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Biology 12U - 2024 > Unit 3: DNA > Flashcards

Unit 3: DNA Flashcards

1
Q

Which scientists were credited with deducing the structure of DNA in 1953?

A

James Watson and Francis Crick

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2
Q

What is DNA composed of?

A

a deoxyribose sugar, a phosphate group, and a nitrogenous base; together these make a nucleotide
DNA is a nucleotide polymer

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3
Q

Characteristics of DNA:

A

DNA is a thread-like molecule: 1 strand of DNA from one cell is about 1.6m
It is twisted in a clockwise direction to form a double helix
DNA consists of 2 antiparallel strands of nucleotides
5’—–3’
3’—–5’
The 5’ end terminates with a phosphate group
the 3’ end terminates with the hydroxyl group of the sugar

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4
Q

Explain complementary base pairing:

A

Only certain nitrogenous base pairing prodcue stable bonds
Adenine bonds with thymine A-T
Cytosine bonds with guanine C-G

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5
Q

Explain purines and pyrimidines:

A

Adenine and guanine are purines: having a double ring structure
Cytosine and thymine are pyrimidines: having a single ring structure
The complementary base pairing maintaining a constant width in the DNA molecule:
5’-AGTACGAGTTT-3’
3’-TCATGCTCAAT-5’

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6
Q

What are the 3 forces contributing to molecular stability of the DNA molecule?

A

a) Phosphodiester linkages:
- Link the sugar/phosphate of one nucleotide to another (stabilizing the ‘handrails’
b) Hydrogen bonding:
- Keeps the 2 strands together as well as stabilizing the inner core
c) Hydrophilic/Hydrophobic reactions
- Causes the bases (hydrophobic) to remain inside the structure while the phosphate group and sugar (hydrophilic) face out into the watery nucleus of the cell (similar to the cell membrane)

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7
Q

If the nucleotides of all the chromosomes in a genome could be stretched out in one large double helix….

A

They would measure 1.8m in length… but an individual nucleotide is 5um (micrometres)

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8
Q

What are Histones?

A

Every 200 nucleotides, DNA is coiled around a group of 8 stabilizing proteins called histones (positively charged)
The complex of histones supporting coiled DNA is called nucleosomes
final chromosome structure is obtained by supercoiling of chromatin fibres

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9
Q

Who discovered semi-conservative replication?

A

Meselsohn + Stahl in 1957

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10
Q

What did Meselsohn and Stahl do?

A

They grew e.coli bacteria in a nutrient medium rich in N15 (heavy isotope of N-meaning it has a higher atomic mass) for several generations to ensure that the 15N would be incorporated into the DNA
THe bacteria were then transferred to a culture medium containing the light isotope 14N (regular N)
Centrifugation was used to isolate the DNA strand
(centrifugation uses contrifugal force and buoyant force to seperate material of differing densities.

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11
Q

In semi-conservative replication, what do the parental strands act as?

A

Involves seperating the two parental strands and building a new complementary replacement strand for each. The two parental strands thus act as templates for replication and remain seperated from each other, incorporated into 2 new molecules.

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12
Q

What is semi-conservative replication?

A

a mechanism of DNA replication in which each of the two strands of parent DNA is incorporated into a new, double stranded DNA molecule

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13
Q

What is DNA replication?

A

Semi-conservative
Each new DNA strand is composed of an existing (parent) half and a newly synthesized (daughter) half combined together
experiments conducted by Meselson and Stahl confrimed this (1957)

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14
Q

Initiation: Seperating the parent strands

A
  • Protiens bind to specific cites on the DNA known as replication origins
  • DNA HELICASE: unwinds the double helix by breaking hydrogen bonds
    SINGLE STRANDED BINDING PROTIENS: keep the DNA strands seperated by blocking reformation of hydrogen bonds
    DNA GYRASE and TOPOISOMERSE: relieves tension in the strands by cutting DNA (allowing the strands to untwist and swivel aorund) and then reseals the cut strands
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15
Q

Elongation - Building complementary strands

A

DNA POLYMERASE III: builds complementary strand
a) only synthesizes DNA in the 5’ to 3’ (thus adds free DNTP to the 3’ end of the elongated strand)
b) requires an existing starting point for attachment - supplied by an RNA primer inserted on the DNA template by a PRIMASE enzyme.
c) uses the energy from the breaking of phosphate bonds to join nucleotides together

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16
Q

What are the Leading and Lagging stands?

A

LEADING STRAND: strand which uses the 3’ - 5’ template strand and is synthesized continuously (5’ to 3’) in the direction of the replication fork.
LAGGING STRAND: - strand which uses the 5’ to 3’ template strand and is synthesized discontinously (5’ to 3’) in short fragments called okazaki fragments in the opposite direction of the replication fork.

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17
Q

What is the function of DNA polymerase I?

A

Removes DNA primers from the leading strand and fragments of the lagging strand and replaces them with the correct deoxyribonucleotide

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18
Q

What is the function of DNA ligase?

A

Joins the okazaki fragments together via phosphodiester bonds

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19
Q

What is termination?

A

As strands are built, they automatically rewind to form double helix

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20
Q

What do DNA polymerase III and I do to ensure accuracy?

A

DNA polymerase III and I can recognize whether hydrogen bonding has taken place. (proof reads strands and puts nucleotides correctly)
If not, a mismatch has occurred and polymerase excises incorrect base and inserts correct one.

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21
Q

What are telomeres?

A
  • Long sequences of repetitive non-coding DNA that act as buffer zones at the ends of chromosomes that help to guard against the loss of valuable genetic material during replication.
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22
Q

DNA Vs. RNA

A

Sugar: DNA-Deoxyribose RNA-Ribose
Structure: DNA-Double helix RNA-Single helix
Size: DNA: large molecule (can be thousands of nucleotides long) RNA: smaller molecule (transcribes only a section of DNA)
Amount: DNA-few molecules of cell RNA-many molecules in the cell
Where: DNA-nucleus RNA-nucleus and cytoplasm
Kinds: DNA-one type RNA-3 types (mRNA, tRNA, rRNA)
Nitrogenous Bases: DNA-A,C,G,T RNA-A,C,G,U

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23
Q

What is a gene?

A

A sequence of nucleotides in DNA or RNA that encodes the synthesis of a protein and are not spaced regularly along chromosomes

Size of the genome and number of genes is not directly related.

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24
Q

What is an exon?

A

a coding region

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25
Q

What is an Intron?

A

Introns

non-coding regions

In general, the frequency and the length of introns is loosely related to the development and complexity of the organism
Yeast - only 5% of genes have introns and it is rare for one gene to contain more than one intron
Vertebrates - 95% of genes have introns

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26
Q

What are Multi-gene families?

A

Contain from a few hundred up to hundred of thousands of copies of the same of very similar gene (may or may not be on the same chromosome)

In some cases they code for a high in demand protein (eg. Histone proteins and RNA products)

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27
Q

Explain the triplet hypothesis:

A

genetic code codons are made up of nucleotide triplets - Francis Crick

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28
Q

Genetic code Central Dogma -

A

The genetic code reveals the amino acid that each codon (nucleotide triplet/3 letters) codes for.

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29
Q

Characteristics of the code:

A

Continuity, Redundancy, Universitality

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30
Q

Explain continuity:

A

Reads as a set of 3 letter codons with no spaces

Has a correct reading frame (grouping of codons)

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31
Q

Explain redundancy:

A

64 possible codons but only 20 amino acids
Offers some protection against mutation
Not random (codons that code for the same amino acid often only differ in the identity of the last base pair)

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32
Q

Explain universality:

A

Genetic code is essentially the same in all living organisms (ie. Same mRNA codons correspond to the same amino acids)

Provides evidence that most organisms share a common ancestor

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33
Q

What is a genome:

A

IS THE COMPLETE SET OF GENES IN AN ORGANISM

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34
Q

Protien synthesis recall…

A

1 protein → hundreds of amino acids
The sequence of amino acids is determined by the sequence of nucleotides in an organism
A protein is composed of combinations of 20 amino acids
There are 3 types of RNA
→ ribosomal RNA (rRNA)
→ transfer RNA (tRNA)
→ messenger RNA (mRNA)

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35
Q

mRNA..

A

mRNA long single strand of RNA
Passes from nucleus to cytoplasm through nuclear pores
Brings information from chromosomes to ribosomes to direct protein synthesis
We have already seen that mRNA is spliced, capped and tailed before leaving the nucleus

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36
Q

rRNA…

A

rRNA provide the site on the ribosome where the polypeptide is assembled

37
Q

tRNA…

A

tRNA is smaller than rRNA
There are a maximum number of the kinds of tRNA, though may vary from organism to organism
Float freely in the cytoplasm
Transport amino acids to the ribosome and position amino acids on the chain

38
Q

2 MAIN PROCESSES IN PROTEIN SYNTHESIS

A

Transcription, Translation

39
Q

Transcription:

A

RNA copy of a gene is produced (mRNA), which is transcribed from DNA
This is initiated when the enzyme RNA polymerase binds to a sequence of nucleotides on one DNA strand

40
Q

Translation:

A

Synthesis of polypeptide by a ribosome
Information on mRNA directs the choice of amino acids
Ribosomes moves along in steps of three (codons)

41
Q

DNA to mRNA - Transcription

A

Initiation
RNA polymerase contains a binding site that only recognizes a promoter sequence on the DNA

Promoter Sequences
Rich in A and T nucleotides
Sequences are not palindromic so RNA polymerase will bind in only one orientation
This sequence does not get transcribed only serves as the attachment site for RNA polymerase

42
Q

Elongation

A

RNA polymerase works in the 5’ to 3’ direction
Does not require a primer to begin
Transcribes only one strand (template strand)
RNA polymerase opens the helix one section at a time and arranges the correct RNA nucleotides according to the DNA template
Oce the RNA polymerase passes a given point the DNA helix reforms and the mRNA strand separates from the DNA
RNA polymerase has no proofreading capability

43
Q

Termination

A

Transcription stops when RNA polymerase encounters a terminator sequence (highly specific)

44
Q

Processing of mRNA Transcript (a)

A

a) Capping and Tailing
5’ cap - made of modified guanine nucleotides which is added to the start of the primary transcript (precursor mRNA)
Poly A tail - string of 200 adenine ribonucleotides is added to the 3’ end by poly A polymerase
Both additions protect the mRNA from digestion by enzymes and assists in the initiation of translation

45
Q

Processing of mRNA Transcript (b)

A

b) Splicing
Eukaryotic genes contain exons and introns
Exon - coding region
Intron - non coding region
Spliecsomes cut out the introns and join exons together to create a continuous coding region on the mRNA transcript

46
Q

From mRNA to Protein - Translation (RIBOSOMES)

A

Ribosomes consist of 2 subunits (one large and one small) and rRNA
Two subunits bind mRNA between them
Moves along the mRNA transcript in the 5’ to 3’ direction

47
Q

From mRNA to Protein - Translation (tRNA)

A

tRNA is a small single stranded RNA with a 3 lobed structure resembling a clover leaf
Anti codon region - contains a nucleotide triplet complementary to a codon on mRNA (pg. 325)

Amino acid attachment site - across from anti codon region where the appropriate amino acid bonds

Aminoacyl tRNA - a tRNA bound to its particular amino acid

48
Q

Initiation

A

1st tRNA is brought into the P (peptide) site carrying methionine since it corresponds to the start codon AUG

2nd tRNA enters the A (acceptor) site

49
Q

Elongation (of polypeptide)

A

A peptide bond is formed between the 2 adjacent amino acids
The ribosome translocates (shifts) one codon over in the 5’ to 3’ direction and the next tRNA enters the A site
Process is repeated until a stop codon is reached ( a codon that does not code for an amino acid)

50
Q

Termination

A

A release factor protein aids in dismantling the ribosome - mRNA complex realising the polypeptide chain
Polypeptide chain may undergo further processing

Sugar (glycosylation) or phosphate (phosphorylation) may be addeD
Polypeptide may be cleaved
Two or more polypeptides may combine together

51
Q

The LAC Operation

A

E. coli produce the enzyme B-galactosidase, responsible for breaking down lactose only when lactose is present

The gene for B-galactosidase is part of an operon

52
Q

Operon

A

a cluster of genes under the control of one promoter and one operator in prokaryotic cells

53
Q

Operator

A

regulatory sequences of DNA governing whether or not RNA polymerase can bind to the promoter sequences to begin transcription of the genes

54
Q

Availability of Lactose…

A

If lactose is NOT available for the E.coli a repressor protein binds to the operator region making it impossible for RNA polymerase to bind to the promoter

If lactose IS present in the E.coli’s environment the cell will take up the lactose and some will bind to the repressor, causing a conformational change in the repressor resulting in it detaching from the operator site - lactose acts as an inducer in this case

55
Q

The TRP Operon

A

Trypoperon is an amino acid that is used by E.coli cells for the production of protein
If concentration of tryptophan is high the genes for this amino acids production are no longer transcribed
With high levels of tryptophan it binds to the trp repressor protein, altering its shape so that it can now bind to the trp operator
Tryptophan is required to inactivate the trp operon - repressor
OPPOSITE! When trp is not present, this person is turned on. When trp is present, it is turned off because more trp is NOT needed

56
Q

Gene Expression Regulation In Eukaryotes - Pre- transcriptional control

A

Cell controls the extent to which DNA is exposed to transcription enzymes (the more condensed regions of DNA are not transcribed)

57
Q

Gene Expression Regulation In Eukaryotes - Transcriptional Control

A

The cell controls whether or not exposed DNA is transcribed - involves regulatory proteins

58
Q

Gene Expression Regulation In Eukaryotes - Post - transcriptional control

A

Cell controls the rate of processing of pre mRNA into finished mRNA
Accomplished by not adding the cap, or tail

59
Q

Gene Expression Regulation In Eukaryotes - Translational control

A

Regulatory proteins can bind to the 5’ cap of the molecule preventing the small ribosomal subunit from attaching to the mRNA

60
Q

Gene Expression Regulation In Eukaryotes - Post- translational control

A

Regulatory proteins may breakdown the polypeptide before its able to reach its destination

61
Q

What type of DNA ends do restriction endonucleases produce?

A

Sticky and zig-zagged

62
Q

What are the steps of PCR?

A

Denaturation, annealing, and extension

63
Q

In Sanger sequencing, what are ddNTPs missing?

A

A hydroxyl group

64
Q

How have plasmids helped scientists?

A

All of the above (farm insulin, clone genes, produce recombinant proteins)

65
Q

What are the two types of gene therapy?

A

Somatic and germ-line

66
Q

In gel electrophoresis, DNA fragments move in what direction?

A

Positive to negative

67
Q

What is it called when targets bind to their complementary probe in microarrays?

A

Hybridization

68
Q

What are the three steps in forming transgenic organisms?

A

Identification, isolation, transformation

69
Q

Which nuclease is involved in CRISPR?

A

Cas9

70
Q

What is a benefit of Nanopore sequencing?

A

Is pretty cheap: $750

71
Q

Plasmids are circular pieces of DNA.

A

T

72
Q

Transgenic organisms can be made for human desires like glowfish.

A

T

73
Q

Ethical concerns for CRISPR involve duplicating human DNA.

A

F

74
Q

Sanger sequencing sets the gold standard for DNA sequencing.

A

T

75
Q

Therapeutic genes are the ‘unhealthy genes’ in gene therapy.

A

F

76
Q

Gel electrophoresis separates DNA fragments based on shape and odour.

A

F

77
Q

Kary Mullis is the inventor of PCR.

A

T

78
Q

Microarrays can detect precancerous lesions early.

A

T

79
Q

Restriction endonucleases cut DNA fragments cleanly.

A

F

80
Q

Nanopore sequencing detects and interprets changes in noisy currents.

A

T

81
Q

Role of each in protein synthesis:

A
82
Q

Role of each in protein synthesis: mRNA

A

Template for Translation
The mRNA serves as the template for translation, containing codons that dictate the sequence of amino acids in the protein. The ribosome reads the mRNA in a 5’ to 3’ direction, ensuring accurate protein synthesis.

83
Q

Role of each in protein synthesis: Peptide bond

A

Joins Amino Acids
A peptide bond forms between the carboxyl group of one amino acid and the amino group of the next. This bond links amino acids together, creating the primary structure of the protein.

84
Q

Role of each in protein synthesis: Anticodon

A

Binds to mRNA Codon
The anticodon on tRNA is complementary to the mRNA codon and ensures that the correct amino acid is added to the growing polypeptide chain. This base-pairing maintains the accuracy of translation.

85
Q

Control Mechanism - Lac Operon

A

Q: What is the name of the control mechanism?
* A: The Lac Operon.
* Q: Is it turned ON or OFF?
* A: ON (lactose binds to the repressor).

86
Q

Who discovered base pairing rules (A=T, C=G)?

A

Chargaff

87
Q

What is a histone?

A

Positively charged protein

88
Q

At what level is a protein added to a high-energy phosphate?

A

Post-translational

89
Q

What phase of DNA replication involves helicase?

A

Initiation

Biology 12U - 2024 (5 decks)

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