Human genome Flashcards
What are the names of the short & long arms in chromosomes?
How many autosomes & chromosomes in the human somatic cells?
What happens after pre-mRNA splicing?
What is alternate splicing?
What do the products of alternate splicing allow for?
How would you define exons within a gene?
P = small, Q = large
23 chromosome pairs - 46 total chromosomes (22 autosome pairs)
PolyA tail added & mRNA transported from nucleus to cytoplasm
Exons from different genes joining together after splicing
More possibilities of different proteins
Percentage of gene that is protein coding
What are gene families?
How are genes arranged in the globin gene families on their chromosomes?
Why is this significant in evolutionary terms?
Set of similar genes formed from duplication of an original gene with base changes/mutations
In order of genes from embryo, to fetus, to adult
Genes organised in way needs to transcribe to progress in development
Why are there multiple histone genes in the histone gene family for DNA packaging?
What is unique about the histone genes across the different chromosomes?
What is the evolutionary significance?
What are the outcomes after gene duplication? (3)
Need lots of histone available when DNA replicates so it can constantly condense the chromatin as DNA replicated
Each member of histone gene family code for the same protein (histone)
Kept the same sequence due to the function of the histones in DNA replication & storage - huge selective pressure
- Genes stay similar: selective pressures on both genes (like globin & histone gene families)
- One copy mutates & loses function (pseudogenes) - selective pressure on 1 gene
- One copy acquires a new function - selective pressure on 1 gene
What is a LINE?
What do they do?
What do they encode as a result of their function?
How large is a full length L1 element?
What is contained on the LINE DNA?
Long interspersed nuclear element (L1)
Copy themselves & re-insert copy (transposition) into different locations in chromosome - autonomously active
Proteins/enzymes to replicate their own DNA & insert it into chromosomes
6000bp
Promoter
ORF1: binds RNA & DNA & acts as chaperone
ORF2: encodes poly protein with reverse transcriptase & endonuclease activities
PolyA stretch at 3’ end
What are the first 3 steps in target-site-primed reverse transcriptase of LINE prior to recognising the chromosome site?
What are the next 3 steps in LINE mRNA recognising the chromosome site & producing the cDNA strand?
What are the last 3 steps for forming double stranded DNA & full insertion into the chromosome?
- LINE promoter recognise by human RNA polymerase II & transcribes into LINE mRNA
- mRNA transported into cytoplasm & ORF1 & ORF2 proteins translated
- ORF1 & ORF2 proteins bind to mRNA & chaperone activity escorts mRNA back into the nucleus
- LINE mRNA anneals to rich T region in DNA through rich 3’polyA sequence tail
- ORF2 endonuclease activity cleaves one strand of the chromosome liberating a 3’OH of the DNA
- 3’OH provides primer for ORF2 to form cDNA complimentary strand with reverse transcriptase activity using the mRNA as a template
- RNaseH degrades mRNA strand by cleaving phosphodiester bonds in mRNA that is H bonded to DNA in hybrid
- DNA polymerase replaces RNA strand with DNA to form double-stranded DNA
- DNA ligases catalyses formation phosphodiester bonds between LINE and chromosome
How can LINE disrupt gene transcription? 2 ways
What diseases are caused by LINE insertion?
What happens at the 5’ end of some LINES?
In what cells are LINES more abundant?
What modification is often made to a lot of LINES?
What is the function of the FMO1 gene in mammals?
What happens to this gene as a result of LINE insertion in humans?
- Insertion into promoter region - silences a gene
- Insertion into intron makes gene longer - transcription is slowed down
X-linked muscular dystrophy, haemophilia & colon cancer
Truncated - meaning reverse transcriptase can’t transcribe entire LINE mRNA which prevents transcription of truncated LINEs
Germline
Methylated
Enzyme (flavin containing monooxygenase) to detoxify foreign chemicals
LINE inserts into promoter & inactivates its transcription in liver
What are SINES?
What length are they?
To what kind of organisms are they specific to?
The Alu1 repeat is the most abundant family of SINES, how many occur?
How did they discover the Alu1 repeat?
Short interspersed elements
280-300bp
Primates - event in evolution
1.2 million times
Digestion of the human genomic DNA with enzyme Alu1 & run on agarose showed a bright band of a specific DNA repeat - named Alu1
What are the elements on the Alu1 DNA repeat?
What is the origin of the alu1 sequences?
How does SINE transposition occur?
How is SINE inserted into the chromosome? 2 steps but largely speculation
What diseases does insertion of SINE cause?
Why is the Alu1 repeat not capable of being autonomously active like L1/LINE?
Sites A & B are internal promoters - binding sites for host RNA pol III
Rich PolyA region at 3’
7SL RNA or tRNAs - both transcribed by RNA pol III
Via RNA transposon/intermediate by human RNA pol III
- SINE mRNA copied by reverse transcriptase by L1 element
- SINE mRNA integrated into human chromosome similarly to L1
Haemophilia, chromic haemolytic anaemia & cystic fibrosis
Doesn’t code for proteins with chaperone, reverse transcriptase or endonuclease properties - relies on L1 for integration & copying by RNA pol III
What is a psuedogene?
What is a type 1 pseudo gene?
What is significant about type 1 pseudogenes in different species?
What is an example of a type 1 pseudogene?
What is a type 2 pseudogene called?
How is it different to type 1?
What happens to it on mutation?
Why is the mutation not fatal?
What is an example of a type 2 pseudo gene?
Resembles a functional gene but doesn’t code for a functional RNA or protein
Gene duplication causes a copy to be silent/inactive
Can be functional in 1 species but not in the other
Globin genes
Unitary pseudogene
Not a member of a gene family- only occurs once
Silenced & becomes a pseudogene - but compensates for a product of gene on silencing (e.g vitamin C)
Can be tolerated as usually the gene product can be accumulated through another means e.g diet
L-gulono-gamma-lactone oxidase pseudogene (synthesises absorbic acid/vitamin C)
What is a type 3 pseudogene?
How does it become a psuedogene?
How is it produced?
What are its features and how have these derived?
What is a benefit of processed pseudogenes?
Processed pseudogene
Functional gene, transcribed & then becomes pseudogene on reverse transcription (cDNA product)
Reverse transcription of mRNA functional gene results in cDNA integration into chromosome as a processed pseudogene instead of a functional gene
Has no promotor or introns & has a 3’A rich region - due to its mRNA origin
Do not interfere with functional genes - don’t affect our health
What are the mitochondria’s 37 genes?
How is the mitochondrial genome arranged with its two strands?
What is the control region?
What happens after transcription?
How many RNA molecules are formed?
What are there not? (2)
How do the anticodons compare in mitochondrial & nuclear genome?
Why is mitochondrial DNA more prone to mutation? (2)
rRNA genes, tRNA genes & polypeptide coding genes for oxidative phosphorylation
Circular genome - heavy strand encoding 28 genes rich in G on the outside, and light strand encoding 9 genes rich in C on the inside
Where RNA polymerase binds to transcribe the genes
Whole strand is cleaved to produce individual RNA molecules
2 - heavy & light
Gene overlap, introns
Has different anticodons so mitochondrial genome encodes its own tRNA
- Not protected/packaged by histones as circular
- Reactive oxygen species concentration is high in mitochondria
Why is the gut microbiome significant?
How do microbes help us?
How can you analyse the microbiome cheaply?
What aspect of the 16S rRNA gene allows for PCR?
What happens after PCR of the variable regions?
What is the limitation?
Microbes encode proteins that we cannot produce
Feed - process food & provide vitamins
Form - help form immune system development
Protect - fight off pathogenic bacteria
Associated with obesity, immunity, mental health, cancer, drug response
Take a fecal sample & amplify bacterial 16S rRNA gene with PCR
Conserved regions between the variable regions allow to design primers for PCR to determine sequence of variable regions
Analyse sequences by comparing against data base of known 16S rRNA sequences
Can only amplify what is known - require conserved sequences
What is the metagenomic approach to sequencing bacterial DNA in gut?
What are the pros?
What are the cons?
Sequencing the entire DNA (not just 16S rRNA) & performing bioinformatic analysis (from fecal sample)
Can’t culture all bacterial species in a lab
Expensive
Contains both human & bacterial DNA so need extra bioinformatics analysis
What is the transcriptome?
What do rRNAs do?
What other RNAs make up the transcriptome?
What does the ribosome assembly RNA look like?
What are these different aspects?
How is it transcribed & what is the end product?
What happens to the product?
All RNAs produced by the cell
Components of the ribosome
tRNA, short noncoding RNA, long-non-coding RNA
RNA pol I promoter, ETS1, 18S gene, 1TS1, 5.8S gene, 1TS2, 28S gene, ETS2
rRNA of subunits for ribosome assembly, ETS are externally transcribed sequences, ITS are internally transcribed sequences
RNA pol I & produces 47S rRNA containing 18S, 5.8S & 28S genes
Cleaved into individual rRNA by endonuclease
Where are the 47S rRNA in the human genome?
Where does transcription of 47S rDNA occur, & what happens after?
How can you end up with an individual rRNA profile?
What 4th rRNA gene is crucial for ribosomal assembly?
Where is it located?
How is it transcribed?
What follow transcription of all rDNA genes?
Copies spread across 5 chromosomes on their short arms
Nucleolus where rRNA produced & then binds to ribosomal subunits to form small & large subunits (in nucleolus)
Repetitive 47S rRNA sequences lead to recombination in meiosis
5S rRNA gene
Chromosome 1 - separate to 47S rRNA
by RNA pol III - so gene has internal promoter & trimmed by exonuclease activity into RNA transcript
Association with ribosomal subunits
