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Genes and genomes

55 important questions on Genes and genomes

What type of cells are mitochondria and chloroplasts?

Endosymbiotic cells.

What is the Symbiogenesis/Endosymbiotic theorie?

The idea that eukaryotic mitochondria and chloroplasts are descended from formerly free-living prokaryotes.

How do you calculate the weight of a chromosome?

First you multiply the number of basepairs by the molecular weight per bp (660 g/mol) to get the total molecular weight and then you devide that by the avogadro constant.

How do you calculate the contour length of a chromosome?

You multiply the amount of base pairs by the length per bp.

Where are the prokaryote chromosomes found in the cell?

Since they don't have a nucleus they just float around, which means the genes are ready to function.

Why is bacterial translation faster?

Co-transcriptional translation.

Where are the chromosomes in animals and fungi?

The nucleus and mitochondria.

Where are the chromosomes in plants?

Mitochondria and chloroplasts.

Why is ribosomal RNA easier to obtain than ribosomal protein genes?

Due to higher abundance.

When is an nucleotide change a mutation?

If it is present in less than 1% of the population.

What is a nucleotide change when it is present in more than 1% of the population?

A polymorphism.

How can species hybridization occur?

Point mutations, deletions, insertions, inversions or local duplications.

What is a Mendalian trait?

A trait that depends only on a single locus whose alleles are either recessive or dominant.

What is spatio-temporal gene expression?

The activation of genes within specific tissues of an organism at specific times during development.

Why are bacteria the most evolved and optomized organisms?

Every gene in their genome has a function.

What is a functional group in a bacterial genome?

One mRNA with multiple genes on it.

What does the Sigma (σ) subunit DNA sequence determine?

The transcription start site in promoters.

How is the promoter strength in bacteria determined?

The binding strength to the sigma subunit or RNA polymerase.

What is the enzyme in transposons that can cut and paste called?

Transposase or integrase.

Chromosomal genes in eukaryotes are mono-cistronic, what does this mean?

That one mRNA usually codes for one protein, each mRNA molecule only has one ORF.

What is alternative splicing?

A process during gene expression that allows a single gene to produce different splice variants. Some exons of a gene may be included or excluded from the RNA product.

Via what proces can one gene code for many different RNAs?

Alternative splicing.

Why is the eukaryotic transcription way slower than prokaryotic transcription?

Because our primary RNA transcript is highly processed via splicing, capping and polyadenylation.

What is the C-value paradox?

The fact that the amount of DNA does not correlate with the complexity of an organism.

How does the C-value paradox emerge?

Because some genomes contain a lot of transposons.

What are Long interspersed nuclear elements (LINE)?

A type of retrotransposon that is characterized by their longer sequences.

What are Short interspered nuclear elements (SINE)?

A type of retrotransposon that is characterized by sequences of non-coding DNA present at high frequencies in various eukaryotic genomes.

What are Long terminal repeat (LTR) retrotransposons?

Transposable elements characterized by the presence of long terminal repeats that directly flank an internal coding region.

How do retrotransposons mobilize?

Through reverse transcription of their mRNA and integration of the newly created cDNA into another genomic location.

What is LINE-1/L1?

An autonomous non-LTR retrotransposon in mammals.

What does L1 ORF2 encode?

A reverse transcriptase/integrase.

What is the function of L1 ORF2?

Reverse transcribing of L1 mRNA and intergrading the L1 CDNA in the chromosome.

What are the majority of retrotransposons?

Single long terminal repeats, products of homologous recombination-mediated deletion of DNA between the two original LTRs.

What serves as binding sites for a transposase in short inverted repeat transposons?

Inverted repeats.

Where are pseudogenes most often derived from?

Genes that have lost their protein-coding ability due to mutations.

Which two pseudogenes does a human have?

Processed and non-processed.

How can non-processed pseudogenes still have all their introns and their promoter?

They are generated via a segmental DNA duplication event and not via an RNA intermediate.

What is the effect of sigma factor switch on operon expression?

Switching of sigma factors changes which operons are actively transcribed.

How does gyrase play a role in operon expression?

It tunes how efficiently operons are transcribed by modulating DNA supercoiling.

How does the cut-and-paste mechanism of DNA transposons work?

The transposase cuts the DNA at the terminal inverted repeats, moves the DNA segment to a new location and integrates it.

What are two characteristics of processed pseudogenes?

They emerge via retrotransposons and are splices and don't have a promoter.

What are two characteristics of non-processed pseudogenes?

They emerge via a segmental DNA duplication event and still have all their introns and the promoter.

Why is genome size not equal to complexity?

This is because some genomes contain a lot of transposons, which can greatly expand genome size. But they do not contribute to genome complexity.

What are three examples of Cis-elements?

Enhancer, promoter and silencer.

What is the effect of an enhancer on the transcription?

It enhances the transcription by providing binding sites for transcription factors.

What is the effect of a promoter on the transcription?

A strong promoter binds RNA polymerase efficiently → high transcription rate. A weak promoter binds RNA polymerase less efficiently → low transcription rate.

What is the effect of a silencer on the transcription?

It binds repressor proteins that inhibit transcription and reduces or completely represses transcription.

What is temporal co-linearity?

When genes are activated in a specific order over time, matching their order on the chromosome.

What is spatial co-linerarity?

When genes are expressed in body regions that match their position on the chromosome.

Why would metabolomics be closest to phenotype?

Because it captures the real-time biochemical state of a cell or organism to reflect what the system is actually doing.

What is the difference between transciptomics and epigenomics?

Epigenomics reveals why certain genes are turned on or off, whereas transcriptomics shows what genes are actually being expressed.

What is the advantage of transciptomics over proteomics?

Nucleic acids are more tractable than proteins and RNA can be amplified with a PCR.

What bacteria produced oxygen for the first time?

Cyanobacteria.

What are individual bacterial ORFs called?

Cistrons.

What are HOX clusters?

Gene clusters that have 4 copies of genes, because of whole genome duplications.

The question on the page originate from the summary of the following study material:

Genomics for Health and development

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