Integrity: Maintaining the Genome & Maintaining the Cell Flashcards
Broadly describe the structure of a chromosome in decreasing size
Chromosome -> wound up chromatin fibre -> nucleosome (DNA wrapped up around protein complex) -> DNA
What is chromatin?
This is the substance in a cell nucleus which is formed by DNA wound around protein cores.
When unravelled it resembles beads on a string
What is a nucleosome?
One unit of chromatin
Why is chromatin formed?
It allows DNA to occupy a smaller space
What is a nucleotide?
The basic building block of DNA
What are the three componants that make up a nucleotide?
What is the name of the sugar present in a nucleotide?
2-deoxyribose
The bases in nuceotide are either ____ or ____
Pyrymidines or Purines
How do you know if a base is either a pyrimidine or a purine?
Is cytosine a pyrimidine or a purine?
Pyrimidine
Is adenine a pyrimidine or a purine?
Purine
Is thymine a pyrimidine or a purine?
Pyrimidine
Is guanine a pyrimidine or a purine?
Purine
How are DNA strands bonded?
Hydrogen bonds between the bases
What bases pair with which bases?
Remember : GCAT
How do the three componants of a nucleotide come together to form DNA?
The back bones are made of the phosphate and sugar which are bonded by the bases
What is a nucleoside?
Just the sugar and base componant
How are nucleosides named?
Not going to bother remembering this. Just a refresher
On what carbon groups are the sugar linked by the phosphodiesters?
5,3
What is the advantage to linking the sugars by two different carbon groups?
It gives DNA direction, it wll always go from a 5 end to a 3 end. The 5 end has a free phosphate while the 3 end has an OH
What defines the DNA sequence?
The order of the bases
As well as protein what else is found in a nucleosome?
Histones - these bind the DNA to the protein
How many histones are in a nucleosome and what are the 4 names?
What is the advantage to the 4 unique base pairings?
Each strand can be used as a template to replicate it’s partner
How does DNA begin splitting for replication?
Origins of replication are areas where splitting can begin with the help in initiator proteins
Where does replication begin?
Replication fork begin at the origin of replication and branch out bi-directionally unzipping as they replicate
Most important enzyme in DNA replication?
DNA-polymerase
Which direction in DNA synthesised in?
A 5’ -> 3’ direction
DNA ploymerase adds new nucleotides to the 3’ end of the growing chain
How does the polarity of the two newly synthesised DNA strands at a replication fork differ?
Opposite polarity
What problem does the opposite polarity of the two new replicated strands creat?
DNA can’t replicate bidirectionally
How is the problem of directional synthesis overcome to ensure by-directional syntheses?
What are the lagging strands called?
Okazaki fragments
What is the enzyme that joins together okazaki fragments?
DNA ligase
DNA polymerase can only continue existing chains, how are new chains started?
What enzyme helps unwind the double helix?
DNA helicase
DNA polymerase is highly accurate
However if an error does occur a missmatch actually wont bind, so how does it stay? (the occasional mutation must occure for evolution)
If unrepaired it is cemented in in the next round of replication
How are errors usually spotted?
By proofreading
What is the occurence of errors with and without proofreading
1 in 10^7 bases without proofreading
In reality with proofreading more like 1 in 10^9 bases
How does DNA missmatch repair occure?
DNA repair proteins bind forming an “oxbow lake” and cutting off the error
5 Things that can damage DNA
- Synthesis missmatch
- UV light
- Radiation
- Chemicals
- Cellular metabolism
How does UV light specifically damage DNA
It created Thymne dimers
How does common damage repair look like? Why is it often not that bad?
It’s not that bad because information is redundent in the other strand so it can often remake it self the same
What is Xeroderma pigmentosum
Genetic defect
* Affected individuals cannot
repair thymine dimers (caused by UV)
* Severe skin lesions, including
skin cancer
How does mitochondial DNA differ from nuclear DNA?
Only other place DNA is found that isn’t the nucleus?
Mitochondria
What is RNA?
It is a short single stranded copy of a single gene (one strand of DNA will contain many many genes)
It is then used to make proteins
What are six differences between DNA and RNA
What does RNA contain in place of thymine?
Uracil
What are the codes for the four bases on RNA?
GCAU
Thymine replaced by uracil
What is the difference between deoxyribose and ribose?
When transcribing DNA which strand is the coding strand and which is the template strand?
The one being copied into RNA is the coding strand
The one being used to make the copy is the template
Names for which strand is being copied and which is used to make the copy?
Copied: coding strand
Other: template strand
Another name for the template and coding strands?
Coding strand: sense strand
Template strand: anti-sense strand
What is the enzyme that synthesises RNA?
RNA polymerase
What direction is RNA synthesised?
5’ to 3’
same as DNA polymerise
What does DNA stand for?
deoxyribonucleic acid
What does RNA stand for?
Ribonucleic acid
Difference between mRNA and RNA
mRNA is the main type of RNA and is the instructions or blueprint for the protein to be synthesised int he ribosome
Other types are tRNA (transfer RNA) and ribosomal RNA (rRNA) which help the ribosome actually build the proteins
What is the specific enzmyme that makes mRNA?
RNA polymerase II
All cells contain all genes. So how do cells become specialised?
Through gene expression
Gene expression turns on certain genes
What are promotors and enhancers?
What are transcription factors?
Three steps to gene expression
- Promotors and enhancers in place for gene you want expressed
- Transcription factors bind to the promotors and enhancers
- RNA polymerase can then bind to transcription start site
Often gene expression is more complicated that simply ON or OFF. What are the different ways the same gene can be expressed to make differing RNA?
Expression of a single gene can be controlled at various
levels to give different products:
- alternative promoters - different regions of DNA that can initiate transcription of a gene found upstream of the gene resulting in different RNA, basically just starting transcription at different points
- alternative splicing - can splice different parts of the same gene together
- alternative polyadenylation - the polyadenylation can cut off differing sections of the transcribed RNA essentially changing the tail length of the RNA
What are the key sections which lead to splicing?
Introns and Exons
Introns: parts which are non-coding
Exons: coding parts
How do introns and exons lead to alternative splicing?
The whole thing is initially transcribed into a primary transcript.
Later the introns are removed by something called the spliceosome creating the final peice of mRNA.
Different spliceosomes recognise different boundaries between introns and exons known as splice sites. Splice sites can also remove exons sandwiched between introns resulting in multiple different sequences of mRNA
What is Capping and Polyadenylation?
Its is the sealing on the RNA.
Capping is at the 5’ end and polyadenylation is at the 3’ end
What does the cap consist of?
a guanine nucleotide that has a methyl group attached to the 5’ end of
the RNA in an unusual way
What is Polyadenylation?
- A polyA tail is a string of adenylate residues added to the 3’ end of anmRNA
- Not found on rRNAs or tRNAs
How can alternative polyadenylation create differing final RNAs?
The polyadentlation cuts off a portion of the transcribed RNA (clevage). By changing the point at which it does this it can create differing mRNA sequences
What are the purposes of the untranslated regions?
- 5’ untranslated (5’UTR) is the region of an mRNA that is
found upstream of the translated region - function of 5’UTRs is mostly unclear, may affect
translational control - 3’ untranslated (3’UTR) is the region of an mRNA that is
found downstream of the translated region - 3’UTRs can determine the stability of the mRNA
What is a non-coding RNA?
This is any RNA that is not used to make proteins but instead the RNA is the final product in itself.
Examples being rRNA - makes up the structure of the ribosome and help catalyse protein synthesis
Spliceosomes - these are made up of RNA
Where is RNA transcribed and processed and where is it translated?
In the nucleus: transription and processing
In the cytoplasm: translated into proteins
Translation: what is a codon?
A condon is a set of three bases which corresponds to a specific amino acid
How many possible codons are there?
4 different bases, and each codon is made of three bases read in an order of 5’ to 3’
Therefore there is 4^3 combinations = 64 codons
61 codons specify for 1 in 20 amino acids
3 are stop codons
Why is readng frame important?
Because a codon is made of three bases there are three possible reading frames that will give completely different amino acids
How does the 5’ cap relate to translation?
Thought to be involved in initiation
Most mRNAs need a 5’cap to be translated efficiently (there
are some exceptions e.g. polio virus RNAs are uncapped)
How is translation initiated?
the pre-initiation complex (PIC) scans the mRNA for the translational start site (AUG codon)
The PIC consists of the 40S ribosome (small ribosome) bound to elongation
initiation factor 2 (eiF2), GTP and most importantly the initiator MET-tRNA.
MET-tRNA has the anti codon to AUG and binds it.
Once it binds it this draws in 60S ribosome which combines to form the final 80S ribosomal complex.
Now translation can begin (elongation)
What codon is the initiation codon?
AUG
Also known as the Kozak (Consensus) sequence
What come after initiation of translation?
Elongation
What is elongation?
All the reactions involved in translation from the formation of the
first peptide bond to the addition of the last amino acid
How does elongation work?
Each unique aminoacyl-tRNA can come into to bind to it’s corresponding codon if it’s being read by the ribosome 80S complex.
Once it binds to the corresponding mRNA codon it attaches it’s amino-acid to the growing polypeptide chain
How is the correct amino acid bound to the correct tRNA in order to make the corresponding aminoacyl-tRNA?
It is bound using the corresponding tRNA-synthetase enzyme
Example shown is the amino acid tryptophan and the tRNA-tryptophan. The corresponding enzyme is therefore tryptophanyl tRNA synthase
What is the function of the 40S (small) ribosome vs the 60S (large) ribosome?
The 40S helps match the correct aminocytl-tRNA to the correct codon
The 60S ribosome catalyses formation of peptide bonds that
covalently link amino acids
Elongation in more detail, what are the three docking sites and how does the process work?
There are three docking sites:
E - ejection
P - polypeptide
A - amino acid
- The correct aminocytl-tRNA binds to A dock
- polypeptide is transfered from the peptidyl-tRNA (P dock) to aminocytl-tRNA by the creation of a new bond
- Large subunit translocates
- Small subunit translocates
What is the complex called that is dock in the P-dock?
Peptidyl-tRNA
Three stop codons?
UAA, UAG and UGA
What happen when a stop codon is reached (termination)
The stop codon aren’t recognised by of the aminoactyl-tRNAs.
Instead they are recognised by a single class 1 release factor
protein (eRF) which transfers a hydroxyl group from water to
hydrolyse the polypeptide-tRNA linkage and, thereby, lead to
release of the polypeptide chain from the last tRNA.
What is the name of the thing that recognises the stop codon?
Class 1 release factor
protein (eRF)
What defines cell differentiation?
The presence of different transcription factors
You can put the nucleus of a liver cell into a muscle cell and it will still become a muscle cell because of the presence of muscle specific transcription factors MyoD
How do transcription factors know what genes to bind to?
They can form bonds with specific promotors ascciated with different genes
What is the difference between a promotor and a transcription factor?
Promotor: Like a shop sign but for genes. The sign specifying “hey it’s me, toy shop”. Present in all DNA (the shopping center)
Transcription factor: Looks for specific promotors. Shoppers who are looking for toy shops. If they are the only shoppers prensent in the shopping center then the shopping center basically becomes a toy shop
When differentiated cells divide they generally remain the same cells. How?
The genes activated by transcription factors generally contain instruction to create more of the same transcription factors. The transcription factors are inherited by the daughter cells
What is chromatin remodelling?
This is where transcription factors can actually re-model chromatin and histones in order to further express their target genes
What is DNA methylation?
This is a form of cell differentiation memory through silencing.
By adding (and maintaining) a methyl group to certain part of the DNA this can block the binding of transcription factors thus preventing them from accessing genes.
What is X-inactivation?
Eaely on in female mammal embryonic development one of the X-chromosomes randomly condenses in each cell.
These then clone themselves and females end up with a patchwork of X-chromosomes from each parent.
What is a multipotent hematopoietic stem cell?
A multipotent stem cell can be inferred by the
ability of a single stem cell to reconstitute a
complete blood & immune system when
transplanted to an individual lacking bone
marrow
What is GATA1
This is the transcription factor which defines a RBC.
It binds to the genes expressing alpha-globin and beta-globin
What are stromal cells?
These are cells present in bone marrow that encourage stem cells to remain stem cells and not differentiate
What is assymetric stem cell devision vs independent choice?
Assymetic: fate deceided on devision, one will always be a stem cell and one always a differentiated cell
Independent: both new cells can be either stem cells or differentiates cells witht he choice being influenced by outside factors. This is more flexible to needs
What are paneth cells?
These are found in the gut next to intestinal stem cells.
They release WNT which make stem cells proliferate and maintain the stem cell state
In the abscence they will differentiate
Their prescence means that you get intense proliferation from the site of peneth cells which then gradually differentiate into intestinal epithelial cells as they get pushed aways from the paneth cells sites
What is the link between stem cells and cancer?
Many cancer occure at sites containing stem cells as all these cells of proliferation is a breeding ground for uncontrolled proliferation
E.g. intestinal, epithelial, bone marrow and reproductive organs
What is Familial adenomatous polyposis coli (FAP)
This is an inherited conditon making someone more predisposed to colon cancer.
It results in a deletion or inactivation of one copy of the APC gene. If the other then becomes deleted they have no APC.
If you remember the WNT pathway APC inhibits proliferation and in turn is inhibited by WNT. Lacking apc therefore leads to excessive proliferation and you end up with giant intestinal cryps which become cancerous polyps.
Describe the intestinal crypt?
Corn
