Unti 1 Lecture 4

How are genes regulated? study of heritable changes in gene expression that do not involve changes to the underlyding sequence 

Epigenetics

How do genes evolve over time

Genome Evolution

What do gene sequences tell us about evolutionary relationships between species?

Molecular Phylogenetics

What are the functions of the genes in an organism?

Systems Biology and Bioinformatics 

How do genes guide embryological development?

Evolutionary Developmental Biology

A computer algorithm and software package that allows researchers to quickly upload and compare sequences from species against online databases of samples from other species in hopes of finding homologous sequences.

BLAST

Determining the location of every gene on a chromosome, as well as the function of every gene.

Gene Mapping 

Calculating the accumulation of sequence differences between diverse species following a sequence alignment.

Seqence Divergence

Collecting sequence samples from many different individuals from the same species to create a “consensus” sequence that identifies the genes that are shared by all individuals of that species.

Reference Sequences

Collecting and compiling information from reference sequences to create a complete sequence of all the nucleotides, in order, found on every chromosome of a species.

Whole Genome Sequencing 

Genetically modifying a sequence of DNA to include a mutation that inactivates a gene in a model organism so researchers can see what effect that broken gene has on the phenotype of the organism.

-study loss/change of protein function

analyze the role of non-coding regions

investigate mutations that cause disease

Gene Knock-Outs

Arranging sequence data from multiple different species to find where sequences overlap and where homologs are present, as well as where changes to the sequences have accumulated.

Seqence Alignment 

Studying genomes allows for the comparison of diverse taxa even if they do not share any morphological similarities

True

Genes mutate at the same frequency over time, and this stable rate of mutation across all species can be used to calibrate molecular clocks

False

Molecular phylogenies are the most accurate type of phylogeny and do not require revisions

False

Most mutations are selectively deleterious and lead to hybrid breakdown over time

False 

Mutations are caused by environmental factors such as natural selection and gene flow

False 

Gene A and Gene B arose due to a gene mutation within a single species. The functions of the two genes differ. These two genes are:

Paralogous

Genes A1, A2, B1, and B2 indicate common ancestry. These 4 genes are all:

Homologous

Gene A1 in species 1 is identical to Gene A2 in species 2. They encode for nearly identical proteins and are evidence of common ancestry. These two genes are:

Orthologous 

Genome

genetic materal of an organism

Bioinformatics

computer-sciecnce based field

science of collecting and analyzing complex biological data ex. genetic codes

Sytems biolofy

aims to model the behavior of entire biological systems based on the study of the ststems paths

-omics fields careate cataloigues of genes and their products

Point mutations

alter a single gene

Homologous genes

show common ancestry and result from divergent evolution 

Orthologous 

• genes that are present in different species

Paralogous genes

genes that result from duplication of a gene within a singe species, resulting in the potential for different gene functions

• present in different species 

Synonymous mutations

nucleotide is altered but the resulting amino acid stays the same; silent mutations

Non-synonymous mutations

nucleotide is altered and the animo acid sequence cahanges as a result

 

Missense mutation

• altetred protein 

• small change= conservative missense 

• large change= non-conservative 

Nonsense mutation

creates a stop codon that ends translation

Frameshift mutation

Insertion or deletion of nucleotide cause reading frame to shift

Molecular Clocks

mutations accumulate in a fiven seqence at predicatble rates

Neutral theory

many changes are not acted upon by selection

• they occur by chance

A gene that codes for a protein that is needed to build structures or perform functions within a cell

Structural gene 

A sequence of DNA that does not code for the formation of a protein, but has other functions within the genome

Non-coding Gene 

A gene that codes for regulatory proteins that can activate or de-activate other genes

Regulatory Gene

A transposable gene, or transposon, that can move and interrupt gene sequences, leading to dysregulation or a loss of gene expression

Non-Coding Genen 

Structural genes

Code for proteins needed to build structures or perfome functions within a cell

Non-coding genes

some contribute to ene regulation and expression

change in phenotype without change in genotype

epigenetics 

EVO-DEVO

compare the developmental processes of different species

how these traits evolved 

The increased expression of keratin in some reptiles and birds is regulated by histone modification which increases the efficiency of the transcription of the genes necessary to produce keratin proteins in structures like scales, feathers, and beaks

Epigenetics

An alteration to the gene Gap5 controls the expression of eyes in fish and amphibians; modifications to this gene cause eyes not to form during development

Evo-Devo Rule 1

Hox and Gap genes are seen in all species of animal and indicate that all animals evolved from a common ancestor that had homeobox gene sequences

Evo-Devo Rule 2

Evo-devo rule 1: Modular Body plans

changes to developmenttal regulatory genes cause changes tp body segment arrangements 

HOX genes

genes in animals contail a similar 180 nucleotide seqence (homeobox)

GAP genes

activate early in embryonic development and help regulate the formationof major body structure 

Evo Devo 2 Conserved genes

developmental regulatory genes are highly conserved over time and across species

control the body plans of organims