describe the structure of a chromosome in decreasing size

A

Chromosome -> wound up chromatin fibre -> nucleosome (DNA wrapped up around protein complex) -> DNA

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2
Q

What is chromatin?

A

This is the substance in a cell nucleus which is formed by DNA wound around protein cores.

When unravelled it resembles beads on a string

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3
Q

What is a nucleosome?

A

One unit of chromatin

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4
Q

Why is chromatin formed?

A

It allows DNA to occupy a smaller space

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5
Q

What is a nucleotide?

A

The basic building block of DNA

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6
Q

What are the three componants that make up a nucleotide?

A
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7
Q

What is the name of the sugar present in a nucleotide?

A

2-deoxyribose

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8
Q

The bases in nuceotide are either ____ or ____

A

Pyrymidines or Purines

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9
Q

How do you know if a base is either a pyrimidine or a purine?

A
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10
Q

Is cytosine a pyrimidine or a purine?

A

Pyrimidine

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11
Q

Is adenine a pyrimidine or a purine?

A

Purine

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12
Q

Is thymine a pyrimidine or a purine?

A

Pyrimidine

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13
Q

Is guanine a pyrimidine or a purine?

A

Purine

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14
Q

How are DNA strands bonded?

A

Hydrogen bonds between the bases

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15
Q

What bases pair with which bases?

A

Remember : GCAT

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16
Q

How do the three componants of a nucleotide come together to form DNA?

A

The back bones are made of the phosphate and sugar which are bonded by the bases

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17
Q

What is a nucleoside?

A

Just the sugar and base componant

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18
Q

How are nucleosides named?

A

Not going to bother remembering this. Just a refresher

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19
Q

On what carbon groups are the sugar linked by the phosphodiesters?

A

5,3

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20
Q

What is the advantage to linking the sugars by two different carbon groups?

A

It gives DNA direction, it wll always go from a 5 end to a 3 end. The 5 end has a free phosphate while the 3 end has an OH

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21
Q

What defines the DNA sequence?

A

The order of the bases

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22
Q

As well as protein what else is found in a nucleosome?

A

Histones - these bind the DNA to the protein

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23
Q

How many histones are in a nucleosome and what are the 4 names?

A
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24
Q

What is the advantage to the 4 unique base pairings?

A

Each strand can be used as a template to replicate it’s partner

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25
Q

How does DNA begin splitting for replication?

A

Origins of replication are areas where splitting can begin with the help in initiator proteins

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26
Q

Where does replication begin?

A

Replication fork begin at the origin of replication and branch out bi-directionally unzipping as they replicate

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27
Q

Most important enzyme in DNA replication?

A

DNA-polymerase

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28
Q

Which direction in DNA synthesised in?

A

A 5’ -> 3’ direction

DNA ploymerase adds new nucleotides to the 3’ end of the growing chain

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29
Q

How does the polarity of the two newly synthesised DNA strands at a replication fork differ?

A

Opposite polarity

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30
Q

What problem does the opposite polarity of the two new replicated strands creat?

A

DNA can’t replicate bidirectionally

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31
Q

How is the problem of directional synthesis overcome to ensure by-directional syntheses?

A
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32
Q

What are the lagging strands called?

A

Okazaki fragments

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33
Q

What is the enzyme that joins together okazaki fragments?

A

DNA ligase

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34
Q

DNA polymerase can only continue existing chains, how are new chains started?

A
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35
Q

What enzyme helps unwind the double helix?

A

DNA helicase

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36
Q

DNA polymerase is highly accurate

However if an error does occur a missmatch actually wont bind, so how does it stay? (the occasional mutation must occure for evolution)

A

If unrepaired it is cemented in in the next round of replication

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37
Q

How are errors usually spotted?

A

By proofreading

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38
Q

What is the occurence of errors with and without proofreading

A

1 in 10^7 bases without proofreading

In reality with proofreading more like 1 in 10^9 bases

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39
Q

How does DNA missmatch repair occure?

A

DNA repair proteins bind forming an “oxbow lake” and cutting off the error

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40
Q

5 Things that can damage DNA

A
  • Synthesis missmatch
  • UV light
  • Radiation
  • Chemicals
  • Cellular metabolism
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41
Q

How does UV light specifically damage DNA

A

It created Thymne dimers

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42
Q

How does common damage repair look like? Why is it often not that bad?

A

It’s not that bad because information is redundent in the other strand so it can often remake it self the same

43
Q

What is Xeroderma pigmentosum

A

Genetic defect
* Affected individuals cannot
repair thymine dimers (caused by UV)
* Severe skin lesions, including
skin cancer

44
Q

How does mitochondial DNA differ from nuclear DNA?

A
45
Q

Only other place DNA is found that isn’t the nucleus?

A

Mitochondria

46
Q

What is RNA?

A

It is a short single stranded copy of a single gene (one strand of DNA will contain many many genes)

It is then used to make proteins

47
Q

What are six differences between DNA and RNA

A
48
Q

What does RNA contain in place of thymine?

A

Uracil

49
Q

What are the codes for the four bases on RNA?

A

GCAU

Thymine replaced by uracil

50
Q

What is the difference between deoxyribose and ribose?

A
51
Q

When transcribing DNA which strand is the coding strand and which is the template strand?

A

The one being copied into RNA is the coding strand

The one being used to make the copy is the template

52
Q

Names for which strand is being copied and which is used to make the copy?

A

Copied: coding strand
Other: template strand

53
Q

Another name for the template and coding strands?

A

Coding strand: sense strand

Template strand: anti-sense strand

54
Q

What is the enzyme that synthesises RNA?

A

RNA polymerase

55
Q

What direction is RNA synthesised?

A

5’ to 3’

same as DNA polymerise

56
Q

What does DNA stand for?

A

deoxyribonucleic acid

57
Q

What does RNA stand for?

A

Ribonucleic acid

58
Q

Difference between mRNA and RNA

A

mRNA is the main type of RNA and is the instructions or blueprint for the protein to be synthesised int he ribosome

Other types are tRNA (transfer RNA) and ribosomal RNA (rRNA) which help the ribosome actually build the proteins

59
Q

What is the specific enzmyme that makes mRNA?

A

RNA polymerase II

60
Q

All cells contain all genes. So how do cells become specialised?

A

Through gene expression

Gene expression turns on certain genes

61
Q

What are promotors and enhancers?

A
62
Q

What are transcription factors?

A
63
Q

Three steps to gene expression

A
  • Promotors and enhancers in place for gene you want expressed
  • Transcription factors bind to the promotors and enhancers
  • RNA polymerase can then bind to transcription start site
64
Q

Often gene expression is more complicated that simply ON or OFF. What are the different ways the same gene can be expressed to make differing RNA?

A

Expression of a single gene can be controlled at various
levels to give different products:

  • alternative promoters - different regions of DNA that can initiate transcription of a gene found upstream of the gene resulting in different RNA, basically just starting transcription at different points
  • alternative splicing - can splice different parts of the same gene together
  • alternative polyadenylation - the polyadenylation can cut off differing sections of the transcribed RNA essentially changing the tail length of the RNA
65
Q

What are the key sections which lead to splicing?

A

Introns and Exons

Introns: parts which are non-coding
Exons: coding parts

66
Q

How do introns and exons lead to alternative splicing?

A

The whole thing is initially transcribed into a primary transcript.

Later the introns are removed by something called the spliceosome creating the final peice of mRNA.

Different spliceosomes recognise different boundaries between introns and exons known as splice sites. Splice sites can also remove exons sandwiched between introns resulting in multiple different sequences of mRNA

67
Q

What is Capping and Polyadenylation?

A

Its is the sealing on the RNA.

Capping is at the 5’ end and polyadenylation is at the 3’ end

68
Q

What does the cap consist of?

A

a guanine nucleotide that has a methyl group attached to the 5’ end of
the RNA in an unusual way

69
Q

What is Polyadenylation?

A
  • A polyA tail is a string of adenylate residues added to the 3’ end of anmRNA
  • Not found on rRNAs or tRNAs
70
Q

How can alternative polyadenylation create differing final RNAs?

A

The polyadentlation cuts off a portion of the transcribed RNA (clevage). By changing the point at which it does this it can create differing mRNA sequences

71
Q

What are the purposes of the untranslated regions?

A
  • 5’ untranslated (5’UTR) is the region of an mRNA that is
    found upstream of the translated region
  • function of 5’UTRs is mostly unclear, may affect
    translational control
  • 3’ untranslated (3’UTR) is the region of an mRNA that is
    found downstream of the translated region
  • 3’UTRs can determine the stability of the mRNA
72
Q

What is a non-coding RNA?

A

This is any RNA that is not used to make proteins but instead the RNA is the final product in itself.

Examples being rRNA - makes up the structure of the ribosome and help catalyse protein synthesis

Spliceosomes - these are made up of RNA

73
Q

Where is RNA transcribed and processed and where is it translated?

A

In the nucleus: transription and processing

In the cytoplasm: translated into proteins

74
Q

Translation: what is a codon?

A

A condon is a set of three bases which corresponds to a specific amino acid

75
Q

How many possible codons are there?

A

4 different bases, and each codon is made of three bases read in an order of 5’ to 3’

Therefore there is 4^3 combinations = 64 codons

61 codons specify for 1 in 20 amino acids

3 are stop codons

76
Q

Why is readng frame important?

A

Because a codon is made of three bases there are three possible reading frames that will give completely different amino acids

77
Q

How does the 5’ cap relate to translation?

A

Thought to be involved in initiation

Most mRNAs need a 5’cap to be translated efficiently (there
are some exceptions e.g. polio virus RNAs are uncapped)

78
Q

How is translation initiated?

A

the pre-initiation complex (PIC) scans the mRNA for the translational start site (AUG codon)

The PIC consists of the 40S ribosome (small ribosome) bound to elongation
initiation factor 2 (eiF2), GTP and most importantly the initiator MET-tRNA.

MET-tRNA has the anti codon to AUG and binds it.

Once it binds it this draws in 60S ribosome which combines to form the final 80S ribosomal complex.

Now translation can begin (elongation)

79
Q

What codon is the initiation codon?

A

AUG

Also known as the Kozak (Consensus) sequence

80
Q

What come after initiation of translation?

A

Elongation

81
Q

What is elongation?

A

All the reactions involved in translation from the formation of the
first peptide bond to the addition of the last amino acid

82
Q

How does elongation work?

A

Each unique aminoacyl-tRNA can come into to bind to it’s corresponding codon if it’s being read by the ribosome 80S complex.

Once it binds to the corresponding mRNA codon it attaches it’s amino-acid to the growing polypeptide chain

83
Q

How is the correct amino acid bound to the correct tRNA in order to make the corresponding aminoacyl-tRNA?

A

It is bound using the corresponding tRNA-synthetase enzyme

Example shown is the amino acid tryptophan and the tRNA-tryptophan. The corresponding enzyme is therefore tryptophanyl tRNA synthase

84
Q

What is the function of the 40S (small) ribosome vs the 60S (large) ribosome?

A

The 40S helps match the correct aminocytl-tRNA to the correct codon

The 60S ribosome catalyses formation of peptide bonds that
covalently link amino acids

85
Q

Elongation in more detail, what are the three docking sites and how does the process work?

A

There are three docking sites:

E - ejection
P - polypeptide
A - amino acid

  1. The correct aminocytl-tRNA binds to A dock
  2. polypeptide is transfered from the peptidyl-tRNA (P dock) to aminocytl-tRNA by the creation of a new bond
  3. Large subunit translocates
  4. Small subunit translocates
86
Q

What is the complex called that is dock in the P-dock?

A

Peptidyl-tRNA

87
Q

Three stop codons?

A

UAA, UAG and UGA

88
Q

What happen when a stop codon is reached (termination)

A

The stop codon aren’t recognised by of the aminoactyl-tRNAs.

Instead they are recognised by a single class 1 release factor
protein (eRF) which transfers a hydroxyl group from water to
hydrolyse the polypeptide-tRNA linkage and, thereby, lead to
release of the polypeptide chain from the last tRNA.

89
Q

What is the name of the thing that recognises the stop codon?

A

Class 1 release factor
protein (eRF)

90
Q

What defines cell differentiation?

A

The presence of different transcription factors

You can put the nucleus of a liver cell into a muscle cell and it will still become a muscle cell because of the presence of muscle specific transcription factors MyoD

91
Q

How do transcription factors know what genes to bind to?

A

They can form bonds with specific promotors ascciated with different genes

92
Q

What is the difference between a promotor and a transcription factor?

A

Promotor: Like a shop sign but for genes. The sign specifying “hey it’s me, toy shop”. Present in all DNA (the shopping center)

Transcription factor: Looks for specific promotors. Shoppers who are looking for toy shops. If they are the only shoppers prensent in the shopping center then the shopping center basically becomes a toy shop

93
Q

When differentiated cells divide they generally remain the same cells. How?

A

The genes activated by transcription factors generally contain instruction to create more of the same transcription factors. The transcription factors are inherited by the daughter cells

94
Q

What is chromatin remodelling?

A

This is where transcription factors can actually re-model chromatin and histones in order to further express their target genes

95
Q

What is DNA methylation?

A

This is a form of cell differentiation memory through silencing.

By adding (and maintaining) a methyl group to certain part of the DNA this can block the binding of transcription factors thus preventing them from accessing genes.

96
Q

What is X-inactivation?

A

Eaely on in female mammal embryonic development one of the X-chromosomes randomly condenses in each cell.

These then clone themselves and females end up with a patchwork of X-chromosomes from each parent.

97
Q

What is a multipotent hematopoietic stem cell?

A

A multipotent stem cell can be inferred by the
ability of a single stem cell to reconstitute a
complete blood & immune system when
transplanted to an individual lacking bone
marrow

98
Q

What is GATA1

A

This is the transcription factor which defines a RBC.

It binds to the genes expressing alpha-globin and beta-globin

99
Q

What are stromal cells?

A

These are cells present in bone marrow that encourage stem cells to remain stem cells and not differentiate

100
Q

What is assymetric stem cell devision vs independent choice?

A

Assymetic: fate deceided on devision, one will always be a stem cell and one always a differentiated cell

Independent: both new cells can be either stem cells or differentiates cells witht he choice being influenced by outside factors. This is more flexible to needs

101
Q

What are paneth cells?

A

These are found in the gut next to intestinal stem cells.

They release WNT which make stem cells proliferate and maintain the stem cell state

In the abscence they will differentiate

Their prescence means that you get intense proliferation from the site of peneth cells which then gradually differentiate into intestinal epithelial cells as they get pushed aways from the paneth cells sites

102
Q

What is the link between stem cells and cancer?

A

Many cancer occure at sites containing stem cells as all these cells of proliferation is a breeding ground for uncontrolled proliferation

E.g. intestinal, epithelial, bone marrow and reproductive organs

103
Q

What is Familial adenomatous polyposis coli (FAP)

A

This is an inherited conditon making someone more predisposed to colon cancer.

It results in a deletion or inactivation of one copy of the APC gene. If the other then becomes deleted they have no APC.

If you remember the WNT pathway APC inhibits proliferation and in turn is inhibited by WNT. Lacking apc therefore leads to excessive proliferation and you end up with giant intestinal cryps which become cancerous polyps.

104
Q

Describe the intestinal crypt?

A

Corn

Baz: Semester 2 (42 decks)

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