Molecular Biology and Genetics Flashcards
What’s the difference between purines and pyrimidines?
Purines are the larger molecules
Which nitrogenous bases are purines and which are pyrimidines?
Purines: A and G
Pyrimidines: T and C
How many hydrogen bonds are there between G-C and A-T?
G-C = 3 H bonds A-T = 2 H bonds
Define ‘nucleotide’
Sugar, phosphate and nitrogenous base
What is present at the 3’ end of DNA?
-OH (hydroxyl) group
What is present at the 5’ end of DNA?
Phosphate group
In which direction does DNA replication occur?
5’ to 3’
What is the role of topoisomerase?
Prevents supercoiling of DNA
How does the antibiotic quinolone work?
Targets topoisomerase to cause supercoiling and double strand breakage
In which direction does DNA editing occur?
3’ to 5’
Name the 3 ways of repairing single strand DNA defects
Base excision repair, nucleotide excision repair and mismatch repair
Name the 2 ways of repairing double strand DNA defects
Non-homologous end joining and homologous recombination
Describe base excision repair
Removal of incorrect base using [BASE] DNA glycosylase enzyme to break phosphodiester bond, then DNA polymerase will insert new nucleotide and DNA ligase will seal
Describe nucleotide excision repair
Dimer forms between two base pairs, nuclease then cleaves ~12 phosphodiester bonds, DNA helicase then unwinds section and allows complementary base pairing again, DNA polymerase facilitates, DNA ligase seals backbone
Describe mismatch repair
If there is an error in a newly made strand then mismatch proofreading proteins bind (MutS binds to mismatched base pair, MutL scans nearby DNA for nicks and triggers strand removal up to mismatch point), this is followed by DNA synthesis once more
Describe non-homologous end joining
Accidental breakage of DNA strand followed by further loss of nucleotides from end degradation, then the ends rejoin in the absence of nucleotide portion (abnormal)
Describe homologous recombination
Accidental breakage of DNA strand followed by further loss of nucleotides from end degradation, then nucleotide structure is copied from a second chromosome in order to fill in gap of missing nucleotides prior to end re-joining
What are the consequences of a defect in xeroderma pigmentosum?
It affects nucleotide excision repair and increases likelihood of skin cancer and increases UV sensitivity
What are the consequences of defects in MutS or MutL?
This affects mismatch repair and increases likelihood of colon cancer
What are the consequences of a defect in BRCA2?
Affects homologous recombination repair, and increases likelihood of getting breast/ovarian cancer
Describe the mitochondrial genome
Has 13 protein coding genes on 1 circular DNA molecule and this DNA is inherited from the mother
Define ‘autosomes’
Chromosomes which aren’t sex chromosomes, therefore 1-22
Define ‘karyotype’
Number and appearance of chromosomes in the nucleus of cell
Outline the structure of a chromosome
Top is the p (short) arm, the bottom is the q (long) arm, the tips are coated by telomeres which is a ‘protein cap’ of repetitive DNA. In the middle of the top body is the G light band, and at the bottom middle is the G dark band, and in the middle is the centromere
What is the G light band?
A gene rich, G and C dense, early replicating part of chomosome
What is the G dark band?
A gene poor, A and T rich, late replicating part of the chromosome
Define ‘aneuploidy’
Abnormal chromosome number
Define ‘exon’
Region of gene that encodes protein sequences
Define ‘intron’
Non-coding regions of DNA between exons in genes
What are genetic ‘control elements’?
Sequences such as promoters and enhancers that regulate transcription
What is a pseudogene?
A non-functional copy of a gene that arises from gene duplication followed by a deleterious mutation in one copy
What happens to intron regions after transcription?
There is splicing to remove them and leave only the exons
Describe ‘robertsonian translocation’
The joining of two chromosomes at the centromere (vertically)
Outline Down Syndrome
Trisomy of chromosome 21 –> muscle hypotonia and congenital heart malformations
Outline Edwards Syndrome
Trisomy of chromosome 18 –> multiple malformations including clenched hands with overlapping fingers
Outline Patau syndrome
Trisomy of chromosome 13 –> incomplete brain lobation, cleft lip and congenital heart disease
Outline Klinefelter syndrome
47 chromosomes, having XXY (affects males) and leads to infertility, lack of testosterone and tallness
Outline Turner syndrome
45 chromosomes, just X (females) –> infertility, short stature and webbed neck (excess skin)
When do females experience X chromosome inactivation?
Early in embryonic development
Describe X inactivation in women
X inactive specific transcript (Xist) is a long non-coding piece of RNA in the X-inactivation centre on the X chromosome, and this works to associate closely with the chromosome in order to cause changes to the chromatin and special reorganisation of the chromosome to cause transcriptional inactivation
Describe the role of Y chromosomes in male sex differentiation
SRY region of Y chromosome (sex-determining region of Y chromosome), which then encodes proteins of the HMG group of transcription facotrs
What is different about DNA in B and T cells?
Been rearranged
Which RNA polymerase makes rRNA?
Pol I
Which RNA polymerase makes tRNA?
Pol III
Which RNA polymerase makes mRNA?
Pol II
Describe the stages of mRNA synthesis
Initiation - RNA polymerase binds to gene
Elongation - polymerase transcribes gene
Termination - polymerase stops transcribing
Processing - mature mRNA formed
Export - mRNA leaves nucleus to be translated
What is the structure and function of the promoter region of genes?
The promoter region lies upstream of the gene exon and acts as template for the preinitiation complex, bringing Pol II to the gene so it can be transcribed
What are transcription factors?
DNA binding proteins which either enhance or repress the assembly of the pre-initiation complex
Define ‘proteome’
the entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time
How is immature mRNA processed prior to translation?
Processed by capping, slicing and polyadenylating
What do antibiotics target?
Ribosomes
In what direction to RNA polymerases work?
5’ to 3’ direction
What is a missense mutation?
A single base change that changes the amino acid coded for
What is a nonsense mutation?
Single base change leading to a stop codon
What is a splice-site mutation?
Insertion/deletion of nucleotides at which intron splicing takes place, so this will alter the protein
What is a silent mutation?
Base change which doesn’t affect amino acid coded for
What is a frameshift mutation?
Addition of one base which shifts the entire reading frame
What is a regulatory mutation?
Mutation on promoter or other element
What genetic mutation causes sickle cell disease?
Base pair change of A to T in B-haemoglobin gene
What genetic mutation causes cystic fibrosis?
Deletion of CTT nucleotides in CFTR gene
What genetic mutation leads to chronic myelogenous leukaemia?
Chromosome 9 and 22 translocations
Give some examples of autosomal dominant conditions
Neurofibromatosis, marfan syndrome, Huntington’s disease
Give some examples of autosomal recessive conditions
Cystic fibrosis, sickle cell disease, thalassaemia
Give some examples of X-linked recessive conditions
Haemophilia, colour blindness, DMD
Define ‘genotype’
Combination of alleles seen in any one person
Provide the equations of the Hardy Weinberg principle
p + q = 1
p2 + 2pq + q2 = 1
What are the exceptions to the Hardy Weinberg principle?
No inbreeding
Describe the structure of tRNA
Has L-shape 3D fold wit one end attached to specific amino acid and other has anti-codon (3 exposed bases)
Which enzyme catalyses the attachment of a specific amino acid to tRNA?
aminoacidacyltransferase
Why is tRNA required to error check it’s amino acid?
Binding site for amino acids is large so smaller molecules may be able to attach, in this case they must be removed
What is meant by the ‘tRNA wobble’?
That tRNA can pick up different amino acids due to the redundancy of codons,
Describe the structure of rRNA
It has two subunits: large and small and mRNA binds to small subunit, and there are two binding sites for tRNA on large subunit
What is the start codon?
AUG
What is the first amino acid in translation?
Methionine
Describe what happens in the elongation phase of mRNA translation
GTPase hydrolyses GTP to provide energy for tRNA binding, and amino acid is joined to existing AA via peptidyl transferase enzyme
Describe what happens in the termination phase of mRNA translation
When stop codon is reached, releasing factors 1 and 2 bind to the protein to cause it’s release and then GDP and releasing factor 3 bind to the mRNA (in small subunit) where GTP is hydrolysed and RF1,2 and 3 are released as well as GDP
Why are the processes of transcription and translation good targets for antibiotics?
These processes are different in eukaryotes to prokaryotes, so won’t affect our structures
What is ‘DNA methylation’?
Gene methylation inactivates genes, and this involves adding methyl group to cytosine site
What are ‘histone modifications’?
Activating or repressive modifications of histone proteins that associate with the DNA
How can bisulfite sequencing be used to study epigenetic modification?
Investigates DNA methylation: add sulfite to genes and those cytosines which aren’t methylated (so are active) will be converted to uracil, then PCR is used, converting the uracil to thiamine if they are methylated (so inactive genes will show)
