Molecular basis of inheritance Flashcards
(90 cards)
1
Q
What is DNA?
A
polymer of nucleotides (polynucleotide)
2
Q
What does DNA consist of?
A
Deoxyribose: H at 2’ position on sugar ring
Phosphate ( PO4 )
Nitrogenous bases
3
Q
What is structure of ribose?
A
OH at 2’ position on sugar ring
4
Q
What are purines?
A
N bases with double ring structure that altogether have 9 Cs
5
Q
What are pyrimidines?
A
N bases with single ring structure that altogether have 6 Cs
6
Q
Which N bases are purines?
A
A + G
7
Q
Which N bases are pyrimidines?
A
C + T
8
Q
What is a nucleoside?
A
Sugar + base
9
Q
What is deoxyadenosine?
A
deoxyribose + adenine
10
Q
What is nucleotide and how is formed from nucleoside?
A
- sugar + base + phosphate
- nucleoside phosphorylated at 5’ hydroxyl group of the sugar
11
Q
What are 3 examples of nucleotides?
A
deoxyadenosine 5’ monophosphate = dAMP
deoxydenosine 5’ diphosphate = dADP deoxydenosine 5’ triphosphate = dATP
12
Q
What’s special about dADP + dATP?
A
contain high energy phosphate groups
13
Q
What’s special about nucleotide triphosphates e.g. dATP?
A
building blocks of DNA
14
Q
How do nucleotides attach to each other and what enz catalyses this reaction?
A
- 3’ OH groups
- form 3’ to 5’ Phosphodiester bonds liberating inorganic pyrophosphate (PPi)
- DNA polymerase
15
Q
What’s special about ends of polynucleotide chains?
A
- have polarity – diff ends due to 5’ end (phosphate) and 3’ end (hydroxyl group)
16
Q
What is shape of DNA and how is it formed?
A
two polynucleotide chains coiled around a central axis, forming a right hand double helix.
17
Q
What is the internucleotide distance in double helix?
A
0.34nm
18
Q
What is length of one full twist in double helix?
A
3.4nm
19
Q
How many nucleotides are there per turn in double helix?
A
10
20
Q
How are the DNA strands held together in double helix?
A
- base pairing + H bonds between complementary base pairs
21
Q
How many H bonds between A + T and C + G?
A
A + T - 2
C + G - 3
22
Q
Which direction do the DNA strands run in double helix?
A
Antiparallel – strands running opp to each other
23
Q
How are the bases arranged in the double helix?
A
perpendicular to the helical axis (twisted at 90 degrees)
24
Q
What is process of semi-conservative replication and why does it occur?
A
- The parent molecule unwinds.
- Two new daughter strands are assembled based on base- pairing rules (A + T, C + G)
- Since the base sequences of the two strands of DNA are complementary each strand can act as a template for building a new strand.
25
What is the haploid size?
23 pairs of chromosomes = ca. 3.2 x 109 nucleotides (3.2bn)
26
What is average size of protein-coding DNA in a gene and what does this mean?
- 2000 bases
| - 2000 bases to specify production of 1 polypeptide chain
27
How many genes is there coding capacity for?
> 1 m
28
What % of genome encodes protein and how many genes is this?
- 1.1%
| - 20 000 genes
29
What is structure of prokaryotic gene?
- 5' end - PROMOTER
- Coding sequence (exon)
- 3' end - TRANSCRIPTION TERMINATOR
30
What happens to mRNA after its transcribed?
translated by the ribosome to give a polypeptide
31
What is structure of eukaryotic gene?
- promoter
- EXON
- INTRON
- transcription terminator signal
32
What is a promoter?
- proteins that bind which switch on transcription
| - control when and where to transcribe gene
33
What are exons and what % do they make up of human genome?
– encodes polypeptide sequence
- 1.1%
- start and stop codon
- transcribed into mRNA.
34
What are introns and what % do they make up of human genome?
– intervening sequence which doesn’t encode polypeptide sequence
- sequences corresponding to introns are not found in mature mRNA (do not code for any amino acids in mature protein).
- 23%
35
What is transcription terminator signal?
– sequence tells transcription to stop
36
What is structure of pre-mRNA in nucleus?
- cap
- exon
- intron
- poly A tail
37
Describe process of formation of mRNA from eukaryotic gene in nucleus
- transcription by RNA polym of pre-mRNA from eukaryotic gene in nucleus
- add of cap and poly A tail
- splicing of pre-mRNA to form mRNA
38
What is splicing?
Sequences corresponding to introns removed and exon sequences spliced together
39
Where does mRNA go after transcription in nucleus?
sent to rib for decoding in cytoplasm just composed of exon sequences
40
What % of human genome are regulatory proteins and what are some examples?
- 4%
| - includes promoters and transcription terminators
41
What % of genome is non-repeating sequences and composition?
- 44%
- 23 % introns
- 21% other unique sequences
42
What % of human genome is repeating sequences and composition?
- 51.6%
- 45% transposon based repeats
- 6.6% heterochromatin
43
What is heterochromatin?
Highly condensed DNA that’s never transcribed but of clinical importance as DNA fingerprint is analysis of this 6.6.%
44
What are retrotransposable elements and where are they found?
- move from one part of genome and insert themselves in randomly selected new location.
- move via a ’copy and paste’ mechanism involving an RNA intermediate
- found in all eukaryotic and bacterial genomes
45
How to retrotransposable elements move?
- Transposable element transcribed into RNA
– RNA moves to another part of genome
– reverse transcribes into DNA
- DNA inserts somewhere else into genome at random.
46
What are types of retrotransposon elements?
1. LINES (Long Interspersed Elements)
| 2. SINES (Short Interspersed Elements)
47
What is L1?
- e.g. of LINES
48
How long is L1?
6,500 bp repeats which exists in approx. 500,000 copies.
49
What is are 2 properties of L1?
- Contains its own reverse transcriptase – can control where it went/when it moved in genome.
- Most L1 copies are inactive (don’t move anymore) owing to re-arrangements and mutations
- but some (ca. 100) are still actively transposing and moving around in genome
50
What can be a problem with moving L1, how and an example?
- cause disease - overall, retrotransposon insertions account for 1 in 250 of disease-causing mutations
– some 100 L1 elements that can move around insert themselves into exon and disrupt protein function in corresponding protein
e.g some cases of haemophilia A are due to L1 transposition into an exon/the Factor VIII gene on X chromosome.
51
Are genomes identical in autosomal cells?
- Technically, 2 cells adj to each other may not have same genome if one of transposon events has happened
- or could be diff due to mutations so genome identical in autosomal cells not quite true – can be diff.
52
What is an example of SINES?
e.g. Alu repeat is ~160 bp and exists in 1.2 million copies.
53
What is the structure of heterchromatin?
- Composed of long arrays of high-copy-number tandemly (2 repeats, 2 repeats etc) repeated DNA sequences,
- (v. short repeats) - repeat units are small ranging from 4 to ca. 171bp
54
What are 2 properties of heterochromatin?
- Tends to be transcriptionally inactive (because of its compact state – its so condensed)
- also referred to as satellite DNA as base composition slightly diff to rest of genome so when genomic DNA extracted and sep by density – layer of DNA lighter than rest which floats above in a gradient.
55
What is clinical relevance of heterochromatin?
- Number of repeats varies immensely between individuals – unique to everyone, provides a genetic “fingerprint”
- Used in paternity testing & forensic science – count no. of repeats in 1 part of genome and look in 10 diff locations and no. of repeats = gen fingerprint
56
What is non-coding RNA (ncRNA)?
- not translated further into protein
– created for mechanical purposes required for exon splicing
- and de-coding mRNA – deconding info in exons
- 1000s play important regulatory roles (mirco RNAs).
57
What are small nuclear RNAs (snRNAs) and function?
– stay RNAs forever – not translated,
- up to 360 nucleotides in length.
- Form complexes with proteins to form small riboucleoprotein particles (snRNPs), required for splicing pre-mRNA – splicing exons together and removing introns
- message processing
58
What are e.g.s of decoding-mRNA and function?
- ribosomal RNA (rRNA)
– large chunks of genome devoted to genes that encode it.
- Made + incorp into rib structure
- transfer RNA (tRNA)
– match codon on mRNA + tRNA carrying aa
- many tRNA result in joining lots of aa to make polypeptide chain
59
How many genes code for long ncRNAs?
> 3000
60
What is an e.g. of long ncRNA with known function?
Xist which makes a 19.3kb RNA that controls mammalian X inactivation
61
How many genes does human X chromosome have?
1500
62
How many X genes do females have compared to males?
- twice as many but twice the amount of transcription is not observed (suggesting such a situation would be lethal).
63
Why isn't there twice as much transcription in female X chromosomes and reason for this?
- In each autosomal female cell – 1 X chromosome switched off = mammalian X inactivation
– all genes on that X chromosome not transcribed
- Dosage compensation is achieved because one of the X chromosomes in females is transcriptionally silent so it corrects for the unprop dose of X related genes
64
What is process of dosage compensation?
- Xic (X inactivation centre) contains the Xist gene
– RNA persuades DNA to form tightly packed heterochromatin
– no access for RNA polym to transcribe any of the genes – mass compression of 1 of X chromosomes . Transcribed to a long non-coding RNA - heterochromatin formation spreads from inactivation center - condensed DNA which can't be transcribed
65
When does X inactivation occur and why?
early in embryogenesis – stage in lifetime of female where both X are active
- Once it has occurred, all cells descended from the initial cell in which inactivation took place will exhibit inactivation of the same chromosome (inherited somatically/mitotically)
66
Which X is inactivated (maternal or paternal)?
The choice of which X to inactivate is random – sometimes paternal switched off + other times maternal one – 50/50
67
How does X inactivation lead to tortoise-shell cats?
- Gene for brown or orange is on the X chromosome at 1 particular locus
– 1 allele makes black pigment and another makes orange.
- Heterozygous cat – 1 black and 1 orange allele.
- Black cells derived from 1 cell where X chromosome carrying black gene switched on X chromosome carrying orange gene switched off
- All cells in an orange patch are descended form one cell in the early embryo in which the X bearing the gene for black pigment was inactivated.
68
Name 2 examples of X-linked recessive disorders that reveal X inactivation in humans
1. Anhidrotic ectodermal dysplasia (defective sweat glands)
2. red green colour blindness
69
What is Anhidrotic ectodermal dysplasia (defective sweat glands) and what is its cause?
- Heterozygous females have random patterns of tissue with and without sweat glands.
- genes causing this located on X chromosome
- Patches of her can sweat and patches of her can’t bc of the mosaic fashion of X chromosome inactivation
- non-sweat patch - Derived from 1 cell where normal X switched off
- sweat patch - Derived from cell where mutant X switched off – leaving normal X with wild-type allele switched off
70
Why does red green colour blindness mainly affect males?
- Heterozygous females have mosaic retinas with patches of defective colour perception – 1 copy of mutant allele – parts of retina can’t distinguish between red and green and other parts can depending on which X was switched off.
- Males are fully colour blind if they carry the mutant allele as they only have 1 X so 1 version of gene.
71
What are micro RNAs (miRNA)?
>3000
- 21-22 nucleotides long
- regulate expression of specific genes
72
How are miRNA syn?
- RNA encoded by miRNA gene
– transcribed by RNA polym (short piece of RNA which isn’t going to be decoded into protein).
- Sequence folds in on itself and froms hairpin structure so it can base pair with itself – capped and polyaddenated like normal RNA - get precursor miRNA
- Processing event in nucleus
- Export into the cytoplasm and processing by nuclease
- This leaves a single strand of RNA that base pairs with a coding mRNA
73
What happens to mRNA that's formed from miRNA syn and what are 2 effects as a result?
- Binds to message encoded by exon
1. translational repression – prevent rib from working so it doesn’t translate
2. deadenylation (mRNA instability) – activates enz which removes poly A tail – destabilises mRNA and gets degraded
74
What can mutations in miRNA genes cause and 3 examples?
- cause disease
- mutation in miRNA miR-96, causes hereditary progressive hearing loss.
- mutation in miRNA miR-184, causes hereditary keratoconus and cataract (EDICT syndrome - degenerative eye disorder)
- Many miRNAs are upegulated or down regulated in cancer and contribute to tumor progression of the disease and makes them drug targets.
75
How does the no. of miRNAs (and other types of small RNA) compare with protein coding genes?
- The number of protein coding genes has remained static (acc went from 30 000 to 20 000),
- but the number of miRNAs (and other types of small RNA) is constantly being revised upwards, and may even match or exceed the number of protein coding genes.
76
What does the mit genome encode, what genes are involved and properties?
- mtDNA, encodes 13 polypeptides
– 13 of proteins that constitute mitochondrion made by mit genome (remainder made by genes encoded in nuclear genome plus rRNA and tRNA)
- A Highly compact genome
- no introns & no repetitive DNA.
77
How are mit inherited and what type of inheritance is this?
- Mitochondria are inherited exclusively from the mother (sperm cell mitochondria are excluded from the zygote).
- This is Non-Mendelian (only coming from 1 side), cytoplasmic, extranuclear inheritance (not genes in nuclear genome)
78
Where does transcription and translation occur in mit?
Mit matrix
79
What are mitochondrial cytopathies (diseases) caused by and which organs are most affected?
- mutations in mtDNA.
- those that use high amounts of energy (ATP) e.g. muscle and nerve as main function of mit is to gen ATP so compromising mit genome compromises its ability to gen ATP.
80
What are 2 examples of disorders depending on what location in mit genome mutated?
1. MELAS – myopathy, encephalopathy, lactic acidosis, stroke-like episodes.
2. LHON – Leberʼs hereditary optic neuropathy
81
Why does mitochondrial cytopathy affect both sexes?
- can only be passed on by the mother
- An affected mother would transmit the disorder to
all offspring
- offspring of affected fathers are normal – can’t transmit cytopathy bc he contributes no mit to progeny
82
What does matrilineal inheritance mean?
does not follow any of the autosomal or sex-linked inheritance patterns
83
How can a mother who has passed on mitochondrial diseases have a child free of mitochondrial cytopathy?
- if healthy mitochondria from another female are used.
- The child would have three parents (three person IVF)
- Nuclear DNA from couple and mit DNA from someone else
84
Describe process of three parent in vitro fertilization
1. egg with faulty mitochondria - nucleus removed
2. Donor egg with healthy mitochondria (nucleus removed)
3. Transported to donor egg with healthy mitochondria, then egg is fertilized.
4. Embryo free of mitochondrial
disease
85
What is cytoplasmic transfer?
- egg with defective mitochondria
- Receives cytoplasm from healthy egg (includes good mitochondria)
- New egg (good + bad mitochondria) then fertilized by IVF
- Abnormal mitochondria still there, but no medical follow up for these children
86
What is structure of adenine?
NH2 group
87
What is structure of guanine?
- C=O
| - NH2 group
88
What is structure of cytosine?
- C=O
| - NH2 group
89
What is structure of thymine?
- 2 C=O groups
| - CH3 group
90
What is structure of uracil?
2 C=O
