nucleic acids Flashcards
how is DNA found in eukaryotic cells?
chromosomes within a nucleus
how is DNA found in prokaryotic cells?
dispersed within the cytoplasm
what are the 3 shapes of bacteria?
spirilla, bacilli, cocci
what is gram stain used for?
the staining and differentiation of bacteria
describe the stages of the gram staining process
fixation stained with crystal violet treated with iodine decolorization counter stain with safronin
what colour does gram +ve bacteria stain?
purple
what colour does gram -ve bacteria stain?
pink
what does the gram stain bind to in bacteria?
peptidoglycan in the cell wall
why do gram -ve bacteria not stain with gram stain?
second, outer lipid membrane that is not present in Gram positive bacteria which prevents the stain binding properly
what did the Frederick Griffiths experiment show?
something could be passed between bacteria that would alter the virulence of the bacteria
what did averys experiment do and what did it show?
They extracted and purified DNA, RNA, protein, lipid and carbohydrates from heat killed virulent strains and mixed each substance separately with the non-virulent strain
showed that DNA was the transforming principle
what was the Hershey and chase experiment?
the protein and DNA components of bacteriophage were labelled with different radioactive molecules.
show that only DNA was injected into the bacteria to make new phages. This showed that the DNA and not the protein must contain the genetic information.
what was the Hershey and chase experiment?
the protein and DNA components of bacteriophage were labelled with different radioactive molecules.(sulphur is not found in DNA, whilst phosphorus is not found in protein)
show that only DNA was injected into the bacteria to make new phages. This showed that the DNA and not the protein must contain the genetic information.
what are the 6 key features of DNA?
Antiparallel strands form double helix
Sugar phosphate backbone
Base pairs join strands together by hydrogen bonding (adenine with thymine, guanine with cytosine)
Unit is the nucleotide (base + sugar + phosphate)
Sugar is deoxyribose
Strands are complementary
which bonds link adjacent sugars in DNA?
phosphodiester bonds
what are the 4 bases in DNA and are they purine or pyrimidine?
purine: adenine, guanine
pyrimidine: cytosine, thymine
what does DNA coil around to become more dense?
histones
what are the 4 bases in RNA?
purine: adenine, guanine
pyrimidine: cytosine, uracil
what are the three differences between DNA and RNA?
sugar, U for T base switch, RNA single stranded DNA double stranded
Is DNA replication conservative or semiconservative?
semiconservative
where does the replication of DNA occur?
at the replication fork
which enzymes unwind the DNA?
helicases
what stabilises the denatured DNA in replication?
Single strand binding proteins
what allows replication to commence on the denatured strand and which enzyme controls it?
DNA primase synthesises a short RNA primer to allow replication to commence
In which direction does DNA synthesis occur?
5’ to 3’
In which direction does DNA synthesis occur?
5’ to 3’
which enzyme carries out DNA replication in eukaryotes?
DNA polymerase III
what does DNA polymerase III need to carry out replication?
pool of all four deoxy nucleoside tri-phosphates (dNTPs)
why is a primer needed for replication to occur?
requires a free 3′-OH
what are the two stands of DNA called during replication?
lagging and leading stands
what occurs on the lagging strand?
okazaki fragments
what does DNA polymerase 1 do?
replaces the RNA primers with DNA
what does DNA ligase do?
seals the gaps between fragments
what is the overall error rate in replication?
1 in 10^9 bases.
what are the 4 different types of mutation that can occur?
Base substitution (eg G to T, G to A, etc)
Deletions of bases (1 or more)
Insertions of bases (1 or more)
Rearrangements of bases
how does Ethyl methane sulphonate (EMS) cause mutation?
reacts directly with DNA to form the O6-ethylguanine adduct
The O6-ethylguanine adduct mispairs with thymine during replication
This produces a GC AT mutation
name an example of a base excision repair enzyme and its job.
Uracil N-glycosylase
recognises the presence of uracil in DNA and cuts out this base
important because deamination of cytosine produces uracil, which base pairs with adenine.
list 4 diseases linked to single defective genes.
Duchenne muscular dystrophy
Haemophilia
Cystic fibrosis
Sickle cell anaemia
define genetic susceptibility
carrying a genotype that increases risk of a particular disease, usually if a certain environmental exposure occurs
define genetic susceptibility
carrying a genotype that increases risk of a particular disease, usually if a certain environmental exposure occurs
define genomics
study of the genome; the analysis of sequencing and mapping sets of genes to understanding their organisation and evolution.
define the genome
all of an organisms genetic information, including coding (genes) and non-coding sequences.
describe sanger dideoxy sequencing?
Unknown DNA sequence cloned into plasmid
Each tube contains all four dNTPS but only one ddNTP. Each band represents a length of newly synthesised DNA that has been terminated when the ddNTP was added. Smaller DNA molecules run farther on the gel
By reading each band from the bottom of the gel, the sequence can be read.
define polymorphism
If a mutation occurs in at least 1% of the population ( most commonly single nucleotide polymorphism (SNP)
what is a microarray?
1,000’s of discrete DNA sequences (cDNA or oligos) printed on glass slides
how can microarrays be used?
Compare polymorphisms between different individuals
Compare gene expression between different types of cell
Compare gene expression between normal and diseased tissue
define epigenetics
control of gene expression or cell phenotype by means other than genetic (ie DNA sequence) variation.
give examples of epigenetic change
DNA methylation (at cytosines in CpG sites) and histone modification (methylation, acetylation or phosphorylation)
how has the HGP improved medicine?
Improved understanding of the molecular pathology of disease
Predicting risk of disease
Improved diagnosis
More effective drugs
Targeted more effectively
Tailored to individual (personal gene chips)
Fewer adverse reactions
which strand of DNA is copied in protein synthesis?
template strand (antisense strand)
which strand of DNA is copied in protein synthesis?
template strand (antisense strand)
how is translation initiated?
RNA polymerase binds to the initiation site of the gene in the promoter region
Transcription factors bind to the TATA box to help position the RNA polymerase, and separate the DNA strands
what and where is the TATA box?
The TATA box is a region of the promoter at which transcription factors bind to initiate transcription by binding the RNA polymerase to the region of the gene where transcription begins.
25-35bp upstream from the start site
in which direction does the RNA polymerase travel along the chain?
3’ to 5’
what terminates the RNA synthesis?
polymerase is dislodged, possibly due to secondary structures that form in the RNA.
what 3 modifications occur to the RNA strands in eukaryotes?
5′ end is capped with 7-methylguanosine
3′ end is cleaved at a region called polyA site
Introns are cut out of the pre-mRNA to yield mature mRNA
where are introns spliced out?
complex of small RNAs and proteins called the spliceosome.
which are the coding parts of the gene?
exons
what is the consensus sequence for the spliceosome
at the start and end of each intron?
contain GT dinucleotide at the 5’ end of the intron and AG dinucleotide at the 3’ end of the intron
what does a spliced intron form
a lariat
where is mature mRNA transported to?
cytoplasm through nuclear pores to the ribosomes
how many amino acids are there?
20 amino acids used to make proteins
how many possible reading frames are there?
3
which end does the amino acid attach to the tRNA?
3’
what are the names of the 3 loops on a tRNA
D loop, T loop, anticodon loop
what are the names of the 3 loops on a tRNA
D loop, T loop, anticodon loop
how is an amino acid bound to its tRNA?
aminoacyl tRNA synthetase
what is the start codon and which amino acid does it relate to?
AUG - methionine
where does the start codon bind to?
the small sub unit of the ribosome
which site do new tRNAs enter the ribosome?
A site
what are the 3 sites on a ribosome?
a, p, e
what happens in the P site of a ribosome?
peptide bond is formed between amino acids
when is translation terminated?
when the ribosome reaches one of the stop codons:
UAA, UAG or UGA
release factors bind and the polypeptide chain is released from the ribosome
what are the size of the two sections of eukaryotic ribosomes?
60s and 40s = 80s
what are the size of the two sections of prokaryotic ribosomes?
50s + 30s = 70s
what are the 3 different layers of the Golgi body
cis, medial and trans Golgi
cis is closest to RER
what are the characteristics of cancer cells?
Uncontrolled growth
Loss of contact inhibited cell division
- results in FOCI FORMATION
Immortal
how does UV light cause cancer?
One type of UV induced DNA damage is the thymine dimer, where the input of energy from UV light causes the formation of covalent bonds between adjacent thymine molecules.
how does UV light cause cancer?
One type of UV induced DNA damage is the thymine dimer, where the input of energy from UV light causes the formation of covalent bonds between adjacent thymine molecules.
what is a DNA adduct?
piece of DNA covalently bonded to a (cancer-causing) chemical. This process could be the start of a cancerous cell, or carcinogenesis.
