Genetics and Molecular Biology: DNA, Genes, and Regulation

microfilaments are cytoskeletal elements that can be which of the following? Choose

Genome

The complete set of DNA in a cell or organism including coding and noncoding sequences

Gene

A segment of DNA that is expressed to yield a functional product either RNA or a protein

Coding gene

A gene that produces mRNA which is translated into a protein

Non-coding gene

A gene that produces a functional RNA that is not translated into a protein such as rRNA or tRNA

5′ UTR

A region at the beginning of mRNA that is not translated but regulates translation

3′ UTR

A region at the end of mRNA that is not translated and regulates mRNA stability

Introns

Non-coding sequences within a gene that are transcribed but removed during RNA processing

Exons

Expressed sequences that remain in mRNA and may code for protein

Non-transcribed spacer

DNA between genes that is not transcribed into RNA

Transcribed spacer

RNA sequences that are transcribed but later removed and degraded and are not spliced like introns

Primary RNA transcript (pre-mRNA)

The initial RNA transcript containing both introns and exons

Mature mRNA

The processed RNA after introns are removed and exons are joined

Start codon

AUG signals the start of translation and beginning of the coding region

Stop codon

A codon that signals the end of translation

Iron Response Element (IRE)

A regulatory RNA sequence that binds iron regulatory proteins to control gene expression based on iron levels

Ferritin

A protein that stores iron inside cells

Ferritin IRE location

The IRE is located in the 5′ UTR of ferritin mRNA

Ferritin regulation low iron

IRPs bind the IRE in the 5′ UTR and block translation so ferritin is not produced

Ferritin regulation high iron

IRPs do not bind allowing translation and production of ferritin to store iron

Transferrin receptor

A protein that helps cells import iron from the bloodstream

Transferrin receptor IRE location

The IREs are located in the 3′ UTR of transferrin receptor mRNA

Transferrin receptor regulation low iron

IRPs bind the IREs in the 3′ UTR stabilizing mRNA and increasing receptor production

Transferrin receptor regulation high iron

IRPs do not bind leading to mRNA degradation and decreased receptor production

5′ UTR regulation effect

Binding of proteins in the 5′ UTR blocks or allows translation initiation

3′ UTR regulation effect

Binding of proteins in the 3′ UTR affects mRNA stability and degradation

Opposite regulation principle

Ferritin and transferrin receptor are regulated oppositely to balance iron storage and uptake

Genome size vs complexity

Genome size does not directly correlate with organism complexity

Repetitive DNA

DNA sequences that are repeated many times and make up a large portion of the genome

Gene families

Groups of related genes formed by duplication that have similar but distinct functions

Alternative splicing

A process where one gene can produce multiple proteins by including or excluding exons

Chromatin

DNA packaged with proteins mainly histones to organize and compact it in the nucleus

Histones

Positively charged proteins that bind negatively charged DNA to help package it

DNA replication

The process by which DNA makes an identical copy of itself to pass genetic information to the next generation

Function of genome

To maintain and transfer genetic information and to use that information for cellular activities

DNA polymerase

An enzyme that synthesizes new DNA by adding nucleotides to the 3′ hydroxyl of a growing strand

Direction of DNA synthesis

New DNA is synthesized in the 5′ to 3′ direction

Template reading direction

DNA polymerase reads the template strand in the 3′ to 5′ direction

Substrates of DNA replication

Deoxyribonucleotides and a template strand with a primer

Primer

A short RNA strand that provides a free 3′ hydroxyl group for DNA polymerase to begin synthesis

Primase

An RNA polymerase that synthesizes RNA primers de novo for DNA replication

De novo synthesis

Synthesis from scratch without a pre-existing strand

Origin of replication

A specific location where DNA replication begins

Replication fork

A Y-shaped region where DNA strands are separated and replication occurs

Replication bubble

A region where DNA is being replicated in both directions from an origin

Leading strand

The DNA strand synthesized continuously in the same direction as the replication fork

Lagging strand

The DNA strand synthesized discontinuously in the opposite direction of the replication fork

Okazaki fragments

Short DNA fragments synthesized on the lagging strand

DNA ligase

An enzyme that joins Okazaki fragments by forming phosphodiester bonds

Helicase

An enzyme that unwinds the DNA double helix by breaking hydrogen bonds

Single-strand binding proteins

Proteins that stabilize separated DNA strands and prevent reannealing

Topoisomerase

An enzyme that relieves supercoiling by cutting and rejoining DNA strands

Sliding clamp

A protein that holds DNA polymerase onto the DNA template to increase efficiency

Clamp loading protein

A protein that loads the sliding clamp onto DNA

DNA polymerase III

The main enzyme responsible for DNA synthesis in prokaryotes

DNA polymerase I

An enzyme that removes RNA primers and replaces them with DNA

RNase H

An enzyme that removes RNA from RNA-DNA hybrids

Multiple origins of replication

Eukaryotic chromosomes have many origins to allow faster replication of large genomes

Circular vs linear DNA

Prokaryotes have circular DNA while eukaryotes have linear DNA

End replication problem

The inability to fully replicate the ends of linear DNA after removal of RNA primers

Telomeres

Repetitive DNA sequences at the ends of chromosomes that protect genetic information

Telomerase

An enzyme that extends telomeres using an RNA template

Reverse transcriptase

An enzyme that synthesizes DNA from an RNA template

DNA replication fidelity

The accuracy of DNA replication maintained through multiple mechanisms

Complementary base pairing

Correct nucleotide pairing increases replication accuracy

Proofreading activity

DNA polymerase removes incorrect nucleotides using 3′ to 5′ exonuclease activity

Mutation

A change in DNA sequence that can be spontaneous or induced

Spontaneous mutation

A mutation caused by natural chemical changes such as deamination or depurination

Induced mutation

A mutation caused by external agents such as UV light or chemicals

Thymine dimers

Covalent bonds between adjacent thymine bases caused by UV radiation

Alkylating agents

Chemicals that modify DNA bases and can cause mutations

Direct repair

A mechanism that reverses DNA damage without removing bases

Photolyase

An enzyme that uses light energy to break thymine dimers

Suicide enzyme

An enzyme that permanently modifies itself during repair and cannot be reused

Base excision repair

A process that removes damaged bases and replaces them with correct nucleotides

DNA glycosylase

An enzyme that removes a damaged base from DNA

AP site

A site in DNA where the base has been removed

AP endonuclease

An enzyme that cuts the DNA backbone at an AP site

DNA polymerase and ligase role in repair

They fill in missing nucleotides and seal the DNA backbone

Gene editing

A method to repair DNA by targeting specific sequences

Zinc finger nucleases

Engineered proteins that cut DNA at specific sequences

CRISPR

A gene editing system that uses guide RNA to target specific DNA sequences