Introduction To Genetics Flashcards
(26 cards)
How many coding and non-coding genes are there in the human genome?
Coding: 20,441 including 526 read-through
Non-coding: 22,219 (5952 small, 14, 727 long, 2222 misc)
Significant number of non-coding genes that don’t form functioning polypeptides. Instead they perform regulation, such as translation and transcription. They have lots of functions such as regulation of gene expression.
What are the features of DNA?
- Deoxyribonucleic acid
- 5’ & 3’ according to C position on sugar
- Double helix structure
- Complementarity
- Antiparallel
- 4 base code
- Sugar backbone difference RNA
Secondary structure is: • B form (can also get A form and Z form) • Right handed helix 10 bps per turn • A (more bp/turn) • Z left handed helix
What is a gene?
Part of a DNA molecule that serves as a template for making functionally important RNA
What is a locus?
A unique chromosomal location defining position of a gene
What is an allelle?
Alternative versions of a gene eg ABO locus
What is a genotype?
List of all allelles present at a loci/locus
What is a phenotype?
Observable trait/characteristic – contributed by genotype/epigenetic/env factors
What is a transcript?
A length of RNA that has been transcribed respectively from a DNA template.
What are the features of a protein coding gene?
Exon Exon Exon Exon
| | | |
5’—-⬛️———⬛️——[—🔳- - - -⬜️- - - -⬜️- - - -⬜️- - - -🔲—]—-3’
| | | | | | |
Enhancer Promoter Start Intron Intron Intron Stop
Site Site + intron + Intron
[ ] - open reading frame
Enhancer site: described as being in cis as they are in the same molecule as the gene they are transcribing, also help to control transcription.
Promoter site: acts at a certain site and guides RNA polymerase.
In this way they control and regulate transcription. Described as acting in trans as they are transcribed from a different gene in the genome.
Exons and introns: For RNA production the introns are removed and the exons are made transcribed into a fully fledged polypeptide or protein. Allow alternate splicing - different length transcripts.
What is the central dogma?
The process of replication transcription and translation is know as this central dogma of molecular biology. We originally throught the dogma could only go from DNA - transcription - RNA - translation - protein. But now we know that there are enzymes that can reverse transcribe.
The first step in the central dogma is to separate the two strands. Helicase unzips the two complementary DNA strands resulting in a replication fork. This acts as a template for making a new strand of DNA. Replicase makes a primer as a starting point for new DNA. DNA polymerase binds to the primer and adds bases in only one direction from 5’ to 3’. The leading strand is made continuously, the DNA polymerase? adding bases one by one. the lagging strand runs in the opposite direction so can’t be made this way, instead is added in small chunks know as okazaki fragments. Each fragment is started with an RNA primer. DNA polymerase adds a short row of DNA bases in the 5’ to 3’ direction. The next primer is added further down and a new Okazaki fragment is made, and so on. Once the new DNA has been made exonuclease removes all primers from DNA. Another DNA polymerase then fills in the remaining gaps with DNA. Finally DNA ligase seals off the fragments of DNA in both strands creating a double strand.
DNA production is semi conservative process as it involves one old conserved strand, and one new one.
So leading and lagging are made in different ways but the same enzymes are used for each.
What enzymes are involved in transcription in eukaryotes?
RNA Polymerases I, II, and III are involved in eukaryotic transcription.
RNA polymerase I (localized to the nucleolus) transcribes the rRNA precursor molecules.
RNA polymerase II produces most mRNAs and snRNAs, and miRNAs. It typically has 2 promoters, either a TATA promoter at the - 25 position (usually occurs in genes transcribed by RNA polymerase at a particular stage in the cell cycle), or a GC box. Transcription starts at the +1 base site, so anything upstream (further behind) is described as negative.
RNA polymerase III is responsible for the production of pre-tRNAs, 5SrRNA and other small RNAs. The promoter site is within the gene itself - downstream of the transcription starting base.
The mitochondria and chloroplasts have their own RNA polymerases.
How and why does splicing occur?
During transcription we produce heterogenous RNA or primary messenger RNA transcripts that still contain introns and exons structure like genomic DNA. There are very conserved dinucleotide regions at the ends of the introns - a donor site and an acceptor site.
During splicing these sites are brought together in a mixture of ribonuclear proteins and small RNA molecules to form a complex, bringing these complementary sites together. In doing this they form a loop structure known as a lariat loop.
This whole loop is spliced out of the molecule giving two exons that are spliced next to each other in the spliceosome and an RNA lariat structure.
To the mature messenger RNA, there is addition of a polyamide tail and capping of the 5’ end of transcript (adds a methylated nucleotide that prevents degradation of transcript and assists transportation to cytoplasm).
Splice sites can be weaker or stronger, depending on the tissue the transcript is being modified in.
So you can look at the genomic DNA like a read only molecule, with the premessenger RNA being the editable version.
What is alternative splicing?
Alternative splicing is the mechanism by which ~ 79000 protein coding genes produce ~ 200000 gene transcripts.
Around 90% of human genes are spliced - variants in canonical splice sites (GT and AG) can lead to disease.
E.g. snoRNAs can regulate splice site selection - a sense thought to cause Prader Willi syndrome.
Exon skipping, leading to non-sense mediated decay.
What are the main features of translation?
Code held in mature messenger RNA is decoded to a set of AAs.
RNA transported to cytoplasm.
Translation is initiated in cytoplasmic ribosomes that provide a structure for translation (2 diff subunits 6DS and 4Ds) small holds RNA and A site in the large subunits binds aminoacyl group coming in from tRNA,p site holds the growing polypeptide.
Each AA has its own specific transfer RNA, with an anti-codon (3 base pair complementary to the three base pair corresponding to an AA.
Always starts at AUG - methionine and stops with a STOP codon.
mRNA also has a 5’ and 3’ untranslated regions, have been transcribed but are responsible for stabilising the RNA on the ribosome.
What are the functions of non-coding DNA?
• 1-3% of genomes encodes amino acids/polypeptides
• Much of the non-coding was considered Junk DNA – BUT now know
the intergenic sequence actually transcribed
• A lot of current knowledge came from the ENCODE project
• The great majority of all the genome is transcribed, at least at some
times and in some types of cell.
• Some sort of function (coding, transcribed, protein-binding…) can be
assigned to 80.4% of nucleotides in the genome
- Pervasive transcription
- How do we know this – RNAseq/ transcriptomics
What are the other types of RNA aside from messenger RNA (mRNA)?
Short non-coding rna help produce transcripts. Short non-coding RNA are involved in transcripts.
Transfer RNA that bring AA to the ribosome. And ribosomal rna make up that complex.
MicroRNA (miRNA) - very short, around 22 nucleotides that regulate gene expression at transcription or translation level. Transcribed by RNA polymerase 2 or 3 and produce a primary miRNA transcript that undergoes further processing. Highly tissue specific, eg miRNA 122, is specific to the liver -biomarker for liver disease.
How is DNA compacted within a eukaryotic cell?
DNA helix winds round histone proteins in a ‘beads of string’ style - typically around 8, 1 and 3/4 turns around, to give nucleosomes.
Each nucleosome bunches together to make chromatin.
The chromatin then coils leading to supercoiling allowing them to condense into chromosomes.
What epigenetic modifications can occur?
Epigenetic changes are functional changes to the genome or changes to gene expression - no change to the gene itself.
Can be the source of variation in clinical conditions.
Examples include remodelling of chromatin structure
or
Binding of epigenetic factors to the histone tails, preventing proper coiling of DNA around histones into nucleosomes. This affects availability of gene to be activated as genes become inappropriately accessible (active)/inaccessible (inactive).
E.g. Fragile X syndrome.
What is a karyotype?
• A karyotype is the complete set of all chromosomes of a cell of any living organism.
• The chromosomes are arranged and displayed (often on a photo)
in a standard format: in pairs, ordered by size.
How are chromosome bands labelled?
Petit (p) arm and (q) queue joined by the centromere, with each of the bands labelled from the centromere outwards. Then labelled into regions and sub bands within this.
What are the stages of the cell cycle?
Cell cycle has two parts:
- Growth preparation:
- Interphase: 75% of cell life cycle
- G1: rapid growth
- S: DNA replicates; centrioles replicate.
- G2: cell prepares for cell division; microtubular structures form.
- Cell Division:
- Mitosis: nuclear division
- Cytokinesis: cytoplasm division
What cells undergo mitosis?
- Somatic cells divide by mitosis
- Somatic cells are diploid (2n) i.e two of each chromosome
• During mitosis a 2n nucleus divides to produce daughter nuclei
that are also 2n.
- Mitosis maintains the number of chromosomes.
- Results in cells such as internal organs, skin, bones, blood, etc.
What cells undergo meiosis?
- Sex cells (gametes ) chromosomes divide by meiosis
- Sex cells are haploid (n)
- After cell division the chromosome number is halved
• Results in genetic variation by shuffling of maternal and paternal
chromosomes.
• No daughter cells formed during meiosis are genetically identical to
either mother or father.
What are the potential sources of genetic variation?
Recombination (meiosis), translocation (chromosome level movement).
- Missense mutations: Single nucleotide substitution - effect depends on where in the codon it occurs - if its within the first or second base pair it will likely cause a change in the AA.
- Nonsense mutations: Causes the inclusion of a stop codon, leading to a prematurely shortened transcript or transcript never gets formed -nonsense mediated decay.
- Splice site mutations: Can be detrimental if it affects those conserved dinucleotide or splice site machinery will affect splicing so different splice sites formed. The pathogenicity here is difficult to predict due to alternate splicing and alternate splice sites possible.
- Single aa deletion or insertion – ‘frameshift’ mutations: Insertion or deletion of single nucleotides can lead to stop codons or prevention of stop codon formation leading to very long protein production.
- Repeat variation
- Gene fusions, translocations
