Evolbio LT 4 - Evolution of Genes and Genomes

What is the conundrum of genes and complexity

The number of genes does not reflect what we expect 

How do genes originate

Descent with Modification 

How has Duplication led to the origin of genes

1. Unequal crossing over 

2. Exon shuffling 

3. Horizontal Gene Transfer  

4. Replication slippage  

5. Retro-position- reverse transcribing mRNA. 

What is De novo Gene Synthesis 

1. the physical creation of artificial, double-stranded DNA sequences from scratch using chemical building blocks, without needing a natural DNA template 

importance of Duplication in Evolution

1. gene duplication provides the raw genetic material for creating new traits

importance of Contraction in Evolution

how a population's genetic diversity is periodically constrained or reduced through selective pressures (purifying selection)

What is Exon Shuffling 

1. a molecular evolutionary process where two or more exons from different genes—or duplicated exons from the same gene—recombine to form a new gene 

What is Line-1 (Long Interspersed Nuclear Element 1)

a type of "jumping gene" or retrotransposon that makes up about 17% of the human genome and is found in the DNA of most eukaryotes

What is retro-position

1. a mechanism where an RNA transcript of a gene is reverse-transcribed into DNA and reintegrated into a completely different location in the genome 

2. A mature mRNA transcript is reverse-transcribed back into a complementary DNA (cDNA) sequence and randomly integrated into a new location in the genome. 

What are de novo genes

1. completely new genes which originate from non-coding regions 

2. Rare but still exists in nature 

How does Unequal Crossing Over occur

Occurs during meiosis when homologous chromosomes misalign. Recombination between these misaligned sequences results in one chromosome gaining a duplicated gene block and the other losing it.

What is exon shuffling

1. Two or more distinct exons from different genes are brought together ectopically, or an exon is duplicated within the same gene, creating a new exon-intron combination.

What is Horizontal Gene Transfer

1. The transmission of genetic material between distinct organisms without phylogenetic descent (common via plasmids or viral vectors). 

What is Replication Slippage

1. A DNA polymerase mutation error during replication where the nascent strand loops out and realigns incorrectly on a repetitive template sequence.

What are Gene Families

1. a set of loci that arose by duplication and that code for proteins that typically continue to have similar biochemical function. Two or more genes that originated by duplication are said to be paralogs 

   1. Example : hemoglobin

What are the fate of duplicate genes

1. If it works- it may go to fixation 

2. If it does not- deletion 

3. Neofunctionalization– example– crystallin gene 

How does the death of a gene occur

1. Most duplicates are dead from the onset 

2. When a gene becomes non-functional, it becomes a pseudogene 

Can a deletion undergo selection

1. Yes it can still undergo selection 

   1. because they alter the organism's phenotype in ways that affect survival and reproduction 

How can deletions be used for HIV treatment

1. Timothy Ray Brown: the Berlin Patient 

2. Stem Cell treatment 

How does Evolution of Protein Coding Regions occur

1. Changes in first two nucleotides of a codon are slow to evolve 

   1. Affect the protein being coded

What is the Neutral Theory of Molecular Selection- 

posits that most evolutionary changes at the DNA and protein levels are caused by random genetic drift of mutant alleles that are selectively neutral, rather than by natural selection

What is Positive Selection in the Evolution of Coding Regions

1. occasionally, changes in coding genes are favored, like in a new environment 

What is Codon Bias in the Evolution of Coding Regions

1. Codon Bias- when particular codons for the same amino acid are used more 

   1. Abundance in TRNAs 

   2. Efficiency in translation 

   3. Genome Composition 

Changes in Evolution of Coding Regions

1. Sometimes, the change is in expression (regulatory) 

   1. Not the protein, but how much it is expressed 

   2. Changes in the operon, transcription factors, etc 

How can alternative splicing, overlapping genes contribute to Evolution in gene structure

1. Allows genes to adapt without increasing genome size 

2. Operons

What are operons

1. Operons- a set of genes under the control of one operator 

   1. Evolve together for certain theorized reasons 

      1. Ease of transmission via HGT (selfish gene) 

      2. Their spatial arrangements is selected for because it is more efficient 

How can Transposable Elements increase genome size

1. increase genome size primarily through a "copy-and-paste" mechanism. As TEs replicate and insert themselves throughout the DNA, they continuously add new base pairs