Exam 3 short answers mol gen

What proportion of the human genome consists of protein-coding sequences? 

Only ~1% is protein-coding (exons); genes including introns make up ~25% of the genome

Explain the difference between monocistronic and polycistronic mRNA. 

Monocistronic mRNA codes for one polypeptide (eukaryotes); polycistronic mRNA codes for multiple polypeptides (common in prokaryotes).

What are transposons, and how do they contribute to genome size? 

Transposons are mobile DNA elements that replicate and insert into genomes. They increase genome size and make up much of the noncoding DNA. 

Differentiate between housekeeping genes and luxury genes

Housekeeping genes are expressed in all cells for basic functions; luxury genes are expressed in specific cells for specialized functions. 

Define and contrast abundant mRNA and scarce mRNA. 

Abundant mRNA: few types, many copies; Scarce mRNA: many types, few copies per cell. 

Why are some genes considered non-essential? 

Due to gene redundancy- other genes can compensate for their loss. Not all deletions affect phenotype.

What is the difference between synonymous and nonsynonymous mutations? 

Synonymous: does not change amino acid; Nonsynonymous: changes amino acid

Define fixation and explain its role in molecular evolution. 

Fixation is when one allele replaces all others in a population. It's a key step in molecular evolution

How is the ratio of nonsynonymous to synonymous mutations used to detect selection? 

1 = positive selection; <1 = purifying selection; ≈1 = neutral evolution. 

What are the possible fates of a gene after duplication? 

It can: keep its function (redundant), gain a new function, or become a pseudogene. 

Explain the difference between processed and nonprocessed pseudogenes. 

Processed: from reverse-transcribed mRNA (no introns); Nonprocessed: from gene-duplication with mutations.

How do globin gene clusters illustrate duplication and divergence? 

They evolved from an ancestral gene via duplication and developed distinct but related functions. 

Summarize the neutral theory of molecular evolution. 

Most molecular changes are due to neutral mutations fixed by drift, not selection. 

How does the nearly neutral theory differ from the neutral theory? 

It includes slightly deleterious mutations that can fix in small populations by drift.

What is the molecular clock hypothesis? 

DNA mutations accumulate at a steady rate

Compare the introns early and introns late models

Introns early: ancestral genes had introns. Introns late: introns were added later

What is exon shuffling? 

A process where exons recombine to create new gene variants, contributing to protein diversity

What is genetic hitchhiking? 

A neutral allele increases in frequency because it's linked to a beneficial allele under selection

Define linkage disequilibrium and give an example. 

Non-random association of alleles at different loci, often due to close physical linkage. 

What is codon bias, and what influences it?

Preference for certain synonymous codons. Influenced by translation efficiency, tRNA availability, GC content, and gene conversion. 

What is the 2R hypothesis in vertebrate evolution? 

It proposes that early vertebrates underwent two rounds of whole-genome duplication.

What is genetic linkage and how does it affect the inheritance of traits? 

Genes on the same chromosome tend to be inherited together

Why do genes that are close together on the same chromosome tend to be inherited together? 

Because there’s less chance of crossing over occurring between them. 

What are parental and recombinant types, and how do they arise? 

Parental: same allele combinations as parents; 

Recombinant: new combinations due to crossing over during meiosis

What does a high frequency of parental offspring suggest about the distance between genes? 

That the genes are close together and less likely to be separated by recombination. 

How is a chi-square test used to determine if two genes are linked? 

It compares observed and expected offspring ratios. A significant difference suggests linkage.

What is the null hypothesis in a chi-square test for gene linkage? 

That the genes assort independently and are not linked. 

What does it mean if the chi-square test leads to a rejection of the null hypothesis?

It means the genes are likely linked, not assorting independently. 

How is recombination frequency related to gene distance? 

Greater distance = higher chance of crossing over = higher recombination frequency

What limits the accuracy of recombination frequencies for mapping distant genes? 

Multiple crossovers can go undetected, underestimating true distances. 

List three uses of genetic maps. 

1. Identifying disease genes 

2. Evolutionary studies 

3. Aiding gene cloning 

What do trihybrid crosses help determine? 

The order and distance between three linked genes. 

How does interference affect mapping accuracy? 

It reduces the chance of nearby double crossovers

Why are map distances between closely linked genes more accurate? 

There’s less chance of multiple undetected crossovers, so recombination frequency reflects actual distance better. 

What is the difference between homologous recombination and site-specific recombination? 

Homologous recombination occurs between similar DNA sequences; site-specific recombination occurs at specific, short DNA sequences, regardless of overall homology

What is somatic recombination, and where is it commonly observed? 

Recombination in non-germline cells; commonly seen in the immune system  

During what stage of meiosis does recombination occur, and why is synapsis important? 

Prophase I; synapsis aligns homologous chromosomes to allow crossing over.

What is a bivalent in meiosis? 

A structure of four chromatids: two homologous chromosomes, each with sister chromatids.

What is the synaptonemal complex and its function? 

A protein structure that aligns homologs and facilitates recombination. 

What are recombination nodules? 

Dense protein structures on the synaptonemal complex- likely sites of crossover events. 

What initiates the DSBR model of recombination? 

A double-strand break in DNA. 

What is 5′ end resection and its role in recombination? 

Exonuclease removes 5' ends, leaving 3' overhangs that initiate strand invasion. 

What is a D-loop and how is it formed? 

A displaced loop formed when a 3' overhang invades a homologous duplex.

What is heteroduplex DNA? 

DNA formed by pairing one strand from each parent; occurs during strand invasion. 

What are Holliday junctions? 

Cross-shaped structures formed during recombination; influence whether crossovers occur. 

What determines the outcome during Holliday junction resolution? 

Which pair of strands is nicked; original strands = non-crossover, alternate strands = crossover. 

What is gene conversion, and how is it different from reciprocal recombination? 

Gene conversion is nonreciprocal—one allele is changed, not swapped. 

How can heteroduplex DNA lead to gene conversion? 

Mismatch repair alters one strand to match the other, changing the allele.

What is break-induced replication (BIR)? 

Repair of one-ended breaks using a homologous template- can lead to loss of heterozygosity. 

What can happen when BIR occurs at repeated sequences? 

Nonreciprocal translocations. 

What are the axial, lateral, and central elements of the synaptonemal complex? 

Axial: protein core 

Lateral: condensed sister chromatids 

Central: connects homologs (via Zip proteins) 

What do Zip proteins do in the synaptonemal complex? 

They form the central element, aligning homologous chromosomes. 

What is site-specific recombination and how is it catalyzed? 

Recombination at defined DNA sequences, catalyzed by recombinases like integrase. 

What are attP, attB, and the core sequence? 

attP: phage site 

attB: bacterial site 

Core sequence: shared site where recombination happens 

What enzyme allows phage lambda to integrate? 

Integrase, encoded by the phage int gene. 

How does site-specific recombination resemble topoisomerase activity? 

Both cut and reseal DNA strands; integrases work across DNA duplexes like topoisomerases.