DNA 1

Question 1

No of H bonds between A&T and C&G

Answer 1

A and T: 2

C and G: 3

Question 2

What technique indicated DNA is a helix?

Answer 2

X-ray diffraction

Question 3

Can RNA function as an enzyme?

Answer 3

Yes

Question 4

What is the difference between DNA and RNA?

Answer 4

DNA: maintains protein-encoding info

RNA: carries protein-encoding info and controls how info is used

Question 5

What is the molecular definition or the characteristic of a gene?

Answer 5

• a segment of DNA
• directs the formation of RNA to produce
  protein
• The protein (or functional RNA) creates the
  phenotype
• Information is conveyed by the sequence of the nucleotides

Question 6

What is chromatin composed of?

Answer 6

DNA and associated proteins (mainly histone proteins)

Question 7

How is DNA in chromatin organised?

Answer 7

DNA winds around histone proteins
(nucleosomes),
Other proteins wind DNA more tightly to form a chromosome

Question 8

During mitosis, replication and mRNA
production, DNA is unwound

true or false

Answer 8

True

Question 9

What is the main difference in protein biosynthesis between prokaryotes and eukaryotes?

Answer 9

In prokaryotes, transcription (RNA synthesis) and translation (protein synthesis) are coupled, meaning translation begins while transcription is still ongoing.

Question 10

Prokaryote mRNA is polycistronic while eukaryote mRNA is monocistronic.

True or false

Answer 10

True.

Prokaryote mRNA is polycistronic, meaning one mRNA can encode multiple proteins

Question 11

How are eukaryote mRNA transcripts modified before use as a template for translation?

Answer 11

• Addition of capping nucleotide at the 5’ end
• Addition of polyA tail to 3’ end
• Splicing occurs, removing internal sequences
• Introns are sequences removed

Question 12

Where does mRNA translation occur?

Answer 12

in cytoplasm, within the ribosome

Question 13

In the genetic code, how many start codons and stop?

Answer 13

1 start codon and 3 stop codons

Question 14

What is the universality of genetic code indicate?

Answer 14

evidence of a common ancestor

Question 15

What is the characteristic of the genetic code having some codons that encode same amino acid called?

Answer 15

degenerate

Question 16

Why is the genetic code ‘degenerate’?

Answer 16

some codons encode the same amino acid

Question 17

What assists protein folding?

Answer 17

enzymes and chaperone proteins

Question 18

What happens to misfolded proteins?

Answer 18

tagged and dismantled

Question 19

Give a description of secondary structure of proteins

Answer 19

loops, coils, sheets or other shapes formed by H bonds between neighbouring carbonyl and amino groups

Question 20

Give a description of tertiary structure of proteins

Answer 20

3-dimensional shaped by bonds between pie groups

Question 21

Give a description of quaternary structure of proteins

Answer 21

protein complexes formed by bonds between separate polypeptides

Question 22

Describe the process of misfolded proteins being destroyed

Answer 22

1. ubiquitin* conjugation
2. protein degradation at proteosome

*A small protein that tags misfolded proteins for degradation.

Question 23

What are some diseases caused by misfolding of proteins?

Answer 23

• Alzheimer disease
• huntington disease
• parkinson disease
• prion disease
• lewy body dementia
• familial amyotrophic lateral sclerosis

Question 24

What are prions?

Answer 24

proteinaceous pathogens responsible for a wide range of neurodegenerative diseases in animal and human

Question 25

How are prions formed?

Answer 25

from misfolded, ß-sheet rich, and aggregated conformers (PrPSc) of the host-encoded prion protein (PrPC).

Question 26

Is there genetic material that causes prion replication.

Answer 26

No Prion replication stems from the capacity of PrPSc to self-replicate by templating PrPC conversion and polymerization

Question 27

PrP^Sc (the misfolded and infectious form of the prion protein) and PrP^C (the normal cellular form of the prion protein) have the same amino acid sequence. True or false

Answer 27

True their three-dimensional structures are different, which is what gives them distinct properties.

Question 28

In sickle cell disease, why do red blood cells change shape upon deoxygenation?

Answer 28

because of polymerization of the abnormal sickle hemoglobin

Question 29

What is a restriction enzyme?

Answer 29

endonuclease that recognizes specific short sequence of DNA, usually 4-6 base pairs (bp) in length, and cleaves both strands within this sequence

Question 30

The cuts made by restriction enzymes could be ____________ or ___________.

Answer 30

blunt or sticky

Question 31

What are polymorphisms?

Answer 31

variations in DNA sequences --> point mutations, the substitution of one base for another, deletions and insertions

Question 32

What are restriction fragment length polymorphism (RFLP)?

Answer 32

DNA polymorphism --> restriction fragments different due to mutations create restriction sites or 'remove' restriction site variation in length of restriction fragments is RFLP

Question 33

What is the principle of RFLP based on?

Answer 33

A polymorphic difference in the size of allelic restriction fragments as a result of the presence or absence of a restriction site.

Question 34

How can RFLP be assayed?

Answer 34

Southern blotting or PCR

Question 35

What is an allele?

Answer 35

an alternative version of a gene

Question 36

How can sticky-end restriction fragments covalently link to each other after base-pairing with each other?

Answer 36

covalently linked by the action of DNA ligase

Question 37

Describe the technique of PCR in simple terms

Answer 37

use of polymerase chain reaction (PCR) to allow enzymatic amplification in vitro of specific gene fragments over a million fold.

Question 38

What catalyzes the synthesis of DNA strands in PCR?

Answer 38

heat-stable DNA polymerase

Question 39

What serves as precursors for synthesis of the new DNA strands in PCR?

Answer 39

four deoxyribonucleoside triphosphates

Question 40

Why is PCR preferred over conventional methods for detection and identification of the HIV?

Answer 40

Conventional methods such as Southern blot – DNA hybridization and antigen analysis, are labor intensive, expensive and have low sensitivity

Question 41

What are some conventional methods for detection of HIV?

Answer 41

1. Southern blot – DNA hybridization and 2. antigen analysis

Question 42

Where is DNA extracted from in order to detect HIV infection? What advantage does it serve?

Answer 42

white blood cells --> permits identification of viral infections prior to the presence of antibodies, so called 'seronegative state'

Question 43

What can be used to produce a DNA copy (cDNA) by using mRNA as a template?

Answer 43

reverse transcriptase

Question 44

What is the characteristic of cDNA produced by reverse transcriptase as opposed to DNA fragments cleaved from genome by restriction enzymes?

Answer 44

cDNA produced by reverse transcriptase does not contain introns

Question 45

What is the difference between RT PCR and PCR?

Answer 45

RT PCR: reverse transcription and polymerase chain reaction --> find out how many copies of a particular gene is expressed i.e. quantify RNA --> mRNA---cDNA---more DNA

Question 46

What is RT PCR used for?

Answer 46

Gene expression analysis pathogen detection (SARS) Diagnostics

Question 47

What are short tandem repeats (STR)?

Answer 47

Short (about 2-6 bp) repetitive sequences are found scattered throughout the human genome, at specific location of chromosomes, known as STRs.

Question 48

Do STRs vary from person to person?

Answer 48

Yes. a few nucleotide base pairs repeated in tandem, creating intricate patterns that vary from one individual to the next, except in cases of identical twins

Question 49

Where or how are STRs utilized?

Answer 49

1st step: PCR --> fluorescent labels attached to primers 2nd step: gel electrophoresis or HPLC

Question 50

In what field are STRs (PCR + GE/HPLC) used?

Answer 50

forensic science

Question 51

How has STRs analysis grown over the years? What advantage does it serve?

Answer 51

from 8 loci to 20 loci, improving selectivity and accuracy.

Question 52

Name instances where PCR is used.

Answer 52

1. detection of HIV 2. detection of mRNA of a pathogen (Covid) 3. detection of STR as a forensic tool

Question 53

In what assays could DNA probes be used?

Answer 53

1. Northern blots, 2. Southern blots, 3. in situ hybridization or 4. microarrays

Question 54

What are the steps involved with southern blots?

Answer 54

1. DNA fragments on agarose gel and separate by electrophoresis 2. 'blot' DNA fragments from agarose gel into membrane 3. membrane imprinted with DNA bands 4. add labeled probe to membrane (in buffer solution) 5. detection reveals a band where probe bind to target sequence

Question 55

What is southern, northern and western blot for?

Answer 55

southern: DNA northern: RNA western: protein

Question 56

What are the probes used in southern, northern and western blots?

Answer 56

southern: Labeled DNA northern: Labeled DNA western: Labeled antibodies

Question 57

What are the sources of labels in southern and northern blots

Answer 57

Radioactively and fluorescent labeled deoxynucleotide

Question 58

What are the sources of labels in western blots

Answer 58

Radioactively and fluorescent labeled amino acids

Question 59

At what position can DNA and RNA molecules be labelled?

Answer 59

labelled at their ends or throughout their length

Question 60

How is labelling carried out in DNA and RNA molecules?

Answer 60

using radioactive isotopes, but nonradioactive methods are also available.

Question 61

Describe 'end-labelling' of DNA/RNA molecules

Answer 61

Use enzyme to add a radioactive phosphate to nucleic acids with a free hydroxyl group.

Question 62

Describe random priming to produce DNA probes

Answer 62

Use random hexanucleotides (6-mers) as primers and radioactive nucleotide e.g. dCTP to label the DNA

Question 63

Describe the process of making labelled DNA (DNA probe)

Answer 63

1. denature and anneal DNA of interest in presence of random hexanucleotides 2. klenow subunit of DNA polymerase with dATP, dCTP, dGTP and labelled cCTP 3. extention