Week 9 BIO1011 Test

Central Dogma

The central dogma describes the directional flow of genetic information in cells: DNA → RNA → Protein. DNA stores genetic information

How genetic information is stored in DNA

Genetic information is stored in the sequence of nitrogenous bases in DNA: adenine (A)

Base-pairing rules

In DNA: A pairs with T and G pairs with C. In RNA: A pairs with U and G pairs with C. RNA contains uracil instead of thymine.

Differences between DNA and RNA

DNA is double-stranded

Transcription

The process where DNA is used as a template to produce complementary RNA. RNA polymerase synthesizes an RNA strand complementary to the DNA template strand.

Template strand

The DNA strand used during transcription to synthesize RNA. It is read in the 3' → 5' direction.

Coding strand (non-template strand)

The DNA strand not directly transcribed. Its sequence matches the RNA transcript except DNA has thymine while RNA has uracil.

Direction of RNA synthesis

RNA is synthesized in the 5' → 3' direction by adding nucleotides to the 3' end of the growing RNA strand.

RNA polymerase

The enzyme that carries out transcription by catalyzing the polymerization of ribonucleoside triphosphates into RNA.

Initiation (transcription)

The stage of transcription where RNA polymerase binds to the promoter

Elongation

The stage of transcription where RNA polymerase moves along the DNA template strand and adds complementary ribonucleotides to the growing RNA transcript.

Termination

The stage of transcription where RNA polymerase reaches a terminator sequence

Promoter

A DNA region where RNA polymerase and associated proteins bind to initiate transcription.

Terminator

A DNA sequence where transcription stops and the RNA transcript is released.

TATA box

A common eukaryotic promoter sequence (5'-TATAAA-3') located about 25–35 base pairs upstream from the transcription start site that helps recruit transcription proteins.

−10 and −35 motifs

Promoter sequences in prokaryotes located approximately 10 and 35 base pairs upstream from the transcription start site that help recruit RNA polymerase.

Sigma factor

A bacterial protein that helps RNA polymerase recognize and bind to promoters. After transcription begins

General transcription factors

Proteins required for transcription initiation in eukaryotes. They assemble at the promoter and recruit RNA polymerase.

Enhancers

DNA sequences that bind activator proteins and stimulate transcription.

Transcriptional activator protein

A regulatory protein that binds enhancer sequences and promotes transcription.

Mediator complex

A protein complex recruited by activator proteins that helps recruit RNA polymerase II to the promoter.

RNA polymerase II (Pol II)

The RNA polymerase responsible for transcribing protein-coding genes in eukaryotes.

Transcription bubble

A region where DNA strands separate during transcription so RNA can be synthesized.

Bacterial transcription bubble size

The bacterial transcription bubble is about 14 base pairs long

Polymerization reaction

A reaction where ribonucleotides are joined together during RNA synthesis through formation of phosphodiester bonds.

Pyrophosphate cleavage

The release and cleavage of pyrophosphate during transcription that provides energy and makes the reaction irreversible.

Operon

A cluster of functionally related genes controlled by a single promoter in prokaryotes.

Polycistronic mRNA

A single mRNA molecule containing multiple genes that can produce multiple proteins. Common in bacteria.

Exons

Regions of a gene retained in mature mRNA and expressed as protein.

Introns

Non-coding regions removed during RNA processing.

Primary transcript

The initial RNA molecule synthesized from DNA before processing.

RNA processing

The series of modifications that convert a primary RNA transcript into mature mRNA in eukaryotes.

Steps of RNA processing

1. Addition of 5' cap

2. Addition of poly(A) tail

3. RNA splicing

5' cap

A modified guanine nucleotide added to the 5' end of mRNA that protects RNA

Poly(A) tail

A chain of adenine nucleotides added to the 3' end of mRNA that increases stability

RNA splicing

The removal of introns and joining of exons to form mature mRNA.

Spliceosome

A molecular complex that removes introns and joins exons together during RNA splicing.

Alternative splicing

A process where different combinations of exons are joined to produce multiple proteins from one gene.

Translation

The process where ribosomes synthesize proteins using instructions carried by mRNA.

Codon

A sequence of three bases in mRNA that specifies an amino acid.

Open reading frame (ORF)

The coding region of mRNA containing codons that determine the amino acid sequence of a protein.

Untranslated regions (UTRs)

Regions of mRNA that are not translated into protein but regulate stability and translation.

RNA-binding proteins

Proteins that regulate mRNA transport

Coupled transcription and translation

In prokaryotes

Separation of transcription and translation in eukaryotes

In eukaryotes

Transcriptional regulation

Control of whether transcription occurs. It can be positive or negative.

Positive transcriptional regulation

A form of regulation where an activator protein must bind DNA for transcription to occur.

Negative transcriptional regulation

A form of regulation where a repressor protein binds DNA to prevent transcription.

Allosteric effect

change in protein shape caused by binding of a small molecule

Lac operon

A bacterial operon controlling genes required for lactose metabolism.

lacZ

A gene in the lac operon that encodes β-galactosidase.

lacY

A gene in the lac operon that encodes lactose permease.

Operator

A regulatory DNA sequence where a repressor protein binds to control transcription.

Lac operon in absence of lactose

The repressor binds the operator and blocks transcription.

Lac operon in presence of lactose

Lactose binds the repressor

Constitutive expression

Continuous gene expression regardless of environmental conditions

Chromatin

A complex of DNA and proteins

Chromatin remodelling

The repositioning of nucleosomes to expose DNA for transcription.

Histones

Proteins around which DNA is wrapped in nucleosomes.

Histone code

Patterns of histone modifications that influence chromatin structure and gene expression.

Histone modifications

Chemical modifications such as methylation and acetylation that affect chromatin structure and gene activity.

DNA methylation

The addition of methyl groups to DNA

Epigenetics

Heritable changes in gene expression without changes to the DNA sequence.

X-inactivation

Random silencing of one X chromosome in female mammals.

Xist

A non-coding RNA involved in X-chromosome inactivation by coating the chromosome and recruiting silencing proteins.

Calico cats and X-inactivation

Calico cat fur patterns result from random X-inactivation of coat-colour alleles.

Posttranslational modification

Chemical modification of proteins after translation that affects their structure and function.

Chaperone proteins

Proteins that assist correct protein folding.

Importance of protein folding

Incorrectly folded proteins can aggregate and damage cells

Hierarchy of gene regulation

Gene expression in eukaryotes can be regulated at the levels of chromatin structure

Why different cell types behave differently

Different cell types express different sets of genes even though they contain the same DNA.

Combinatorial transcriptional regulation

Regulation of transcription through multiple transcription factors acting together.

Mutation in regulatory regions

Mutations can increase gene expression by preventing repression or decrease expression by disrupting activator binding.

Incorrect splicing

Incorrect exon joining or intron retention can alter codons and produce non-functional proteins.

RNA transcript from template strand 5' ATC TTT GAT ACC 3'

3' UAG AAA CUA UGG 5'

RNA transcript from coding strand 5' ATC TTT GAT ACC 3'

5' AUC UUU GAU ACC 3'