Gene Expression and Regulation - I Need an 100

What is methylation, and how does it affect transcription?

Methylation is the addition of a methyl group (-CH3) to histone tails or DNA, resulting in more packing of chromatin and reduced transcription.

What roles do histones play in gene regulation?

Histones are proteins that package and order DNA into structural units called nucleosomes, which can be modified through methylation and acetylation to regulate gene expression.

What is acetylation and its effect on transcription?

Acetylation is the addition of an acetyl group (-CH2CH3) to lysine in histone tails, leading to less packing of chromatin and an increase in transcription.

Define genomic imprinting.

Genomic imprinting is an epigenetic influence that occurs during critical periods, typically during embryonic development or gamete formation, affecting gene expression.

What is epigenetics?

Epigenetics refers to environmental factors or external influences that affect gene expression without changing the DNA sequence.

What are the two types of ncRNA?

The two types of non-coding RNA are small interfering RNA (siRNA) and microRNA (miRNA), both of which block translation or degrade proteins.

What is RNA interference (RNAi)?

RNAi is a biotechnology technique used to silence gene expression.

What occurs during the translocation of a gene?

Translocation occurs when a gene moves from one location to another within the genome.

What is the impact of gene amplification?

Gene amplification results in multiple copies of the same gene, leading to increased cell division.

What is the composition of a virus?

A virus is composed of a genome (single or double-stranded RNA/DNA) and a capsid, which is an outer protein coat made of capsomeres.

What are glycoproteins in relation to viruses?

Glycoproteins are proteins with carbohydrate chains that can be present on the surface of viruses, contributing to their structure and function.

What distinguishes lytic viruses from lysogenic viruses?

Lytic viruses immediately infect the host and cause cell lysis, while lysogenic viruses integrate into the host genome and remain dormant until triggered.

What is a retrovirus?

A retrovirus is a type of virus, such as HIV, that uses reverse transcriptase to replicate its RNA into DNA.

How does normal viral replication differ from retrovirus replication?

Normal replication follows DNA --> RNA, while retrovirus replication goes from RNA --> DNA via reverse transcriptase.

What is the difference between viroids and prions?

Viroids are naked RNA that infect plants, whereas prions are misfolded proteins that infect animals and are resistant to treatments.

What are restriction enzymes?

Restriction enzymes are molecular scissors that cut DNA at specific recognition sequences.

What is CRISPR technology used for?

CRISPR is a gene editing technology used to modify DNA sequences in organisms.

What does PCR stand for and its purpose?

PCR stands for polymerase chain reaction, and it is used to amplify specific DNA sequences.

What is gel electrophoresis?

Gel electrophoresis is a technique used to separate DNA fragments by size, where longer fragments travel slower than shorter ones.

Define transformation in bacteria.

Transformation is the process by which bacteria uptake plasmids or small DNA fragments from their environment.

What are operons?

Operons are clusters of genes under the control of a single promoter in prokaryotic cells, allowing coordinated regulation of gene expression.

What is positive gene regulation in the lac operon?

Positive gene regulation in the lac operon involves an activator that binds to DNA to enhance the likelihood of transcription.

What is the role of the p53 pathway?

The p53 pathway is involved in tumor suppression by regulating the cell cycle and preventing the proliferation of damaged cells.

What is the function of the RAS pathway?

The RAS pathway is a G-protein signaling pathway that regulates cell division and growth.

What type of genome do bacteria have?

Bacteria have a circular genome that can contain supplementary genetic elements called plasmids.

What are R plasmids?

R plasmids are plasmids that confer antibiotic resistance to bacteria.

What is an F plasmid?

F plasmids are involved in bacterial fertility, facilitating the transfer of genetic material during conjugation.

What did the recombinant DNA in Bacteria lab focus on?

The lab focused on methods to manipulate and study recombinant DNA in bacterial systems.

Define silencing gene in the context of methylation.

Silencing gene refers to the effect of methylation that leads to reduced transcription and gene inactivity.

What environmental factors influence epigenetics?

Environmental factors such as diet, stress, and exposure to toxins can influence epigenetic changes that affect gene expression.

What two features characterize small interfering RNA (siRNA)?

siRNA blocks translation and degrades mRNA, effectively silencing gene expression.

How do glycoproteins affect viral infections?

Glycoproteins on the virus surface aid in attachment to host cells, facilitating infection.

What is the significance of using reverse transcriptase in retroviruses?

Reverse transcriptase is significant for retroviruses as it allows RNA to be converted into DNA, which can integrate into the host genome.

What are the main parts of a virus?

The main parts of a virus are the genome and the capsid, which protects the genome.

What is a key mechanism for the production of proteins in a positive gene regulation context?

In positive gene regulation, an activator binds to DNA, increasing the likelihood of transcription and leading to protein production.

Helicase

breaks hydrogen bonds (unzipping enzyme)

Primase

creates an RNA primer (makes anti-parallel landing pad)

DNA Polymerase III

adds complementary nucleotides to a DNA strand, only synthesizes DNA from 5’ to 3’

DNA Polymerase I

removes RNA primers (created by primase) and replaces them with DNA

Ligase

seals the DNA fragments (after DNA Pol. I), known as the “genetic glue”

Leading Strand

continuous, keeps on going, uninterrupted (DNA can only be continuous on one strand)

Lagging Strand

discontinuous, interrupted, contains the okazaki fragments

Bacteriophage

(used in hershey/chase) viruses that exclusively infect bacterial cells (not human cells)

Codon/Triplet

a sequence of 3 bases on mRNA that codes for an amino acid

Start codon

AUG

RNA Polymerase

synthesizes mRNA from a gene from 5’ to 3’

Promoter

sequence of bases in front of a gene recognized by RNA polymerase

Transcription Factors

proteins that help RNA polymerase attach to the promoter (some proteins attach to the RNA pol., others attach to the T and A bases in the promotor aka the TATA box), allows for control over RNA polymerase

Control Element

a sequence of bases on DNA that controls transcription of a gene

1. Promotor

2. TATA box

3. Enhancer 

Spliceosome

enzyme that removes introns and joins exons together

RNA Processing

when you convert pre-mRNA to mature mRNA (occurs in nucleus)

1. Remove introns and splice exons together via enzyme

2. Addition of 5’ cap (consists of mostly G’s)

3. Add Poly - A tail (consists of mostly A’s)

Mutation

a change in the base sequence of DNA

Point Mutation

a change in the base in a nucleotide 

1. Substitution– a base is replaced by another base 

2. Deletion - a base is removed

3. Insertion - a base is added

tRNA

(folded RNA) transfers amino acids from the cytoplasm to the ribosome

Anticodon

sequence of 3 bases on tRNA that complement the codon on mRNA

Transcription

the process of making an RNA copy of a gene’s DNA sequence, happens in nucleus, (DNA → mRNA)

Translation

happens in the ribosomes, the process of making protein from mRNA (mRNA → protein)

LacZ gene

Gene codes for β-gal (beta-galactosidase)

Introns

Non-coding regions of a gene, removed by RNA splicing (spliceosome) as RNA matures

Exons

Coding sequences of a gene, covalently bond to one another to create mature mRNA

Operator

found in prokaryotes, it is a sequence of bases on DNA that bind the repressor + controls whether RNA polymerase can access the DNA to start transcribing genes (transcription)

Lac Operon

Catabolic Pathway, contains an active repressor that binds to the operator + a lactose inducer that deactivates the repressor

Repressor

active, binds to the operator

TRP Operon

Anabolic pathway, contains inactive repressor that doesn’t bind to the operator, contains the co-repressor “trp” that activates the repressor

Polycistronic

a single molecule of mRNA that codes for many different proteins (in prokaryotes)

Co-repressor

What trp (tryptophan) is considered to be in the trp operon. Means when trp levels are high, it binds to the trp repressor protein, allowing it to bind to the operator and preventing the transcription of operon genes, effectively inhibiting tryptophan synthesis.

Mutation Result

changes the function/activity of a protein

a) reduced activity

b) loss of function (no activity)

c) gain function (hyperactivity)

results in a new phenotype!

Stop Codons

UAA, UAG, and UGA are all

Operon

found in prokaryotes, it is a unit made up of linked genes which is thought to regulate other genes responsible for protein synthesis.

(also known by P.O.G. acronym meaning Promoter, Operator, and Gene)

Prokaryotes

• no membrane-bound organelles

• 1 circular chromosome

• no transcription factors + TATA box

• no introns + no spliceosomes

• no RNA processing

  (so no 5’ cap or poly A tail)

• contains operon (promoter, operator) and enhancer

Eukaryotes

• contains membrane-bound organelles

• many linear chromosomes

• contains transcription factors + TATA box

• has introns + spliceosomes

• has RNA processing

• does not contain operon (promoter, operator) and enhancer

Frederick Griffith’s 1928 transformation experiment

this experiment with bacterium helped lead to the discovery that DNA was the carrier of genetic information (involved mice and rough/smooth strains)

Hershey and Chase Experiment

this experiment proved that DNA was the genetic material; used bacteriophages to dock and kill e. coli by injecting their DNA + used radioactive elements to track