Unit 6 Gene Expression and Regulation (FULL UNIT)

5’ Cap

A modified form of guanine nucleotide added onto the end of a pre-mRNA molecule

Missense mutation

Changes a nucleotide so the codon codes for a different amino acid → Protein may be partially functional or faulty.

Triplet code

1 codon = 3 nucleotides in mRNA → Each codon specifies 1 amino acid in a polypeptide chain

RNA polymerase

An enzyme that links ribonucleotides into a growing RNA chain during transcription, based on complementary binding to nucleotides on a DNA template strand

Point mutation (silent, missense, nonsense)

A change in a single nucleotide pair of a gene

Frameshift mutation

Insertion or deletion of a nucleotide that shifts the reading frame → Entire amino acid sequence downstream is altered, usually nonfunctional.

Transcription initiation complex

The completed assembly of transcription factors and RNA polymerase that forms promoter region to start transcription of RNA

Nonsense mutation

Changes a nucleotide so the codon becomes a stop codon → Translation stops early, shorter, and usually nonfunctional protein

aminocyl-tRNA synthetase

An enzyme that joins each amino acid to appropriate tRNA

RNA processing

Modification pre-mRNA →mRNA

• A 5′ cap is added to the beginning of the RNA.

• A poly-A tail is added to the end.

• Introns (noncoding regions) are removed and exons (coding regions) are spliced together.

RNA splicing

After synthesis of RNA transcript, (introns) are removed from a (pre-mRNA) transcript and the (exons) are joined together to form a mature mRNA that can be translated into protein.

Codon

A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.

Poly-A tail

A sequence of 50–250 adenine nucleotides added onto the 39 end of a pre-mRNA molecule.

A site

Holds the tRNA carrying the next amino acid to be added to the polypeptide chain. (A stands for aminoacyl tRNA.)

Alternative RNA splicing

Eukaryotic gene expression where the same pre-mRNA transcript can be spliced in different ways, resulting in multiple mature mRNAs from a single gene. This allows a single gene to produce multiple different proteins depending on which exons are included or removed.

EX:A gene has exons: 1 – 2 – 3 – 4

• Splicing Option 1: 1–2–3–4 → protein A

• Splicing Option 2: 1–3–4 → protein B

• Splicing Option 3: 1–2–4 → protein C

Start point

In transcription, the nucleotide position on the promoter where RNA polymerase begins synthesis of RNA.

Signal-recognition particle (SRP)

A protein-RNA complex that recognizes a signal peptide and helps direct the ribosome to the ER by binding to a receptor protein on the ER.

Splicesome

A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.

Signal Peptide

A short sequence of amino acids at the beginning of a newly made protein that directs the protein to a specific location in the cell, usually the ER, where the protein will be processed, modified, or transported out of the cell.

Ribosomal RNAs (rRNAs)

RNA molecules with proteins, make up ribosomes

Wobble

Flexibility in base-pairing between the third nucleotide of an mRNA codon and the first nucleotide of the tRNA anticodon.

Transcription Unit

The stretch of DNA downstream from promoter that is transcribed into a RNA molecule

Gene expression

The process by which information encoded in DNA directs the synthesis of proteins or, RNAs that are not translated into proteins and instead function as RNAs.

Mutation

A change in the nucleotide sequence of an organisms DNA or in the DNA or RNA of a virus

Intron

A noncoding, intervening sequence within a primary transcript that is removed from the transcript during RNA processing

E site (Exit site)

The place where discharged tRNAs leave the ribosome.

Transcription factor

A regulatory protein that binds to DNA and affects transcription of specific genes.

Silent mutation

Changes a nucleotide but does not change the amino acid → no change in phenotype and usually no efffect

Translation

The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. Located in cytoplasm

Steps include:

1. Initiation: ribosome assembles and the start codon is recognized

2. Elongation: amino acids are added to the growing polypeptide

3. Termination: ribosome reaches a stop codon and releases the protein

Transfer RNA (tRNA)

Carries a specific amino acid to the ribosome based on its anticodon to appropriate codon in the mRNA.

Terminator

A sequence of nucleotides in DNA that marks the end of a gene and signals RNA polymerase to release the newly made RNA molecule and detach from the DNA.

Messenger RNA (mRNA)

A type of RNA that carries the genetic message copied from DNA to the ribosome.

Reading Frame

On an mRNA, it is read by the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis.

P site (peptidyl tRNA)

Holds the tRNA carrying the growing polypeptide chain.

Promoter

A specific nucleotide sequence in the DNA of a gene that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place.

Mutagen

A chemical or physical agent that interacts with DNA and can cause a mutation

Transcription

The synthesis of RNA using DNA as a template. Located in Nucleus.

Steps include:

1. Initiation: RNA polymerase binds to the promoter. The DNA strands unwind, and RNA polymerase begins synthesizing RNA at the start point on the template strand.

2. Elongation: RNA polymerase moves along the template strand of DNA, unwinding the DNA and adding RNA nucleotides to elongate the RNA strand in the 5’ to 3’ direction.

3. Termination: The RNA transcript is completed and released, and RNA polymerase detaches from the DNA.

Exon

A sequence within a primary transcript that remains in the RNA after RNA processing; also refers to the region of DNA from which this sequence was transcribed.

Primary transcript/ pre-mRNA

The first copy of RNA made from DNA that still needs to be modified before it can be used to make a protein.

Nucleotide-pair substitution

A type of point mutation in which one nucleotide in a DNA strand and its partner in the complementary strand are replaced by another pair of nucleotides.

Anticodon

A sequence of three nucleotides on tRNA that is complementary to a codon on mRNA and allows it to pair.

TATA Box

A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex

Ribozyme

An RNA molecule that functions as an enzyme, such as an intron that catalyzes its own removal during RNA splicing.

Start codon

• The first codon used during translation on the mRNA. It signals the ribosome where to begin building the protein.

• AUG and codes for methionine.

Stop codon

• A sequence of three nucleotides in mRNA that signals the end of translation. When the ribosome reaches it, it stops adding amino acids and releases the completed polypeptide chain.

• They signal release factors to bind and terminate protein synthesis.

• (UAA, UAG, and UGA.)

Prokaryotes transcription and translation location

Transcription and translation occur in the cytoplasm and can happen at the same time

Eukaryotes transcription and translation location

Transcription occurs in the nucleus and translation occurs in the cytoplasm

Central Dogma

Genetic information flows from: DNA (transcription) → RNA (translation) → Protein

One gene - one enzyme hypothesis (Beadle and Tatum)

• Studying bread mold (Neurospora). They showed that mutations in specific genes caused the mold to lose the ability to produce certain enzymes needed for metabolism.

• Some proteins are not enzymes & Some proteins have multiple polypeptide subunits

• Each gene controls the production of a single enzyme that affects a specific step in a metabolic pathway.

What are 3 ways RNA differs from DNA?

1. RNAs sugar is ribose and DNA is deoxyribose

2. RNA has bases of A, U, C, G (uracil replaces thymine) and DNA has A, T, C, G

3. RNA is single-strand, DNA is double-strand

Why is the genetic code said to be redundant but not ambiguous?

Something is redundant if it is repeated or there is more than one way to do the same thing.

• In genetics: multiple codons can code for the same amino acid

Something is ambiguous if it is unclear or can mean more than one thing.

• In genetics: a code would be ambiguous if one codon coded for more than one amino acid.

• Redundant = multiple codons → same amino acid

• Not ambiguous = one codon → only one amino acid

Stages of initiation for transcription

1. Eukaryotic promoter includes a TATA box about 25 nucleotides upstream from start point

2. Several transcription factors, one of them recognizing the box, must bind to the DNA before RNA pol II can bind in correct position

3. Additional transcription factors bind to DNA along with RNA pol II, forming transcription initiation complex. RNA pol II then unwinds DNA helix, and RNA synthesis begins at start point on template strand

Enhancer

Increases the rate of transcription of a gene by binding specific transcription factors, even if it is located far from the gene it regulates.

microRNAs (miRNAs)

A small, single-stranded RNA molecule, associates with one or more proteins in a complex that can degrade or prevent translation of an mRNA with a complementary sequence.

Operon

A group of genes in bacteria that are controlled together and transcribed as a single unit. It includes a promoter, an operator, and structural genes that work together in the same metabolic pathway. It allows the switch to control required enzyme production.

Activator

A protein that binds to DNA and stimulates gene transcription. In prokaryotes, they bind in or near the promoter; in eukaryotes, they generally bind to control elements in enhancers.

Nucleic acid hybridization

The process of base pairing between a gene and a complementary sequence on another nucleic acid molecule.

Control element

A segment of noncoding DNA that helps regulate transcription of a gene by serving as a binding site for a transcription factor.

Regulatory gene

A gene that codes for a repressor protein.

Complementary DNA (cDNA)

A double-stranded DNA molecule made in vitro using mRNA as a template and the enzymes reverse transcriptase and DNA polymerase. A cDNA molecule corresponds to the exons of a gene.

Repressor

Protein that binds operator to block transcription

Operator

The on/off switch that controls whether the genes in the operon are transcribed.

RNA interference (RNAi)

A technique used to silence the expression of selected genes.

Epigenetic inheritance

Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence of a genome. EX: DNA methylation and Histone acetylation.

Corepressor

A small molecule that binds to a bacterial repressor protein and changes the protein's shape, allowing it to bind to the operator and switch an operon off.

cyclic AMP (cAMP)

A signal molecule that increases when glucose is low. It binds to CAP to help RNA polymerase attach to the promoter, speeding up transcription of the lac operon.

reverse transcriptase–polymerase chain reaction (RT-PCR)

A lab technique used to convert RNA into DNA and then amplify it, allowing scientists to detect and measure gene expression.

Differential gene expression

The expression of different sets of genes by cells with the same genome.

Small interfering RNAs (siRNAs)

Can degrade or prevent translation of an mRNA with a complementary sequence so it can’t be translated into protein.

Nucleic acid probe

In DNA technology, a short, single-stranded DNA or RNA sequence that is labeled and used to detect the presence of a complementary sequence in a sample.

Inducer

A specific small molecule that binds to a bacterial repressor protein and changes the repressor's shape so that it cannot bind to an operator, thus switching an operon on.

Repressible Operon

When transcription is usually on but repressed by a specific small molecule that binds to a protein.

Inducible Operon

When transcription is usually off, but can be induced when a specific small molecule interacts with a different regulatory protein.

lac Operon

Inducible; off unless lactose is present. Regulation involves negative control of genes.

trp Operon

Repressible, on unless tryptophan is present. Regulation involves negative control of genes.

CAP

An activator protein that binds to DNA and stimulates transcription of a gene.

Describe the relationship between glucose supply, cAMP, and CAP

Amount of glucose increase = cAMP concentration fails = CAP detaches the operon = transcription at low level.

Heterochromatin

Highly condensed chromatin, not usually expressed/inactive.

Euchromatin

Loosely condensed, usually expressed/active.

Histone Acetylation

The addition of an acetyl group to an amino acid in a histone tail - appears to promote transcription.

DNA methylation

The addition of a methyl group to a DNA molecule - inactivates transcription.

Explain how enhancers and activators interact with transcription factors to affect gene expression?

Activator proteins bind to enhancer regions of DNA (distal control elements). The DNA can bend so the activators come close to the promoter region. Activators interact with mediator proteins and transcription factors, helping RNA polymerase II start transcription.

Non-coding RNAs

RNA molecules transcribed from DNA but are not translated into proteins. There are many types, but some regulate gene expression (e.g., miRNA, siRNA), others have structural or catalytic roles (rRNA, tRNA)

Steps of gene expression regulation

Packing/unpacking DNA → transcription → mRNA processing → mRNA transport → translation → protein processing → protein transport to cell destination.

Chromatin modification (STEP 1)

Histone Acetylation, DNA methylation, Epigenetic factors.

Transcriptional processes: turning genes off and on (STEP 2)

Transcription factors, Activators & Repressors, Promoter, Enhancer.

Post-Transcriptional Regulation (STEP 3 & 4)

RNA processing or mRNA degradation, mRNA transport to cytoplasm through nuclear pore → Alternative RNA splicing.

Translational processes (STEP 5)

MicroRNAs, RNA interference.

Post-Translation (STEP 6 & 7)

Protein processing and protein transport to destination.

Gene Regulation Negative control

Negative regulatory molecules that inhibit gene expression by binding to DNA and blocking transcription. Operons are switched off by the active form of repressor (EX: repressible and inducible operons).

Gene Regulation Positive control

Promoters (activators). Regulatory proteins interact directly with genome to stimulate transcription (EX: CAP with cAMP).

Direction of synthesis

• DNA/RNA synthesis is always 5’ → 3’

• Template strand is read 3’ → 5’

A &T/U Based pairing

2 H Bonds

C & G Base pairing

3 H bonds

DNA structure

• Nitrogenous Bases: A, T, C, G

• Sugar: Deoxyribose

• Strand: Double-stranded

RNA structure

• Nitrogenous Bases: A, U, C, G

• Sugar: Ribose

• Strand: Single-stranded

Pyrimidines

C, T, U → 1-carbon ring

Purine

A, G → 2-carbon ring

3 parts of a nucleotide

• Phosphate group (backbone of DNA)

• Deoxyribose sugar in DNA(forms sugar-phosphate backbone)

• Nitrogenous base(A,T,C,G)