LM5 DNA and molecular biology Flashcards
how is DNA organised in bacteria
in the nucleoid in plasmids
bacterial chromosomes are usually circular and occupies more than 1/4 of the volume of the cell
how is DNA arranged in most eukaryotes
Nuclear DNA is in linear chromosomes and the mitochondrial genome is circular.
In plants the DNA is in the nuclei, mitochondria and chloroplasts
how does mitochondrial and chloroplast DNA differ
mitochondrial DNA is 5 times smaller
describe histone proteins
they are positively charged proteins that interact with DNA
what is the average structure of a nucleosome
it is around 150bp and 8 histone proteins
what are the types of eukaryotic chromosomal DNA packaging
DNA double helix - nucleosome
chromatin - scaffold associated chromatin - condensed chromatin - compacted chromosome
describe chromatin
nucleosomes pack into a coil that twists into another large coil forming these fibres
describe scaffold- associated chromatin
the chromatin fibre fold to form loop domains attached to a protein scaffold
describe condensed chromatin
further condensed
describe the compacted chromosome
during mitosis the loops coil even further
describe DNA packaging in prokaryotes
supercoiling compacts bacterial DNA and the DNA is attached to a protein core
the E.coli genome has 50 supercoiled domains
what are nucleotides comprised of
a pentose sugar 2’ deoxyribose
nitrogenous base
phosphate group
what are the nitrogenous bases
cytosine, thymine, adenine, guanine
what are purines
purines have 2 rings - Adenine guanine
What are pyrimidines
one ring - thymine and cytosine
how many hydrogen bonds occur between the bases
A=T two bonds
C-=G three bonds
What is Chargaff’s rule
abundance of purines is equal to the abundance of pyrimidines
who discovered the structure of DNA
Rosalind Franklin working with Maurice Wilkins produced x-ray crystallography images from purified DNA
what did the x-ray crystallography suggest about the structure of DNA
bases were on the inside and the sugars and phosphates on the outside and it also suggested the molecule was helical with 10 nucleotides per turn and anti-paralles
what are the 4 key features of DNA
it is a double stranded helix of uniform diameter
it is antiparallel
has major and minor grooves
usually right handed
what does it mean when DNA is right handed
curves in the direction of the fingers on the right hand when the thumbs point upwards
describe the antiparallel nature of the DNA strands
it is determined by the sugar-phosphate bonds
phosphate groups connect to the 3’C of one sugar and the 5’C of the next sugar by phosphodiester bonds, the two chain ends differ, one has a free 5’ phosphate group and the other is a free 3’ OH group
the 5’ end of one of the strands is a base paired to the 3’end of the other strand in a DNA double helix
describe why the helix is of a uniform diameter
Chargaff’s rule
describe major and minor grooves
minor grooves occur when the backbones of two strands are closer together on one side of the DNA helix
what is the significance of major and minor grooves
DNA bonding proteins often bind in the major grooves
when does DNA replicate
during the S phase in the cell cycle
define semiconservative replication
produces molecules containing one parent strand and one new daughter strand
define conservative replication
produces one completely new molecule and preserves the original molecule
define dispersive replication
produces two molecules with old and new DNA interspersed along each DNA strand
where does the initiation of DNA occur
replication origins
how are replication origins bound
bound by replication proteins to initiate replication
what occurs once replication is initiated
the replication origins are recognised by a replication complex and two replication forks are formed moving in opposite directions
describe the differences in replication origins between different chromosomes
humans have large linear chromosomes and can have many hundreds of replication origins, whereas small circular chromosomes have a single replication origin
what drives DNA replication
loss of phosphate groups on the deoxynucleotide triphosphates releasing energy to drive reactions once the DNA polymerase adds it to the strand
describe DNA replication and the enzymes catalysing it
Helicase unwinds the double helix exposing the bases
RNA primer us made which is complimentary to the DNA template and primase synthesises RNA one nucleotide at a time
DNA polymerase synthesises DNA in the 5’3’ directions
RNA primer is later removed and DNA fragments are joined by ligase
what is the leading strand
3’end of the strand as the synthesis of this strand is continuous
what is the lagging strand
5’ start and the synthesis of this strand is discontinuous and Okazaki fragments are formed.
what is the end replication problem
the lagging strand cant be completed right to the end and the end of chromosome =s will get shorter with each round of replication
what are telomeres
chromosome ends
what is the alternative method of replication of telomeres
telomerase uses an RNA template made by primase to extend the telomere and telomerase moves to the new end and DNA polymerase fills the gap and this process can be repeated multiple times to lengthen the telomere
what is the purpose of the sliding clamp in DNA processivity
sliding clamp helps to keep DNA polymerase attached to the template and it can incorporate more nucleotides before detaching compared to without a clamp
define transcription
copies information from a DNA sequence to a complementary RNA sequence
what are the main differences between DNA and RNA
The sugar is ribose instead of deoxyribose
uracil is present instead of thymine
single stranded
can base pair with itself and DNA
what are the different classes of RNA
mRNA
tRNA
rRNA
define transcriptome
all RNA molecules produced from a genome. Not all of these are translated, some are non-coding RNAs
what is a gene
unit of inheritance and a stretch of DNA that encodes a functional product
how are genes orientated
they can be orientated in either direction in the genome so the coding strand be either the top or bottom one but by convention we write it as the 5’3’ strand
define promoter sequence
directly upstream of genes and contain binding sites for transcription machinery
what are enhancers
regulatory sequences located far from genes and can be millions of base-pairs away from the gene
how do enhancers and promoters interact
the 3D conformation of eukaryotic chromosomes.
DNA bending allows transcription factors to interact with RNA polymerase
how can genes be regulated
transcription - which genes can transcribe and when
transcript stability - rate of transcript degradation
RNA processing
translation initiation
post-translational protein modification
what is the major gene control point
transcription initiation
how can DNA sequences instruct protein binding
DNA binding proteins contain domains that can interact with DNA in a sequence-specific manner
for example the helix-turn-helix motif binds to the major groove and first helix interacts with the sugar-phosphate backbone to orient the DNA-binding helix which interacts with the bases
where does protein sequence specificity come from
comes from the protein having a surface that is chemically complementary to the DNA
what kind of effect can transcription factors have
activating or repressing
what are the components of transcription
RNA polymerase
DNA template
Ribonucleoside triphosphates
how does RNA polymerase differ in prokaryotes and eukaryotes
Prokaryotes have one RNA polymerase
Eukaryotes have RNA polymerases
what are the three RNA polymerases in eukaryotes
1 - ribosomal RNA
2- messenger RNA
non-coding RNAs
small nuclear RNA
3- transfer RNA
rRNA and snRNA
what are the three stages of transcription
initiation
elongation
termination
describe the initiation stage of transcription
it initiates at promoters which is a sequence that controls the expression of a gene
promoters contain binding sites for transcription factors and RNA polymerase
directly upstream 5’ of a protein coding sequence
promoters dictate the direction of transcription
DNA helix is unwound
describe the elongation stage of transcription
about 10bp are unwound at a time
RNA polymerase reads the template and uses ribonucleoside triphosphates to generate the RNA strand in a 5’3’ direction
no proofreading
describe the synthesis of RNA
it doesnt require a primer
ribonucleotides are added to the 3’ end of the transcript
describe the termination of transcription
formation of phosphodiester bonds stops and RNA-DNA hybrid dissociates
RNA polymerase dissociates from DNA
describe prokaryotic gene organisation
transcription unit contains a coding region which is linear complementarity between DNA and mRNA
1 protein is produced from 1 gene
describe polycistronic gene organisation
multiple genes are controlled by a single promoter (operon)
multiple proteins are produced and there is a mechanism for the co-regulation of these genes
describe how transcription is coordinated with transcription factors
genes to be regulated simultaneously may be far apart or on different chromosomes and co-regulation can be achieved by having related regulatory sequences
describe eukaryotic gene organisation
transcription units produce pre-mRNA after transcription which contains introns and exons and after splicing a strand of mRNA is produced which contains only exons which are the base sequences that code for proteins
what is splicing
it turns pre-mRNA with introns and exons to mRNA with only exons
how is splicing catalysed
spliceosome in the nucleus
when are introns removed
removed by splicing prior to translation
describe the action of splicing
small nuclear ribonuclear protein particles bind to consensus sequences in RNA near the 5’ donor end and 3’ acceptor splice sites
binding of snRPs recruits other proteins and a cut is made between the 5’ exon and the intron
what kind of structure does tRNA form
cloverleaf where about half the nucleotides are base paired
contain many modified nucleotides such as pseudo uridine
what kind of attachment sites do tRNA have
they are covalently attached to a single charged amino acid
they bind to mRNA with their anticodon
what are aminoacyl -tRNA synthetases
they attach amino acids to tRNAs
what is wobble
reduces the number of tRNAs needed by enabling one tRNA to read more than one codon
what are non-Watson Crick base pairs
G-U base pairs
Inosine can base pair with A,C,U
how are the ribosomal components held together
hydrophobic forces
describe the three tRNA binding sites in ribosomes
A - tRNA anticodon binds mRNA codon
P-amino acid added to the polypeptide chain
E- exit site - uncharged tRNA is released from here
what subunit of ribosomes is mRNA associated with
the small subunit
what are the stages of translation
initiation
elongation
termination
What do most chains initiate with
AUG methionine
Describe translation initiation
5’ cap interacts with the small ribosomal unit kozak consensus sequence used to find the initiation codon and position the ribosomes
tRNA binds to AUG start codon completing the initiation complex then the large ribosomal sub unit joins the complex and occupies the p site
describe translation elongation
bond between the tRNA and its amino acid is broken in the p site and a peptide bond is formed between the amino acid that has just been released from the P site and the one attached to the tRNA in the A site
the ribosome shifts along one codon at a time
describe translation termination
a release factor binds to the complex when a stop codon enters the A site the release factor disconnects the polypeptide from the tRNA in the P site
