MICROBIOLOGY EXAM 3

Sigma Factor

Bacterial protein needed to start transcription by enabling RNA polymerase to specifically bind to gene promoters.

N-formylmethionine (fMet)

The first amino acid to be incorporated into a bacterial protein

Terminator

a sequence of nucleotides in DNA that marks the end of a gene or operon and signals RNA polymerase to stop transcription and release the newly formed RNA strand

Codon

a sequence of three consecutive nucleotides in a DNA or messenger RNA (mRNA) molecule that specifies a particular amino acid or signals the start or end of protein synthesi

Anticodon

is a sequence of three nucleotide bases located on a transfer RNA (tRNA) molecule that binds to a complementary codon on a messenger RNA (mRNA) strand during protein synthesis

Signal Sequence

The portion of a newly synthesized protein that directs it to the secretion apparatus, to which SecA binds, is called the ________

Operon

A group of related genes in DNA that are transcribed together to give a single polycistronic mRNA is known as a(n) ________________

cAMP

second messenger molecule used in intracellular signal transduction — relays signals from extracellular-first messengers (like peptide hormones) to target proteins inside the cell.

Antiseptic

An antimicrobial substance applied to living tissue, such as skin or mucous membranes, to destroy or slow the growth of microorganisms and prevent infection.

Disinfectant

Chemical agent used on non-living objects and surfaces to destroy or inactivate up to 99.9% of harmful microorganisms, including bacteria, viruses, and fungi

How to figure out the MIC of an antimicrobial?

In an Agar plate — The MIC is the lowest concentration of the antimicrobial agent that completely prevents visible growth compared to the control plate

How to figure out which antimicrobial agent is most effective using the agar diffusion assay?

Measure and compare the zone of inhibition (ZOI) formed around each agent

What are the major targets of antimicrobial agents that make them effective against bacteria, but non-toxic to humans?

1. Cell Wall/Peptidoglycan

2. Bacterial Ribosomes

3. Nucleic Acid (DNA and RNA) Structure and Function — ex. Folic Acid production

4. Cytoplasmic Membrane Structure and Function

What are the targets of antimicrobial drugs designed to be effective against

fungal cells?

1. Fungal Cell Membrane (Ergosterol and Sterols)

2. Fungal Cell Wall

3. Nucleic Acid and Protein Synthesis

What factors allow a cell to change from sensitive to resistant?

• Mutation

• R-Plasmid Conjugation

• Transposons

What are some of the common molecular mechanisms of antibiotic resistance?

• Enzymatic Degradation or Modification of the Antibiotic

• Alteration or Protection of the Drug Target

• Reduced Permeability (Altered cell envelope)

• Active Efflux Pumps

Central Dogma

DNA → Transcribed into RNA → Translated into Amino acids

Helicase

Unwinds and unzips the DNA double helix by breaking the hydrogen bonds between nitrogenous bases, creating a replication fork.

Topoisomerase (DNA gyrase)

Relieves tension and prevents supercoiling ahead of the replication fork.

Primase

Synthesizes short RNA primers on both template strands. These primers provide a free 3'–OH group required for DNA polymerase to attach and begin building

Exonucleases

RNase H or DNA Polymerase I - remove the RNA primers from both strands.

DNA Polymerase

Reads the existing template strand in the 3' to 5' direction and builds the new complementary strand strictly in the 5' to 3' direction.

Leading Strand

Synthesized continuously in the same direction that the replication fork is opening.

Lagging Strand

Synthesized discontinuously moving away from the fork, producing short segments of DNA called Okazaki fragments, each requiring its own RNA primer

Why are histones positively charged?

They have a high abundance of basic (alkaline) amino acids, specifically lysine and arginine — Binds to DNA’s strong negative charge

DNA Ligase

Seals the nicks and joins the Okazaki fragments on the lagging strand (along with the backbone gaps) into one continuous sugar-phosphate backbone.

TATA-binding protein

a crucial universal general transcription factor that binds to the TATA box promoter sequence

TATA-Box

a non-coding DNA sequence found in the core promoter region of many eukaryotic and archaeal genes

Eukaryotic DNA Structure

Multiple linear chromosomes, many ORIs, histones

Bacterial DNA Structure

1 circular chromosome, 1 origin of replication, NO histones

Archael DNA Structure

1 circular chromosome, 1-3 ORI, histones

Eukaryotic Gene Structure

• Only monocistronic

• Always have introns (non-coding regions removed after

transcription

Bacterial Gene Structure

• Mono/polycistronic mRNA

• No introns (rare)

• Transcription and translation are coupled

Archaeal Gene Structure

• Mono/polycistronic mRNA

• No introns (rare)

tRNA

• Acts as the molecular "decoder" between mRNA codons and amino acids

• Features an anticodon loop that base-pairs complementarily with the mRNA codon

• Charged tRNA: A tRNA covalently linked to its specific amino acid at its acceptor end

Shine-Dalgarno sequence

Ribosomal binding site in prokaryotic (bacterial and archaeal) messenger RNA (mRNA) that recruits and aligns the ribosome to start protein synthesis

SecA

brings unfolded protein into periplasm so it can fold there

Signal Recognition Particle

Target new proteins to the endoplasmic reticulum (ER) in eukaryotes or the plasma membrane in prokaryotes for secretion or membrane insertion.

Twin Arginine System (TAT)

Exports fully folded proteins

What is an inverted repeat sequence in DNA?

A single-stranded nucleotide sequence followed downstream by its reverse complement on the same strand. DNA-binding proteins can identify these sequences by dimerizing and using two symmetrical structural units.

Prokaryotic Ribosomal Subunit Size

Large: 50S

Small: 30S

Eukaryotic Ribosomal Subunit Size

Large: 60S

Small: 40S

What is the standard start codon and what amino acid does it code for?

AUG/ATG — codes for Methionine

mRNA

Messenger RNA — carries genetic instructions from DNA in the cell nucleus to the ribosomes in the cytoplasm to build proteins

tRNA

Transfer RNA — a small RNA molecule—typically 76 to 90 nucleotides long—that acts as an adapter to link the genetic code in mRNA with the amino acid sequence of proteins during translation

rRNA

Ribosomal RNA — non-coding RNA molecule that serves as the primary structural and catalytic component of ribosomes, the protein-building factories in cells.

Protein Chaperones

specialized proteins that assist the correct conformational folding, unfolding, assembly, and translocation of other target proteins while preventing random, non-specific aggregation

Operators

a specific segment of DNA in a genetic unit called an operon where a regulatory protein (such as a repressor or activator) binds to control gene transcription — located within a gene’s promoter region

Co-repressor

A molecule or protein that cannot bind to DNA directly and instead binds to an inactive or active repressor to assist or activate its inhibitory function

Diauxic Growth

a two-phase cell growth pattern that happens when microorganisms grow in a culture medium containing two different nutrient or sugar sources

2-Component Regulatory System

a sensor histidine kinase and a response regulator that work together to detect environmental changes and alter gene expression

Quorum Sensing

a cell-to-cell communication system that lets bacteria and other microbes track their population density and change their behavior together as a group using autoinducers

RNA Polymerase

Binds to a specific DNA sequence called a promoter. The enzyme unwinds the DNA double helix to form an open transcription bubble. No primer is required

Catabolite Repression

allows microorganisms to preferentially metabolize a preferred carbon source (such as glucose) while repressing the genes and enzymes needed to utilize less favorable alternative carbon sources

What causes the production of cAMP in a cell?

A lack of glucose