Developmental genetics

Are genes named after a protein product or the phenotype?

whichever came first

What does an italicised word mean?

species and gene names

Is the following a gene or protein? In which species? SHH

Protein in homo sapiens, mus musculus, gallus gallus

Is the following a gene or protein? In which species? Shh

Protein in xenopus laevis and danio rerio

Is the following a gene or protein? In which species? SHH

gene in homo sapiens, gallus gallus

Is the following a gene or protein? In which species? shh

gene in xenopus laevis and danio rerio

What are 4 types of mutations that can occur?

 point mutations (single base-pair), deletion, insertion, translocation

Name 2 examples of extrinsic causes for mutations

radiation (X rays) and chemical (base modifiers)

What types of mutations are not inherited?

somatic mutations

What types of mutations are inherited?

germline mutations

Explain forward genetics

random mutagenesis (induced mutations) in model organisms to study resulting phenotypes

Explain reverse genetics

induce a specific mutation with a hypothesised effect in humans and confirm/refute based on the observed phenotype

What are 2 techniques used in reverse genetics? Which specific technology is used for this?

• gene knock-out

• gene replacement/knock in

CRISPR

What is a transgene?

segment of DNA that's been moved from one organism to another

What can CRISPR be used for?

knock-out or knock-in

Phenotype → gene

Forward genetics

Gene → phenotype

reverse genetics

What are 3 types of sequences that mutations can affect? What’s the consequence of each?

• regulatory - affects transcription

• non-coding - RNA splicing, stability or translation

• coding - alter amino acid = alter folding of protein or premature stop codon — truncated protein

What does a missense mutation mean?

single amino acid substituted

What is a nonsense mutation?

premature stop codon made

Describe a domain in proteins

functional unit in a protein

Describe a dimer in proteins

2 of a same protein bind together

Describe a conformational change in proteins

change in protein structure

What could an amorphic mutation be caused by?

missense mutation inactivating binding domain

What are 2 possible outcomes of an amorphic mutation?

• haplosufficiency - enough gene product from the one WT copy

• inactivated DNA binding domain - strong phenotype bc no transcriptional activation

What could a hypomorphic mutation be caused by?

missense mutation that weakens the DNA binding domain

What are 2 possible outcomes of a hypomorphic mutation?

• haplosufficiency: enough gene product from the one wild-type copy. The mutant form may also dimerize with wild type and still activate transcription. 

• recessive: mild phenotype due to poor transcriptional activation. The dimer forms on DNA but is often falling off.

What could an antimorphic mutation be caused by?

missense mutation that destroys the dimerisation domain

What are 2 possible outcomes of an antimorphic mutation?

• dominant: mutant form binds DNA but does not dimerise with the WT and thus does not go through a conformational change to become active

• completely inactive

Can a mutated dimerisation domain still bind to DNA? How does this impact the wild type?

sits on DNA but can’t dimerise so doesn’t give the gene a spike in activity

gets in the way of the WT

What could a hypermorphic mutation be caused by?

missense mutation that results in activation that is independent of dimerization

What is the outcome of a hypermorphic mutation?

mutant form binds DNA is active all the time. We call this constitutively active. This increases the overall activation of transcription. This is dominant.

Name 3 loss of function mutations

amorphic, hypomorphic, antimorphic

Name a gain of function mutation

hypermorphic

Which function-related mutations are usually recessive? Dominant?

amorphic, hypomorphic

hypermorphic

What type of mutant is termed dominant negative?

antimorphic

What are Muller’s Morphs?

system of classifying mutations based on how they behave in different genetic situations - hypo, hyper, anti, a - MORPHIC

An albino phenotype is encoded by a genetic pathway, what would an amorphic mutation cause? What would it be disrupting?

interrupt the pathway, eg if B not made then neither is C or D.

biosynthesis of melanin

What are mutations in a same gene called?

alleles

What are mutations on different genes but impacting a same phenotype called?

genes in a same genetic pathway

How does a protein fluoresce? In the specific example of GFP?

absorbs wavelength (excitation) then emits another

475 nm into protein, 510 nm emitted - looks green

What are 3 steps that allow the making of a GFP transgenic line?

• genomic DNA with all regulatory elements

• genetically engineer GFP onto the end of the last exon (gene fusion) or replace the gene (reporter construct)

• re-introduce the new gene into the animal

What is a GFP transgenic line?

genetically modified organism that expresses GFP

List 3 uses for GFP transgenic lines?

• follow expression of a gen

• follow the behaviour of cells in vivo

• follow subcellular localisation of a protein

How can understanding phenotypes inform on protein function?

allowing researchers to observe the visible effects of genetic/protein variations

Which model organism did Muller (of the famous Muller’s Morphs) use to come t his conclusions?

drosophilae