Micro bio exam 2 (redo)

Transcription in Prokaryotes

Transcription and translation are coupled, occurring at the same time and in the same place within the cell.

Transcription in Eukaryotes

Transcription occurs in the nucleus, and translation occurs in the cytoplasm.

mRNA Structure in Prokaryotes

often produce polycistronic mRNA (one mRNA containing multiple genes).

mRNA Structure in Eukaryotes

monocistronic mRNA.

Processing in Eukaryotic RNA

RNA undergoes extensive processing, including splicing (removing introns), capping (5' end), and polyadenylation (3' tail).

RNA Polymerases in Prokaryotes

use a single RNA polymerase.

RNA Polymerases in Eukaryotes

use three RNA polymerases (RNA pol I, II, and III).

Chromosome in Bacteria

The main genetic element, usually a single, circular, double-stranded DNA molecule containing housekeeping genes.

Plasmid (bacteria)

A genetic element that is expendable and replicates separately from the chromosome.

Function of Plasmids

Carry genes that offer selective advantages, such as antibiotic resistance or virulence factors.

Replication Fork

The zone where the DNA double helix is unwound and replication occurs.

Leading Strand

DNA synthesis is continuous in the 5' to 3' direction because the 3' end is oriented toward the fork growth.

Lagging Strand

DNA synthesis is discontinuous, synthesizing short segments called Okazaki fragments in the direction away from the fork.

DNA Helicase

Unwinds the DNA double helix.

DNA Primase

Synthesizes short RNA primers required to start DNA synthesis.

DNA Polymerase III

The primary enzyme for replicating the new DNA strands.

DNA Polymerase I

Removes the RNA primers and replaces them with DNA.

DNA Ligase

Seals the nicks between DNA fragments (especially between Okazaki fragments).

Sigma Factor

A protein needed only for the initiation of RNA synthesis; it ensures RNA polymerase binds to the correct site.

Pribnow Box

A consensus sequence (TATAAT) located 10 nucleotides upstream from the transcription start site in bacteria. It binds RNA polymerase to initiate transcription.

Rho-independent Termination

Controlled by specific DNA sequences; an inverted repeat followed by a string of adenines causes the mRNA to form a stem-loop structure.

Rho-dependent Termination

A specific protein called Rho binds to the newly formed RNA and causes the RNA and polymerase to release from the DNA.

tRNA Structure

Small, stable RNA molecules (73-93 nucleotides) with a 'cloverleaf' secondary structure containing an anticodon and an amino acid attachment site.

tRNA Function

Acts as an adapter molecule that carries specific amino acids to the ribosome and matches them to mRNA codons via the anticodon.

Degenerate Code

The genetic code is redundant; multiple codons can encode for a single amino acid.

Wobble

Flexible base pairing at the third position of the codon, allowing a single tRNA anticodon to recognize and pair with more than one mRNA codon.

Initiation of Protein Synthesis

The small ribosomal subunit (30S) binds to the Shine-Dalgarno sequence on mRNA.

Termination of Protein Synthesis

Occurs when the ribosome reaches a stop codon (UAA, UAG, or UGA).

Freeing a Trapped Ribosome

If a ribosome stalls on an mRNA without a stop codon, a molecule called tmRNA enters the A-site to finish the protein. It carries an amino acid and a small "tag" sequence that mimics mRNA, allowing the ribosome to finish the protein and adding a signal that targets the incomplete protein for degradation.

Properties of DNA-Binding Proteins

Most DNA-binding proteins are homodimers, consisting of two identical polypeptide subunits.

Role of DNA-Binding Proteins

These proteins interact with DNA in a sequence-specific manner to regulate transcription.

Negative Control

A regulatory mechanism that prevents transcription.

Repression

Preventing the synthesis of an enzyme in response to a signal.

Arginine operon

When arginine (the corepressor) is plentiful, it binds to the repressor, which then binds to the operator to block transcription.

Induction

Production of an enzyme in response to a signal.

Inducer

A substance that turns on gene expression (e.g., allolactose).

Corepressor

A substance that binds to a repressor to turn off gene expression (e.g., arginine, tryptophan).

Positive Control

A regulator protein called an activator facilitates the binding of RNA polymerase to the DNA.

Activator Protein

A protein that binds to an activator-binding site (not an operator) to help RNA polymerase recognize the promoter.

Maltose Metabolism

In the presence of maltose, the Maltose activator protein binds to maltose (the inducer), which then allows the protein to bind to the activator-binding site and initiate transcription of the maltose operon.

Catabolic Repression

A global control system that ensures the 'best' carbon source (usually glucose) is used first, repressing the use of other sugars.

Diauxic Growth

A growth pattern where a cell shows two exponential growth phases separated by a lag phase while it switches from using one sugar (glucose) to another (lactose).

Global Control

Systems that regulate many different genes simultaneously.

CRP (Cyclic AMP Receptor Protein)

An activator protein required for the expression of the lac operon and other sugar operons.

Cyclic AMP (cAMP)

A regulatory nucleotide. Its levels are high only when glucose levels are low. Transfers extracellular signals (hormones, neurotransmitters, etc.) to regulate cellular functions

Two-Component System

A regulatory mechanism that allows cells to sense and respond to environmental signals.

Sensor Kinase

Located in the cytoplasmic membrane. It detects an environmental signal and undergoes autophosphorylation at a specific histidine residue.

Response Regulator

A cytoplasmic protein that receives the phosphate group from the sensor kinase.

Quorum Sensing

A process by which bacteria assess their population density using secreted chemical signals called autoinducers.

Quorum Sensing role in Virulence

Many pathogens use this to coordinate the release of toxins or the formation of biofilms only when there are enough bacteria present.

Stringent Response

A global control mechanism triggered by nutrient starvation (amino acid or energy deficiency).

Heat Shock Response

A response to high temperatures or other stressors that cause proteins to denature.

General Stress Response

Allows the cell to survive varied harsh conditions (acid, oxidative stress, etc.).

Small RNAs (sRNAs)

Non-coding RNA molecules that regulate gene expression by base-pairing with mRNA.

Riboswitches

RNA domains in the 5' end of mRNA that bind small molecules directly, changing the mRNA's secondary structure.

Attenuation

A form of transcriptional control in bacteria where transcription is terminated prematurely after it has already begun.

Feedback Inhibition

A mechanism where the end product of a metabolic pathway shuts down the first enzyme in that pathway.

Anti-sigma factors

Proteins that bind to sigma factors and inhibit their function.

Point Mutation

A mutation that changes only one base pair.

Silent Mutation

A change in the DNA that does not change the amino acid sequence.

Missense Mutation

A change in DNA that results in a different amino acid being incorporated into the protein.

Nonsense Mutation

A change in DNA that creates a premature stop codon.

Frameshift Mutation

Insertions or deletions of nucleotides that shift the entire reading frame of the mRNA.

Reversion

A second mutation that restores the original phenotype of a mutant.

Homologous Recombination

A process that results in the physical exchange of DNA between genetic elements with nearly identical sequences.

Transformation

A genetic transfer process by which free DNA is incorporated into a recipient cell.

Generalized Transduction

Any portion of the host genome is packaged into a mature virus particle by mistake.

Specialized Transduction

Only specific DNA from a particular region of the host chromosome (adjacent to the phage integration site) is integrated into the virus.

Phage Conversion

An alteration in the phenotype of a host cell caused by lysogeny (the presence of a prophage).

Gene Transfer Agents (GTAs)

Defective bacteriophages produced by some bacteria that function specifically to package and transfer random DNA fragments between cells.

Conjugation

Horizontal gene transfer that requires cell-to-cell contact.

F (Fertility) Plasmid

A circular DNA molecule that contains genes for DNA replication and for the formation of a sex pilus.

Mechanism of Conjugation

A donor cell (F+) uses a pilus to pull a recipient (F-) close. A single strand of the F plasmid is transferred and then replicated in both cells.

Hfr (High Frequency of Recombination) Strains

Cells where the F plasmid has integrated into the host chromosome. During conjugation, these cells attempt to transfer the entire chromosome.

F' (F-prime) Plasmid

An F plasmid that has previously integrated into a chromosome and then 'excised' incorrectly, carrying some chromosomal genes with it.

Archaea HGT

Archaea use transformation, transduction, and conjugation.

Archaeal Conjugation

Some archaea (like Sulfolobus) form specialized structures called cell aggregates or nanotubes to transfer DNA.

Transposable Elements

DNA sequences that can move from one location to another on a DNA molecule (also called 'jumping genes').

Insertion Sequences (IS)

The simplest type; they carry only the gene for transposase and have inverted repeats at their ends.

Transposons

Larger elements that carry transposase plus additional genes, such as antibiotic resistance.

Conservative Transposition

The element is cut out of the original location and moved to a new site ('cut and paste').

Replicative Transposition

The element is replicated, and the new copy is inserted at a new site while the original remains in place ('copy and paste').

CRISPR

Stands for 'Clustered Regularly Interspaced Short Palindromic Repeats'. It is a prokaryotic immune system against viral infection.

Role of CRISPR

To recognize and destroy foreign DNA (from viruses or plasmids) that has previously infected the cell.

Mechanism of CRISPR

Adaptation: Small pieces of foreign DNA are integrated into the CRISPR region as spacers.

Expression: The CRISPR region is transcribed and processed into small crRNAs.

Interference: The crRNA guides Cas proteins (endonucleases) to matching foreign DNA, which the Cas proteins then cut and destroy.

Identification of ORF

Computers search for a start codon (e.g., AUG), a stop codon, and a ribosome-binding site (Shine-Dalgarno) positioned correctly upstream of the start codon.

Hypothetical Proteins

Proteins predicted by genomic analysis whose function is unknown.

Small Genomes

Devote a higher percentage of their genes to translation (protein synthesis) because these are essential housekeeping functions.

Large Genomes

Devote a higher percentage of their genes to transcriptional regulation and signal transduction, allowing them to adapt to diverse and changing environments.

Transcriptome

The entire complement of RNA molecules produced by an organism under a specific set of conditions.

Chromosomal Islands

Regions of a bacterial chromosome that appear to have been acquired by horizontal gene transfer.

Metagenomics

The study of all the genetic material (the 'metagenome') recovered directly from environmental samples.

Microbiome

The collection of all microorganisms (and their genes) living in a particular environment, such as the human gut.

Microarray

An older technology that uses DNA probes on a chip to detect the presence and abundance of specific mRNA sequences.

RNA-Seq

The modern standard for transcriptomics; it involves sequencing all the cDNA generated from the RNA in a sample.

Proteomics

The genome-wide study of the structure, function, and regulation of an organism's proteins.

Metabolomics

The complete set of metabolic intermediates and other small molecules produced by an organism.

Single-Cell Genomics

Sequencing the genome of an individual cell.