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AMS Semester 1 > PM-155 > Flashcards

PM-155 Flashcards

1
Q

What was Frederick Griffith’s transforming principle (1928)?

A

Bacteria are capable of transferring genetic information through transformation.

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2
Q

What were the 2 strains of streptococcus pneumoniae and what were there properties?

A

Smooth- secrete a polysaccharide capsule, produce smooth colonies, virulent
Rough- unable to secrete a capsule, produce colonies with rough appearance, avirulent

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3
Q

What was the outcome of Griffith’s experiment?

A

R strain bacteria had been transformed by S strain bacteria. R strain bacteria inherited some ‘transforming principle’ from the heat killed S strain, which made them virulent. He assumed the transforming principle was genetic material. The newly acquired trait of pathogenicity was inherited by all the descendants of the transformed bacteria.

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4
Q

What was the hypothesis for Avery’s transformation experiment (1944)?

A

The genetic material of the cell is either protein or nucleic acid (DNA or RNA).

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5
Q

What was the method for Avery’s transformation experiment (1944)?

A

Remove lipids and sugars from a solution of heat killed S cells. Proteins, RNA and DNA remain. Treat solutions with enzymes to destroy protein, RNA or DNA. Add to culture containing R cells. Observe for transformation by testing for the presence of virulent S cells.

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6
Q

What was the conclusion for Avery’s transformation experiment (1944)?

A

No S cells appeared in the solution with no DNA- transformation requires DNA, therefore it is the genetic material of the cell.

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7
Q

What are the steps in a lytic cycle?

A

The phage injects its DNA. The phage DNA circularises. Phage DNA and proteins are synthesised and assembled. The cell lyses, releasing phages.

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8
Q

What was the method for Hershey Chase’s Bacteriophage experiment (1952)?

A

One phage protein labelled with 35S. One phage DNA labelled with 35P. The phages infect cells and agitation frees outside phage parts from the cell. The centrifuged cells form a pellet. Radioactive phage protein found in the liquid but phage DNA found in the pellet.

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9
Q

What was the conclusion from Chase’s experiment?

A

Only phage DNA entered the host cell so DNA must be the molecule carrying the genetic information.

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10
Q

What did Erwin Chargaff prove in 1950?

A

The base composition varies between species. Each species the % A & T and C & G are roughly the same.

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11
Q

How many hydrogen bonds are formed between cytosine and guanine?

A

Three.

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12
Q

How many hydrogen bonds are formed between adenine and thymine?

A

Two.

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13
Q

Who produced X ray diffraction images of DNA and what did they prove?

A

Rosalind Franklin proved that DNA was helical in shape and there was a double helix. It showed the width of the helix and the spacing if the bases.

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14
Q

What did James Watson and Francis Crick prove in 1953?

A

They used the X-ray diffraction images to show that a purine and pyrimidine bonded together as it matched the width of the helices on the X-ray.

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15
Q

What is semi conservative replication?

A

The complementary strand allows each strand to serve as a template for the synthesis of the other.

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16
Q

What is the model of conservative replication?

A

Two parental strands reassociate after acting as templates for new strands.

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17
Q

What is the model of dispersive replication?

A

Each new strand contains a mixture of old and newly synthesised DNA.

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18
Q

What was the Meselson and Stahl experiment?

A

Proved semi conservative replication. Bacteria cultured in medium containing 15N then transferred to medium containing 14N. After two replications and centrifuges the bands of DNA showed semi conservative replication.

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19
Q

Define genome.

A

Complete set of an organisms DNA.

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20
Q

How many base pairs does a human cell nucleus contain?

A

6.4 billion.

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21
Q

What is interphase?

A

G0- Cell cycle arrest.
G1- Cellular contents excluding the chromosomes are duplicated.
S- Each of the 46 chromosomes is duplicated by the cell.
G2-The cell checks the duplicated chromosomes for errors and makes repairs.

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22
Q

What is mitosis?

A

Separation of DNA and formation of two new cells.

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23
Q

What are the steps of DNA replication?

A

Primase synthesises RNA primers required to start DNA replication. Helices untwist the double helix at the replication fork. Single-strand binding proteins prevent the parent strands repairing. Topoisomerase relieves the strain by breaking, swivelling and rejoining the DNA strands.

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24
Q

What happens to the leading strand during replication?

A

Primase starts a RNA primer in the 5’-3’ direction. Constructed in the direction of the replication fork. DNA polymerase III catalyses addition of complementary nucleotides to the 3’ end of primer. One primer and continuous elongation. DNA polymerase I removes nucleotides of primer and completes the DNA strand. DNA ligase closes the backbone.

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25
Q

What happens to the lagging strand during replication?

A

Runs in the direction away from the replication fork. Synthesised in Okazaki fragments of 100-200 nucleotides in Eukaryotes. DNA polymerase III adds new nucleotides to 3’ end. DNA polymerase I removes nucleotides of the primer and completes the DNA strands. DNA ligase closes the backbone.

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26
Q

What happens as each nucleotide joins?

A

Two phosphate groups are lost as a molecule of pyrophosphate, which generates energy.

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27
Q

What is the function of helicase?

A

Unwinds parental double helix at replication fork.

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28
Q

What is the function of single strand binding proteins?

A

Binds to and stabilises single-branded DNA until it can be used as a template.

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29
Q

What is the function of topoisomerase?

A

Relieves overwinding strain ahead of replication fork.

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30
Q

What is the function of primase?

A

Synthesises RNA primer at 5’ end of leading strand and each Okazaki fragment of the lagging strand.

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31
Q

What is the function of DNA polymerase III?

A

Uses parental DNA as a template to synthesise a new DNA strand by adding nucleotides to 3’ end (RNA primer or DNA).

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32
Q

What is the function of DNA polymerase I?

A

Removes RNA nucleotides of primer from 5’ end and replaces them with DNA nucleotides.

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33
Q

What is the function of DNA ligase?

A

Joins Okazaki fragments of lagging strand. Joins 3’ end of DNA that has replaced the primer on leading strand.

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34
Q

What is the damage that requires mismatch repair?

A

Base mismatches caused by replication errors or small insertions/ deletions due to replication slippage.
Increases the risk of developing disease, particularly cancers of the colon.

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35
Q

What is mismatch repair?

A

MMR proteins remove and replace incorrectly paired nucleotides that have been missed by the proof reading ability of DNA polymerase.

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36
Q

What is the damage that requires base excision repair?

A

Small scale, single base modification (oxidation, deamination, methylation etc). Single base deletion- an abasic site resulting from hydrolysis.

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37
Q

What is base excision repair?

A

Damaged bases are removed by a specific DNA gycosylase, which cleaves the sugar-base bond to delete the base. The sugar-phosphate residue is removed. DNA polymerase inserts the correct base.

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38
Q

What is the damage that requires a nucleotide excision repair?

A

Thymine distorts DNA by UV damage. Bulky, helix-distorting DNA lesions (large DNA adducts; DNA intrastrand cross-lines, and so on)

39
Q

What is a nucleotide excision repair?

A

A nuclease enzyme cuts the damaged DNA strand at two points. Repair synthesis by a DNA polymerase fills the gap. DNA ligase seals the remaining nick.

40
Q

What happens when a double strand DNA breaks?

A

Can be highly dangerous if left unprepared. Requires homologous recombination or non homologous end joining.

41
Q

What is homologous recombination?

A

Accurate DNA repair that requires a homologous intact DNA strand to act as a template. It uses a DNA strand from the undamaged sister chromatid to act as a template for guide repair.

42
Q

What is non-homologous end joining?

A

Broken ends are fused together by specific proteins. No template strand required.

43
Q

Define gene expression.

A

Process by which information from the gene is used to synthesise functional gene product (protein).

44
Q

What is alkaptonuria?

A

Patients inherit a non-functional enzyme. Inability to break down tyrosine and phenylanine. Build up of homogentisic acid and its oxidised form alkapton, which turns black on exposure to air when excreted in the urine.

45
Q

What is a prototroph?

A

Any microorganism that can synthesise all its amino acids.

46
Q

What is an auxotroph?

A

A mutant organism that has lost the ability to synthesise certain substances required for growth.

47
Q

How does a eukaryotic gene code for a set of closely related polypeptides?

A

Alternative splicing.

48
Q

How many protein coding genes does the human genome have?

A

20,000.

49
Q

What is tRNA?

A

Transfer RNA. Adapter molecule involved in decoding genetic information during protein synthesis.

50
Q

What direction is mRNA synthesised during transcription?

A

5’ to 3’ direction.

51
Q

What is the gene structure of eukaryotes?

A

Long non coding strands called introns that lie between coding regions called exons. RNA polymerase transcribes the whole gene from the start site to the new polydenylation (poly-A) site. Introns are spliced out during RNA processing in eukaryotes.

52
Q

How is transcription initiated?

A

Common promoter element in eukaryotes is called a TATA box. Transcription factors recognised bind to the promoter element. TFs must be able to gain access and bind to the promoter element to recruit other proteins and RNA polymerase to initiate transcription.

53
Q

What is the process of transcription?

A

After RNA polymerase II has blinded to the promoter region to form a transcription initiator complex, elongation in 5’ to 3’ direction occurs. In eukaryotes transcription terminates at the polydenylation signal sequence (AAUAAA). Once the mRNAhas been transcribed from the DNA, this is the primary transcript.

54
Q

What is mRNA splicing?

A

Introns are removed and exons are joined together. There are donor and acceptor sites at the exon-intron boundaries, which RNAs within the spliceosome can recognise and they cleave the mRNA at the boundaries and then piece the axons together.

55
Q

What is alternative splicing?

A

Creates different polypeptide isoforms by using different exons within a gene.

56
Q

What are the three steps of mRNA processing?

A

1) Capping: 5’ end receives a cap. This prevents degradation and facilitates attachment to ribosomes.
2) Polydenylation: 3’ end receives a poly-A tail, which helps stabilise mRNA and facilitates movement of mRNA out of nucleus.
3) RNA spliced to produce mature transcript.

57
Q

What are the 3 steps in translation?

A

INITIATION
ELONGATION
TERMINATION

58
Q

What is a tRNA molecule?

A

Single RNA strand (~80 nucleotides long). Translates the mRNA codon into an amino acid.

59
Q

What is a wobble base?

A

The third position on the mRNA codon (3’ end). The base pairing is relaxed.

60
Q

What is initiation?

A

The ribosome scans along the mRNA until it REACHES THE START CODON AUG. That brings the initiation tRNA containing methionine that initiates translation.

61
Q

What is elongation?

A

Once the beginning of the polypeptide starts to form the next tRNA comes in. ANTI-CODON of tRNA binds to codon on mRNA at the A SITE- a peptide bond forms between the amino acids. Peptide bond formation between A SITE & P SITE. The empty tRNA in the P site is moved to the EXIT site and released.

62
Q

What is termination?

A

STOP CODON on mRNA in A site accepts a protein called RELEASE FACTOR. This hydrolyses the bond between tRNA in the P site and last amino acid. Polypeptide chain is released and the assembly dissociates.

63
Q

Where does transcription occur?

A

Gene is transcribed to mRNA in the nucleus.

64
Q

Where does translation occur?

A

mRNA is translated into a polypeptide chain in the cytoplasm attached to a ribosome.

65
Q

What is universal genetic code?

A

61 triplets code for amino acids. 3 stop codons.

66
Q

What is the first amino acid?

A

Methionine (AUG)

67
Q

How much of the human genome codes for proteins?

A

Approximately 1.5%.

68
Q

What is the structure of a nucleosome?

A

8 histone proteins. Two H2A, H2B, H3 and H4. Linker DNA between nucleosomes would be open for transcription and for TFs to get in. These nucleosomes can move up and down the DNA double helix so areas can open up for transcription.

69
Q

What is the structure of a genome?

A

DNA wraps twice around histone proteins to form a nucleosome. Histone proteins are positively charged and DNA is negatively charged.Nucleosomes wrap around themselves to form a helical fibre. The fibre organises itself into loops, scaffolds and domains to form the final chromosome structure.

70
Q

What is eurochromatin?

A

Less condensed.
Transcriptionally active.
Contains virtually all eukaryotic gene.

71
Q

What is heterochromatin?

A

Highly condensed nucleoprotein.
Largely transcriptionally inactive.
7% of our genome.

72
Q

What are homologous chromosomes?

A

Maternal & Paternal.
Same length and centromere position.
Carry genes controlling same inherited characteristics but different traits.

73
Q

What are telomeres?

A

Protect the ends of the chromosomes.
Tandem repeats of TTAGGG.
Single stranded overhand that folds back and base pairs with complementary strand. Stem cells produce telomerase to maintain the telomere.

74
Q

What is telomerase?

A

A strand of parent DNA remains unreplicated. Telomerase binds and adds deoxyribonucleotides to the end of parent DNA. Additional repeats are added. Primase, DNA polymerase and ligase synthesise the lagging strand in the 5’ to 3’ direction restoring the original length of chromosome. PREVENT LOSS OF GENES

75
Q

How does chemical modifications or changes to protein structure affect chromatin condensation?

A

Effects on packaging and gene activity.

76
Q

Why transposition?

A

Can increase genetic diversity.
Exon or gene duplication can enable the production of more/less altered or new polypeptide chains.
Insertion mutations.
Pathogenicity.

77
Q

What are transposons?

A

Cut and paste or copy and paste mechanism using transposes. Either DNA sequence is moved or copied from one site to another.

78
Q

What are retrotransposons?

A

More common mechanism. RNA is transcribed and converted to DNA by reverse transcriptase. Inserted into the new site.

79
Q

What are the properties of mitochondrial DNA?

A

Single circular double stranded DNA molecule
16,569 base pairs.
13 protein coding genes (no introns)
2 ribosomal RNA genes
22 transfer RNA genes
Encode proteins and RNAs important for replication protein production and respiration
Inherited solely from mother

80
Q

Define epigenetics.

A

Mechanisms that alter gene expression without altering the underlying DNA sequences.

81
Q

What types of gene regulation occur in the nucleus?

A 
Chromatin remodelling- enable it to open up to allow TFs to get in to promoter regions.
DNA methylation- long term, switches areas off so they can't be transcribed
Transcription factors
RNA processing (alternative splicing)
82
Q

What types of gene regulation occur in the cytoplasm?

A

Degradation/ inhibition of mRNA
Protein processing/ modification
Degradation of protein

83
Q

What is chromatin remodelling by histone modification?

A

Protruding N-terminal tails on the histone proteins are subject to histone modification at specific amino acid positions.
Acetylation and phosphorylation- act to neutralise the positive charge on the histone proteins.
Methylation of various amino acids along the histone protein tail can shut down or open up transcription.

84
Q

What is DNA methylation?

A

Methylation of cytosine residues when they come before a guanine residue. They are called CPG dinucleotides. Represses transcription. DNA methylation attracts other proteins which block TFs from binding to the promoter region.

85
Q

Define Transcription Factors.

A

Bind to specific DNA sequences within promoters and enhancer control elements to increase or decrease gene expression- activators or repressors.

86
Q

What are the types of TFs?

A

General- can work on host of different promoters on genes. Able to switch on multiple genes.
Specific- work in specific cell types to only switch on specific genes
Activator- activate gene transcription
Repressor- repress gene transcription

87
Q

What are enhancers?

A

Regulatory sequences upstream or downstream or downstream of the transcription start site.
DNA looping: The TFs bound to the enhancers bind to the TFs bound to the promoter element. The enhancer bound TFs ( activators or repressors) control the rate of gene expression.

88
Q

What is competitive DNA binding?

A

Activator and repressor TFs compete for binding to the same regulatory sequence. Both bind to the DNA but the repressor binds to the activation domain of the activator, inhibiting it.

89
Q

How does alternative splicing work?

A

Proteins bind to the regulatory sequences within the primary transcript to control the splicing pattern. SPLICE ENHANCER SEQUENCES- hold spliceosome in place. SPLICE SUPPRESSOR SEQUENCES- remove the spliceosome.

90
Q

What is RNA interference?

A

micro RNA- coded for by nuclear genome, then bind into a hairpin loop
small interference RNA- double stranded RNA molecules naturally in cell or introduced experimentally
Silence gene expression by degrading mRNA or inhibiting translation

91
Q

Define differential gene expression.

A

Expression of different genes by cells with the same genome.

92
Q

What is the genome structure of prokaryotes?

A

1 double stranded circular chromosome and plasmids. No histone proteins- DNA packaged by supercoiling. Plasmids may provide cell with advantage e.g antibiotic resistance.

93
Q

What is transcription/translation in prokaryotes?

A

Transcription proceeds through a terminator sequence where the RNA polymerase detaches from the DNA and an mRNA transcript is created. The mRNA transcript can be immediately translated without additional processing (no splicing).

AMS Semester 1 (2 decks)

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