Genome Duplication Flashcards by Joey Pang

Q

How big is the human genome

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Q

What is the c paradox

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Q

What are the percentages of coding and non coding dna in the human genome

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Q

Whats the most common way to make new genes

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What is the impact of gene duplication

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What are pseudogenes

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What are paralogues

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What are orthologues

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What is concerted evolution

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Q

Why is gene duplication good

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What is sub functionalisation of genes

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What is meant by synteny

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Q

Give the history of the study of genome sequencing

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Q

What are the 2 human genome projects

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Q

What did Craig venter do

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What was the results of the 2 human genome projects

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Q

What does ENCODE do

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Q

What are the different transposable elements that make up the human genome

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Q

How do we infer conservation of genomic elements across species?

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Q

What are orthologues good for

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Q

What does conservation in coding gene sequences imply

A

Implies conservation in functionality

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Q

Does conserved cis regulatory elements mean conserved function

A

No it does not mean conserved function

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Q

What does the fact that enhancers with conserved sequences across species may not always have the same function show

A

The majority of human enhancers has
functionality NOT conserved across mammals

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Q

How similar are human and chimp genomes

A

98% similar

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How similar are human and mice genomes

What is LUCA

What are molecular clocks and what are the used for

What an rate of mutation info be used for

What is the mitochondrial eve

How can a genome acquire new genes

How can gene duplication occur during dna replication

Explain trypsin and chymotrypsin as an example of subfunctionalism

Name the two types of pseudogenes

Non processed pseudogenes Processed pseudogenes

Explain what is meant by non processed pseudogenes

Explain what is meant by processed pseudogenes

Give an example of psuedogenes

What are multigene families *

Multigene families are groups of related genes within an organism's genome that share a common origin and often similar DNA sequences. These genes likely arose from a single ancestral gene that duplicated over evolutionary time

What are HOX transcription factors main role

What is the homeodomain of HOX proteins

Where is the normal antennapedia gene expressed

Insects have one cluster of Hox genes (8 genes)

What can a mutation is the antennapedia gene cause + homeotic meaning

What are the two gene clusters that the 8 major HOX genes (in drosophila) are found in called

How many HOX gene clusters do humans have

What can mutations in the following genes respectively cause ; HOXD13, HOXA2, HOXB1

Deformed toes/fingers Deformed ears Variable Ear, Hearing, and Skeletal/Brain Anomalies

1) What is thought to be the HOX vertebrate common ancestor 2) What is the oldest known animal with 4 HOX gene clusters

2) Sea lamprey

What effects could larger/ entire genome duplication have on an organism

What is polyploidy and in what organisms are they commonly found in

Multiple complete sets of chromosomes

Name the two types of polyploidy

- ‘Autopolyploidy’ (‘Auto’ = same) - ‘Allopolyploidy’ (‘Allo’ = other)

What is autopolyploidy

Autopolyploidy is a type of polyploidy (having more than two sets of chromosomes) that occurs when an organism has multiple copies of chromosomes from the same species

What are the issues with autopolyploidy

What is allopolyploidy

What are the benefits of whole genome duplication

What is a locus?

Each gene has a locus, which is a specific position on a pair of homologous chromosomes

What is an allele?

( Ignore red writing - incorrect . Meant to say chromosome. Bands on chromosome is the allele)

What is the meanings of : genotype, heterozygous, homozygous, dominant and recessive alleles, phenotype

A phenotype is the physical manifestation of a genotype. (Physical trait)

What is an SNP

Why are SNPs important

Where can SNPs occur and what is the effect of an SNP appearing in that location

What are the two categories that diseases associated with SNPs fall into

What are coding SNPs and what are the two types

Explain the two types of substitutions

What are the two types of Alzheimer’s What alleles are associated with Alzheimer’s and their risk levels for developing Alzheimer’s

What are non coding SNPs

What is the OAS1 gene associated with

What could happen if a splice site is disrupted due to an SNP

What could indel mutations cause

What are Genome Wide Association Studies (GWAS)

How are Genome Wide Association Studies (GWAS) findings visualised

What are the aims of genome projects

What are the challenges of GWAS

What is meant by linkage disequilibrium and how does it relate to GWAS

What are eQTLs and how do they relate to GWAS

Integrating GWAS with gene expression data is now largely routine The association between GWAS and eQTL identified SNPs can lead to identification of disease causing genes

What are cis and trans eQTLs

Explain one way SNPs can be studied