Micrb 265 lec 9
What is a protein?
A protein is a polymer of amino acids linked by peptide bonds.
What are the main parts of an amino acid?
A central alpha carbon, an amino group, a carboxyl group, a hydrogen, and a variable side chain.
What determines the properties of an amino acid?
Its side chain or R group.
What are the three broad classes of amino acid side chains?
Nonpolar, polar uncharged, and charged.
What is a peptide bond?
A covalent bond formed between the carboxyl group of one amino acid and the amino group of another.
What direction are proteins written in?
From the N-terminus to the C-terminus.
What is the N-terminus?
The end of the protein with the free amino group.
What is the C-terminus?
The end of the protein with the free carboxyl group.
What is translation?
Translation is the process of synthesizing a protein from an mRNA template.
What is the first step of translation initiation in bacteria?
The mRNA binds to the 30S ribosomal subunit.
What helps the 30S subunit bind the mRNA in bacteria?
The Shine-Dalgarno sequence.
What is the Shine-Dalgarno sequence?
A purine-rich ribosome-binding site just upstream of the start codon that base pairs with 16S rRNA.
What is the second step of translation initiation?
The initiator tRNA carrying N-formylmethionine binds the start codon.
What is the third step of translation initiation?
GTP hydrolysis by initiation factors brings in the 50S subunit.
What codon usually starts translation?
AUG.
What is the first amino acid inserted in bacterial translation?
N-formylmethionine.
Where does the initiator tRNA start in the ribosome?
The P site.
What are the three ribosome sites?
A site, P site, and E site.
What does the A site do?
It binds the incoming aminoacyl-tRNA.
What does the P site do?
It holds the tRNA attached to the growing peptide chain.
What does the E site do?
It briefly holds the empty tRNA before it exits.
What are the three phases of elongation?
Aminoacyl-tRNA binding, transpeptidation, and translocation.
What happens during aminoacyl-tRNA binding?
The correct aminoacyl-tRNA enters the A site based on codon recognition.
What factor brings aminoacyl-tRNA into the ribosome?
EF-Tu.
What powers aminoacyl-tRNA entry?
GTP hydrolysis.
What happens during transpeptidation?
A peptide bond is formed and the growing peptide is transferred from the P-site tRNA to the A-site tRNA.
What catalyzes peptide bond formation?
The peptidyl transferase activity of 23S rRNA.
Why is the ribosome called a ribozyme in this step?
Because the catalytic activity is performed by rRNA, not protein.
What happens during translocation?
The ribosome moves forward one codon, the peptidyl-tRNA moves from A site to P site, and the empty tRNA moves to E site and exits.
What factor drives translocation?
EF-G.
What powers translocation?
GTP hydrolysis.
What are the stop codons?
UAA, UAG, and UGA.
What happens at a stop codon?
Release factors recognize the stop codon and terminate translation.
What do release factors do?
They help free the completed polypeptide and dissociate the ribosome.
Does termination require energy?
Yes, GTP hydrolysis is required.
What are the main stages of translation?
Initiation, elongation, and termination.
What is protein maturation?
The set of processes that make a new polypeptide into a functional protein.
What are the four parts of protein maturation emphasized here?
Folding, post-translational modification, complex formation, and localization.
What do chaperone proteins do?
They help proteins fold properly.
What are molecular chaperones?
Proteins that assist folding of nascent or misfolded polypeptides.
Why are chaperones important during heat stress?
They help protect cells from thermal damage by refolding partially unfolded proteins.
What are examples of bacterial chaperones mentioned?
DnaK, DnaJ, GroEL, and GroES.
What does GroEL/GroES do in simple terms?
It provides a protected environment for a protein to fold properly.
Why are hydrophobic regions important in folding?
They tend to be buried inside the protein and help stabilize the folded structure.
What is a post-translational modification?
A chemical change made to a protein after translation.
What are examples of post-translational modifications from this lecture?
Acetylation, methylation, phosphorylation, glycosylation, uridylylation, proteolysis, and addition of prosthetic groups.
What can post-translational modifications change?
Protein activity, localization, stability, or binding partners.
Are all post-translational modifications permanent?
No. Some last for the protein’s lifetime and some are dynamic and reversible.
What is the nitrogen-regulation example meant to show?
That post-translational modifications can control gene expression in response to environmental conditions.
When ammonia is limiting, what key modifications occur in the example?
Uridylylation and phosphorylation help activate nitrogen-assimilation gene expression.
What is complex formation in protein maturation?
Assembly of multiple protein subunits into a functional complex.
What is localization in protein maturation?
Getting a protein to the correct place in or out of the cell.
What does the Sec system transport?
Unfolded proteins across the membrane.
What else is the Sec system important for?
Helping integral membrane proteins fold and insert properly.
What does the Sec system require?
An N-terminal signal sequence and ATP hydrolysis.
What does the Tat system transport?
Folded proteins across the membrane.
What signal sequence is associated with the Tat system?
A twin-arginine signal sequence.
What powers the Tat system?
Proton motive force.
What is the key difference between Sec and Tat?
Sec transports unfolded proteins, while Tat transports folded proteins.
Why do bacteria export proteins?
To obtain nutrients, protect themselves, attach to surfaces, interact with other cells, and help form biofilms.
What is the Type I secretion system?
An ABC transporter that can move proteins from the cytoplasm directly to the outside.
What do Type II and Type V secretion systems have in common?
They rely on Sec or Tat first to get proteins into the periplasm.
What does the Type III secretion system do?
It injects proteins directly into another cell.
What is another name for the Type III secretion system?
Injectosome.
What is the Type VI secretion system used for?
Injecting proteins, often toxins, into other cells, especially other bacteria.
What is the Type IV secretion system used for?
Transfer into another cell, especially during conjugation, and it requires ATP.
What is the corrected point about Type IV pili versus Type IV secretion systems?
Type IV pili used for twitching motility are not the same as the Type IV secretion system. The Type IV secretion system is associated with conjugative pili and transfer between cells.
What is a mutation?
A change in DNA sequence.
What is the wild type?
The strain found in nature or the standard reference form.
What is a mutant?
A strain that carries a DNA sequence change.
What is genotype?
The genetic makeup or nucleotide sequence of an organism.
What is phenotype?
The observable traits resulting from the genotype.
What is a spontaneous mutation?
A mutation that arises without an external mutagen, often from replication errors or tautomeric shifts.
What is an induced mutation?
A mutation caused by an external agent such as radiation or chemicals.
What is a point mutation?
A change in a single nucleotide.
What is a missense mutation?
A point mutation that changes one amino acid to another.
What is a nonsense mutation?
A point mutation that creates a stop codon.
What is a silent mutation?
A point mutation that changes the DNA sequence but not the amino acid.
Why are silent mutations common at the third base?
Because wobble and code degeneracy often make third-base changes non-disruptive.
How can UV light cause mutations?
It can create pyrimidine dimers that distort DNA and lead to replication errors.
What are the three major ways bacteria acquire new DNA?
Transformation, transduction, and conjugation.
What is transformation?
Uptake of free DNA from the environment.
What is transduction?
Transfer of DNA by a bacteriophage.
What is conjugation?
Transfer of DNA directly from one bacterial cell to another through cell-to-cell contact.
Which horizontal gene transfer process requires a Type IV secretion system?
Conjugation.
What is a biofilm?
A community of microbes attached to a surface and embedded in a self-produced extracellular matrix.
What is the biofilm matrix mainly made of?
Mostly polysaccharides, plus proteins and extracellular DNA.
What kinds of surfaces can biofilms form on?
Biotic and abiotic surfaces.
What are the major stages of the biofilm life cycle?
Attachment, colonization, development or maturation, and dispersal.
What happens during attachment?
Cells initially stick to a suitable surface.
What happens during colonization?
Cells grow on the surface and begin producing matrix material.
What happens during biofilm maturation?
A three-dimensional matrix community forms, often with water channels.
What happens during dispersal?
Cells leave the biofilm and return to a planktonic state.
Why are water channels important in biofilms?
They help movement of nutrients and waste through the biofilm.
Why are polysaccharides so important in biofilms?
They are the main structural glue that holds the biofilm together.
What kinds of forces help hold a biofilm together?
Hydrogen bonding, ionic interactions, electrostatic forces, and van der Waals interactions.
Why are biofilms protective?
They help resist physical stress, predators, antimicrobials, and environmental fluctuations.
How can biofilms help bacteria get nutrients?
They trap extracellular enzymes and keep cells close to nutrient sources.
How can biofilms help bacterial cooperation?
Cells are close together, so they can exchange signals, genes, and metabolites more easily.
What is cyclic di-GMP?
A bacterial intracellular signaling molecule that strongly promotes biofilm formation and sessility.