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Medicine Year 1 Semester 1 - Part 2 > Molecular Biology 1-4 > Flashcards

Molecular Biology 1-4 Flashcards

1
Q

Describe the structure of DNA

A

Sugar phosphate backbone - outside
Bases - inside

2 complementary strands of DNA bind together.

The DNA double helix is held together by HYDROGEN BONDS formed between the base-pairs across the 2 different strands.

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2
Q

Explain how DNA is packaged within the cell

A

Short region of DNA double helix

“Beads on a string form of chromatin”

30nm Chromatin fibre of packed nucleosomes

Section of chromosome in extended form

Condensed section of chromosome

Entire mitotic chromosome

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3
Q

DNA

A

deoxyribonucleic acid

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4
Q

RNA

A

ribonucleic acid

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5
Q

What links DNA bases together on the DNA chain ?

A

5-3 prime phosphodiester linkage

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6
Q

Name the 4 main bases of nucleic acids

A

Adenine
Thymine
Cytosine
Guanine

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7
Q

What are purines ?

A

Adenine and Guanine

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8
Q

What are pyrimidines ?

A

Thymine and Cytosine

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9
Q

What is the difference between RNA and DNA ?

A

RNA has : Cytosine, Guanine, Adenine and Uracil

DNA has : Adenine, Thymine, Cytosine and Guanine

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10
Q

What is adenine lacking ?

A

Oxygen

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11
Q

Describe the polarity of the double helix

A

The cell reads the helix from left to right (5-3 prime)

On the opposite side of the strand (3-5 prime)

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12
Q

How many hydrogen bonds are between A and T ?

A

2

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13
Q

How many hydrogen bonds are between C and G ?

A

3

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14
Q

What is the term used to describe the inheritance of changes in base sequence ?

A

Genetics

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15
Q

What is important for replication ?

A

Major and minor grooves

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16
Q

How can chromosomes be distinguished by ?

A

Size
G-banding : Staining pattern : interacts with DNA produces darker and lighter areas

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17
Q

What is higher DNA in the form of ?

A

Chromosomes

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18
Q

As cells divide what happens to chromosomes ?

A

They become condensed.

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19
Q

How is DNA organised within the interphase nucleus ?

A

They are spread out in nuclear zones.
Inside the nuclear envelope in the nucleus

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20
Q

Structural features of histones

A

Positively charges
Long N-termini

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21
Q

What is a nucleosome ?

A

A set of histone proteins
H2A, H2B, H3, H4
Makes an octameric histone core
147 base pairs of DNA

Wrapped around histone proteins (H1)
1.7 left-handed turns

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22
Q

How are nucleosomes formed ?

A

The opposite charges of histones (+) and DNA (-) attract, so the double helix wraps twice around each group of 8 histones, forming a nucleosome.

Nucleosomes look a bit like beads on a string, and they can snuggle closer together and be further packaged as chromatin fibers.

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23
Q

What do the histone tails in the structure do ?

A

The amino-terminal tails of histone proteins protrude from the nucleosome

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24
Q

What is the function of histone H1 ?

A

Helps form 30nm fibre
Extra linking histone
Links nucleosomes together in a more compact high end structure

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25
Q

What are the ‘beads on a string’ packaged into ?

A

30nm chromatin fibre of packed nucleosomes and further condensed

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26
Q

How big is the short region of DNA double helix ?

A

2nm

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27
Q

How big is the ‘beads on a string’ form of chromatin ?

A

11nm

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28
Q

What do chromosomes need to allow protein access ?

A

They need to be remodelled by the remodelling complex.

ATP —-> ADP

Condensed chromatin —-> Decondensed chromatin

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29
Q

What is access/lack of access related to ?

A

The histone tails

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30
Q

What % of the genome of genes comprise ?

A

<5% of total content of DNA

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31
Q

Describe the organisation of the human genome

A

3 billion base pairs of DNA
Genes <5%
‘Junk’ DNA
Often repetitive

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32
Q

Heterochromatin location

A

Tends to be at the ends of a chromosome or near the centre (centromere)

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33
Q

Heterochromatin

A

More compact
Telomeres at the end
Centromere - where the mitotic spindle binds

With heterochromatin, on the other hand, nucleosomes are more densely packed, because it contains genes that the cell rarely or never uses.

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34
Q

Euchromatin

A

Most of the genes
Open configuration

Nucleosomes are more loosely packed, because it contains the genes - or regions of DNA - that the cell frequently uses to make proteins that help the cell perform its day to day job.

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35
Q

Repetitive types of DNA

A

Interspersed repeats
Tandem repeats

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36
Q

Interspersed repeats

A

SINE and LINE often derived from retroviruses

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37
Q

Tandem repeats

A

Satellite - telomere TTAGGG
Mini-satellites 7-100 bases repeated up to 40,000 bases
Micro-satellites 1-6 bases repeated >100 bases

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38
Q

What is myotonic dystrophy ?

A

Muscle wasting condition
Can be inherited in families through generations

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39
Q

What is the cause of myotonic dystrophy ?

A

Tri-nucleotide repeat expansion in 3’ UTR of MD gene

More repeats = worse

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40
Q

Mitochondrial DNA

A

mtDNA

41
Q

What is mitochondrial DNA ?

A

Circular
Maternally inherited
Implications for disease
Can be used in forensics
‘Out of Africa’

42
Q

Why are DNA strands antiparallel ?

A

The antiparallel nature of DNA strands is needed to form the hydrogen bonds between the nitrogenous bases.

43
Q

How are 2 strands copied ?

A

The semiconservative model

44
Q

What is the experiment to determine the way that strands are copied ?

A

Matthew Meselson & Frank Stahl’s experiment

45
Q

What is the semiconservative model ?

A

In this model, the two strands of DNA unwind from each other, and each acts as a template for synthesis of a new, complementary strand.

This results in two DNA molecules with one original strand and one new strand.

Each strand of DNA serves as a template to make a new, complementary strand, seemed most likely based on DNA’s structure.

46
Q

How long does it take to replicate the human genome ?

A

8 hours

47
Q

Briefly describe the Meselson-Stahl’s experiment

A

They labeled the DNA of bacteria across generations using isotopes of nitrogen.

From the patterns of DNA labeling they saw, Meselson and Stahl confirmed that DNA is replicated semi-conservatively.

48
Q

In what direction does DNA strand grow ?

A

From 5’ to 3’

49
Q

What is the function of the template strand ?

A

Specifies which base is to be added next

50
Q

What is the difference between the leading and lagging strand ?

A

The replication fork is asymmetrical

51
Q

Leading strand

A

DNA opens up
5’ to 3’ direction
DNA polymerase forms

52
Q

Lagging strand

A

Synthesised in short fragments (Okazaki)
RNA primer required

53
Q

Werners syndrome

A

A premature aging syndrome
Defect in how the ends of chromosomes are replicated

54
Q

What are the ends of our chromosomes called ?

A

Telomere

55
Q

What happens at a DNA end ?

A

Telomerase binds.

Telomerase adds additional repeats to the template strand.

Completion of lagging strand by DNA polymerase.

56
Q

What are mutations ?

A

Mistakes in base pairing, can lead to changes in the DNA sequence.

57
Q

When are errors in DNA corrected ?

A

During synthesis during proofreading
After DNA replication has occurred

58
Q

Hereditary non-polyposis

A

A genetic disease of autosomal dominant inheritance

59
Q

What is the normal mutation rate ?

A

About 1 error for every 3 genomes replicated

60
Q

PCR

A

Polymerase Chain Reaction

61
Q

Function of PCR

A

Polymerase chain reaction (PCR) amplifies DNA using complementary primers for specific target sequences.

Repeated cycles of heating and cooling amplify the target region of DNA.

62
Q

Function of DNA polymerase

A

DNA polymerase adds DNA nucleotides, using complementary base pairing, to the deoxyribose (3’) end of the new DNA strand which is forming.

63
Q

What is produced in the 1st cycle of PCR ?

A

2 double stranded DNA molecules

64
Q

What is produced in the 2nd cycle of PCR ?

A

4 double stranded DNA molecules

65
Q

What is produced in the 3rd cycle of PCR ?

A

8 double stranded DNA molecules

66
Q

What are some uses of PCR ?

A

Detection of presence of infectious agents
Inheritance patterns
Looking for changes in chromosome copy numbers
DNA sequencing - chain termination: Sanger method
Looking for mutations

67
Q

Alexander disease

A

glial fibrillary acidic protein (GFAP)

68
Q

Intron

A

The introns of the primary transcript are non-coding regions and so are removed.

69
Q

Exon

A

The exons are coding regions and are joined together to form the mature transcript.

70
Q

Describe the majority of gene encoding proteins

A

Contain regions of DNA which encode proteins (exons), dispersed by regions which do not encode proteins.

71
Q

Splice site

A

Determined by sequences around each intron/exon junction

72
Q

Promoter

A

Promoters are fairly large nucleotide sequences that initiate the process of transcription.

Repetitive non-coding regions of nucleotides.

73
Q

Enhancer

A

Enhancers are short nucleotide sequences that enhance the transcription rate in the genome.

74
Q

Transcription

A

DNA is used as a template
Complementary to one strand
RNA polymerase (5’ to 3’)
Not as accurate as DNA replication

75
Q

What do transcription factors have ?

A

2 Domains :

  • DNA binding domain
  • Activation domain
76
Q

Why is mRNA processed ?

A

To protect from exonucleases
Aid transport
Identify as mRNA

77
Q

Fraiser syndrome

A

Affects the kidneys
Defect in the glomerulus of the kidneys

78
Q

What is the gene number paradox ?

A

Making many different proteins from limited number of genes.

79
Q

What is transcription ?

A

DNA is converted into useable form via transcription

80
Q

How many bases code for an amino acid ?

A

3 - triplet code

81
Q

What does gene expression involve ?

A

Transcription and translation of DNA sequences.

82
Q

mRNA

A

Messenger RNA carries a copy of the DNA code from the nucleus to the ribosome.

83
Q

tRNA

A

Transfer RNA folds due to complementary base paring.

Each tRNA molecule carries its specific amino acid to the ribosome.

84
Q

rRNA

A

Ribosomal RNA and proteins form the ribosome.

85
Q

Function of RNA splicing

A

Forms a mature mRNA transcript

86
Q

Describe translation

A

Translation begins at a start codon and ends at a stop codon.

Anticodons bind to codons via complementary base pairing, translating the genetic code into a sequence of amino acids.

Peptide bonds join the amino acids together.

Each tRNA leaves the ribosome and the polypeptide is formed.

87
Q

What are frame shift mutations ?

A

Occur as a result of nucleotide insertions or deletions.

88
Q

Name some nucleotide substitutions

A

Missense
Nonsense
Splice-site mutations

89
Q

What is the difference between a a mutation and polymorphism ?

A

Mutations are associated with changes in phenotype.
Only mutations affect gene expression.

Polymorphisms are common and do not contribute to disease.

90
Q

What is the initiation codon ?

A

Defines the beginning of open reading frame.

91
Q

What are the 3 phases of translation ?

A

Initiation
Elongation
Termination

92
Q

Elongation

A

RNA polymerase unzips the coding strand from the template strand, by shearing the hydrogen bonds between complementary nucleotides.

93
Q

Terminator sequence

A

Contains 2 complementary sequences in a row, on a single strand.

When they get transcribed onto the mRNA, the nucleotide sequences bond to each other, forming a Hairpin loop, making the RNA polymerase detach from the DNA strand.

94
Q

Effects of mutations

A

No transcription
Protein incorrectly processed
Inappropriate function
Unstable protein

95
Q

Splisosome

A

Cuts introns out of the mRNA sequence

96
Q

START CODON

A

AUG
Methionine

97
Q

STOP CODON

A

UAA
UGA
UAG

98
Q

What are the 3 amino acid sites for the tRNA to bind on the ribosome ?

A

Aminoacyl site
Peptidyl site
Exit site

99
Q

Termination

A

Ribosome reaches stop codon and releases the polypeptide.

Medicine Year 1 Semester 1 - Part 2 (37 decks)

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