Structure and function of the Human Genome Flashcards
What are the 4 types of chromosomes?
Telocentric is not found in humans
What is a nucelosome?
- DNA double helix binds to histones
- Octamer of histones form nucleosome
- H1 stabiilises this structure
- Histone tails have many + aa side chains which interact with - charged phosphates of the DNA helix. This electrostatic attraction constrains the DNA to wrap around the histone octamers.
What is the difference between euchromatin and heterochromatin?
Euchromatin: Allows gene expression due to loosely compact nucleosomes
Heterochormatin: Highly condensed and wound tightly around the histone, genes not expressed
Euchromatin also stains differently to heterochromatin which gives rise to diff banding patterns
What are centromeres and what is their function?
- Rich in heterochromatin
- Normally is a highly repetitive DNA sequence- characteristic of non geneic sequences
- Keep sister chromatids together
- Attach to microtubules during cell division
What is the function of telomeres?
Protect the ends of the chromosome
Telomerase repairs telomeres but is only active in certain cell types
If telomerase is switched on in the wrong cells this can lead to cancer
What is the nuclear genome and exome?
All the genetic material in a cell. 22 pairs of autosomes and pair of sex chromosomes. The actual DNA sequence and the transcribed units (genes) within the DNA. These are involved in:
- •Protein coding
- •RNA-only coding (non-coding transcripts; make RNA but not protein)
exome: just the parts of the genome which code for protein, i.e. all the coding exons
Give definitions for: Exons, utr, introns, Promoter region
Exons: code for amino acids except for Untranslated Regions (5’UTR & 3’UTR)
UTR: contain regulatory elements (important for control of p.synthesis). Don’t code for any aa.
Introns: non-coding gene regions between exons
Promoter region: 5’ of gene; contains important regulatory elements for transcription
What is mitochondrial genome?
What is the epigenome?
Chemical compounds that attach to DNA or histones and can affect gene activity and expression E.g. DNA methylation, histone acetylation. How do they affect gene activity?
- Alter chromatin structure, recruit histone modifiers
- Repress transcription
- Responds to environmental cues (cellular and external)
What are the different types of gene expression?
This is due to differential gene expression:
In time (temporal)
- Development (i.e. embryos versus adults a different set of genes need to be active)
- In response to hormones, infection, other signals
Spatially
- Diff tissues/cells express different genes (e.g. brain vs liver)
Failure to regulate gene expression tightly may lead to…
What is meant by the term central dogma?
You will always go from DNA to RNA to protein and never the other way round
What is sense and antisense?
The sense strand has the same sequence as the mRNA molecule
The opposite, antisense strand is used as the template to generate this identical mRNA strand
This is important to make sure that the aa sequence is correct
Describe transcription
DNA helicase unzips the DNA
RNA polymerase attaches to a non coding region in front of a gene.
Free RNA molecules form complimentary base pairs w/ DNA strand.
RNA polymerase joins nucleotides juntos to make mRNA
mRNA leaves the nucleus via a pore
What is pre mRNA and what happens to it?
The molecule that’s directly made by transcription in a eukaryotic cell is pre-mRNA. To mature, necesita undergo:
Addition of a 5’ cap to the beginning of the RNA
Addition of a poly-A tail (tail of A nucleotides) to the end of the RNA
Chopping out of introns and pasting together remaining exons
Describe the 5’ cap, the poly-A-tail and splicing process
The 5’ cap is added to the 1st nucleotide in transcription. The cap is a modified G nucleotide. It protects 5’ end from degradation, facilitates transport into cytoplasm
A polyadenylation signal in RNA during transcription causes an enzyme to half the RNA. Polyadenylation polymerase adds 50-200 A nucleotides to the cut end, forming a poly-A tail. The tail protects the 3’ end.
Finally hay intron removal and splicing juntos of exons
What is the triplet code?
- RNA “read” in threes = codons
- 64 possible combinations of 4 bases
- Codon → specific amino acid
- 20 amino acids
- Degenerate = >1 codon can code for same amino acid
What is meant by open reading frame?
How is translation initiated?
The ribosomal binding site in the 5’ UTR is recognised. This binds to comp RNA in the small subunit of the ribosome.
Once that binds, initiator tRNA will look for AUG. This codes for methionine- the aa which starts every protein sequence.
Once that first tRNA molecule has bound to the start codon, the small and large ribosome subunit bind juntos
Describe the next part of translation after initiation
So you have the full ribosome complex. This creates three sites: exit site, peptidyl site, aminoacyl site.
The 1st tRNA is in the peptidyl site. tRNA carries its attached aa residue and comes into the aminoacyl site. The bond between the tRNA and its aa in the peptidyl site breaks, a new bond forms between the tRNA and the a.acyl site. The same happens again, but this time the tRNA comes into the exit site.
This chain continues til a stop codon. A release factor triggers the end of translation, the release of the peptidyl chain, and the disassociation of the ribosomal complex.
What is the cell cycle?
- G1 = Cell makes a variety of proteins needed for DNA replication
- S = synthesis; chromosomes are replicated so that each chromosome now consists of two sister, identical chromatids
- G2 – synthesis of proteins especially microtubules
- Some cells don’t replicate; some are senescent.
- Transcription and translation occurs throughout interphase
What is mutation/variant?
Mutation/variant: a change in the genetic material
A pathogenic mutation (pathogenic variant) results in an alteration of the function of the gene product and can cause a disease phenotype
What are the types of variants?
Differentiate between synonymous and non synonymous variants
Synonymous base substitution: silent mutation
Non synonymous is categorised into missense and nonsense:
- Missense: substitution causes a change in the aa type produced. Effects are difficult to predict
- Nonsense: substitution introduces a premature stop codon.
Indels can be…
In-frame (if the bases inserted/deleted are multiple of three) or frameshift (not multiple of three)
How can variants cause loss of function?
- Variants reduce activity/decrease stability = hypomorph
- Variants which cause complete loss of gene product = null allele/amorph
Eg sickle cell, CF etc. These are recessive, so often 1 healthy copy of gene is sufficient to produce enough protein for a sub clinical individual
Dominant loss of function: Haploinsufficiency (loss of 1 allele is sufficient to cause problem). Full amount of protein product is required, if not disease occurs. Eg MonoMac syndrome, Marfan syndrome
How can variants cause gain of function?
Mutant allele produces a mutant protein which is damaging (upregulated or different role). Mostly in dominant diseases
eg Achondroplasia (gain of function mutation in FGFR3 leads to decreased bone mass by altered regulation of osteoblast/clast activity). Due to overactive protein
What is a dominant negative variant?
Protein produced by mutant allele interferes with role of wildtype (normal) allele. Examples:
- Mutation in transcription factor removes activation domain but still contains DNA binding domain. So it can bind to the DNA, but can’t trigger transcription; blocks wildtype from binding
- Mutation in a dimer protein means it lacks function but can still dimerise with wildtype protein. However the resulting dimer is non-functional (eg sodium channels)
What is the difference between germline and somatic mutations?
Germline affects the gametes, so can be inherited and passed down through generations.
Somatic only affects non-germline cells so cannot be passed down: only affects that individual, not the gametes
Mosaic mutations can affect germline and somatic cells so still have the possibility to be passed down.
