TAMIU MICROBIO LEC 11

Define 'Genetics' in the context of microbiology.

The study of what genes are, how they carry information, how information is expressed, and how genes are replicated.

What is the definition of a 'Gene'?

A segment of DNA that encodes a functional product, usually a protein.

Distinguish between Genotype and Phenotype.

Genotype refers to the genes of an organism, while phenotype refers to the expression of those genes.

What are the three components of a nucleotide?

A pentose sugar, a phosphate group, and a nitrogen-containing base (purine or pyrimidine).

What type of bond connects nucleotides within a single nucleic acid strand?

Phosphodiester bonds, which are covalent bonds between the 3' OH group of one nucleotide and the 5' phosphate of the next.

What is the Central Dogma of molecular biology?

The flow of genetic information: DNA is replicated, transcribed into RNA, and translated into protein.

What is the function of mRNA in protein synthesis?

It encodes polypeptides using three-base combinations called codons that specify amino acids.

What is the role of tRNA during translation?

It converts mRNA information into an amino acid sequence using an attachment arm for the amino acid and an anti-codon region to orient at the ribosome.

What is the function of rRNA?

It serves as a catalytic and structural component of the ribosome, the site of protein translation.

Describe the anti-parallel nature of DNA.

DNA consists of two strands running in opposite directions (5'-3' and 3'-5') that form a double helix.

Which nitrogenous bases pair with each other in DNA?

Adenine pairs with thymine, and guanine pairs with cytosine.

Why is DNA supercoiling necessary in cells?

Because linear DNA is much longer than the cell, supercoiling compacts the DNA to fit within the genome.

What is the difference between negative and positive supercoiling?

Negative supercoiling is twisted opposite to the right-handed helix (common in bacteria), while positive supercoiling prevents DNA denaturation at high temperatures (found in some Archaea).

What is the function of DNA gyrase?

It introduces supercoils into DNA via double-strand breaks.

How does gene expression differ between prokaryotes and eukaryotes regarding transcription?

In eukaryotes, each gene is transcribed individually. In prokaryotes, multiple genes can be transcribed into a single mRNA molecule.

What are plasmids?

Small, usually circular, double-stranded DNA molecules that replicate independently of the chromosome and are often beneficial but not essential for cell function.

What are transposable elements?

Segments of DNA that can move from one site to another on the same or a different DNA molecule.

What is an operon?

A cluster of genes encoding enzymes of a single biochemical pathway in prokaryotes that are transcribed into a single mRNA and regulated as a unit.

What are R plasmids?

Resistance plasmids that confer resistance to antibiotics or other growth inhibitors.

What provides the energy for DNA synthesis?

The hydrolysis of the phosphate bonds when a nucleotide triphosphate is added to the growing DNA chain.

In which direction is DNA synthesized?

DNA is always synthesized in the 5' to 3' direction.

What is the role of primase in DNA replication?

It creates an RNA primer, which provides the necessary 3'-OH group for DNA polymerase to begin synthesis.

What is the primary enzyme responsible for DNA replication?

DNA polymerase III.

What is the significance of the 'primer:template junction'?

It is the specific region of double-stranded DNA where the DNA replication complex must bind to initiate synthesis.

What is the function of helicase in DNA replication?

Helicase unwinds the DNA helix to create single-stranded templates.

Why is an RNA primer necessary for DNA replication?

DNA polymerase cannot start a new DNA strand; it can only extend an existing strand from a 3' end.

What is the role of primase?

Primase binds to open DNA and synthesizes a short RNA primer to initiate replication.

How does the synthesis of the leading strand differ from the lagging strand?

The leading strand is synthesized continuously, while the lagging strand is synthesized discontinuously in Okazaki fragments.

What is the function of DNA ligase?

DNA ligase seals nicks between DNA fragments on the lagging strand.

What is the role of DNA polymerase I in lagging strand synthesis?

It removes the RNA primers and replaces them with DNA nucleotides.

What is the function of the replisome?

It is the DNA replication complex containing DNA polymerase III, gyrase, helicase, primase, and single-strand binding proteins.

What is the purpose of the 3' to 5' exonuclease activity in DNA polymerases?

It allows for proofreading by detecting and removing mismatched base pairs.

How are the two circular chromosomes separated after prokaryotic DNA replication?

Topoisomerase breaks one chromosome and relinks it to separate the linked circles.

In which direction does transcription proceed?

Transcription proceeds in the 5' to 3' direction.

What signals the start of transcription?

Transcription begins when RNA polymerase binds to the promoter sequence on the DNA.

What is the role of the sigma factor in bacterial transcription?

The sigma factor helps RNA polymerase recognize and bind to the promoter initiation site.

What are the two main promoter regions in bacteria?

The Pribnow box (-10 region) and the TTGACA sequence (-35 region).

What is a polycistronic mRNA?

An mRNA molecule that contains multiple open reading frames, transcribed from an operon, encoding multiple proteins.

How does Rho-dependent termination work?

The Rho protein binds to the RNA and causes RNA polymerase to pause at a termination site.

What is the 'TATA' box in eukaryotic transcription?

A 6-8 bp sequence in the promoter recognized by transcription factors to initiate transcription.

What is the function of spliceosomes?

Spliceosomes are complexes of RNA and protein that remove introns and join exons in eukaryotic primary transcripts.

What is the purpose of mRNA capping in eukaryotes?

The addition of methylated guanine to the 5' end is required to initiate translation and assist in ribosome binding.

What is the function of the poly(A) tail on eukaryotic mRNA?

It stabilizes the mRNA molecule and prevents premature degradation.

What are the four levels of protein structure?

Primary (amino acid sequence), secondary (alpha-helix/beta-sheet), tertiary (3-D shape), and quaternary (multiple subunits).

What is the definition of translation?

The process by which mRNA is translated into a polypeptide chain (protein synthesis).

How does RNA differ from DNA in terms of sugar and nitrogenous bases?

RNA contains ribose instead of deoxyribose and uracil instead of thymine.

What are the three types of RNA found in all cells?

mRNA, tRNA, and rRNA.

True or False: Transcription requires a primer.

False. RNA polymerase does not require a primer to initiate transcription.

What is an Open Reading Frame (ORF)?

A sequence starting with an AUG start codon, followed by a series of codons, and ending with a stop codon.

What are the start and stop codons for translation?

Start: AUG. Stop: UAA, UAG, UGA.

What is the primary function of tRNA in translation?

It acts as a decoder, carrying specific amino acids to the ribosome and matching its anticodon to the mRNA codon.

What is the significance of the CCA sequence at the 3' end of tRNA?

It is the attachment site for the amino acid.

What is the role of aminoacyl-tRNA synthetase?

It binds a specific tRNA to its corresponding amino acid, activating the amino acid with ATP to form aminoacyl-AMP.

What does it mean that the genetic code is 'degenerate'?

Multiple codons can encode the same amino acid, and irregular base pairing (wobble) can occur at the third position.

What is the 'wobble' position in the genetic code?

The third position of the codon-anticodon pairing, where irregular base pairing is permitted.

What are the two subunits of a ribosome composed of?

rRNA and proteins.

What is the function of the 16S rRNA in the ribosome?

It facilitates initiation by providing a binding site for the initiator tRNA and mRNA, and helps position the mRNA.

Define the three sites of the ribosome: A, P, and E.

A-site (acceptor): where the next tRNA enters. P-site (peptide): holds the tRNA with the growing peptide chain. E-site (ejection): where empty tRNA is released.

What is the Shine-Dalgarno sequence?

An upstream mRNA sequence that is complementary to the 3' end of 16S rRNA, allowing the ribosome to bind and position itself.

What is the initiator amino acid in Bacteria versus Archaea/Eukarya?

Bacteria use N-formylmethionine; Archaea and Eukarya use methionine.

What are the three main steps of translation?

Initiation, Elongation, and Termination.

Describe the process of transpeptidation during elongation.

The ribosome catalyzes the formation of a peptide bond between the amino acid in the A-site and the growing chain in the P-site.

What occurs during translocation?

The ribosome moves three bases down the mRNA, shifting the tRNA from the A-site to the P-site and the spent tRNA to the E-site.

What is a polysome?

A complex formed by multiple ribosomes simultaneously translating a single mRNA molecule.

How is translation terminated?

Release factors recognize a stop codon, cleave the peptide from the tRNA in the P-site, and cause the ribosomal subunits to dissociate.

List three functions of protein chaperones.

Folding misfolded proteins, refolding denatured proteins, and preventing improper protein aggregation.

What is the role of SecA in protein export?

It recognizes unfolded proteins and transports them to a membrane-bound channel for translocation using ATP.

What is the function of the Signal Recognition Particle (SRP)?

It binds to proteins during translation and moves the ribosome to the membrane surface for insertion.

What is the difference between a codon and an anticodon?

A codon is a three-nucleotide sequence on mRNA; an anticodon is the complementary three-nucleotide sequence on tRNA.

What is the definition of a transcriptional unit?

A segment of DNA that is transcribed into a single RNA molecule.

What is polycistronic mRNA?

An mRNA molecule that encodes multiple proteins, common in prokaryotic operons.

What are the components of the prokaryotic initiation complex?

The 30S ribosomal subunit, mRNA, formylmethionine tRNA, and initiation factors (IF1, IF2, IF3).

Still learning (4)

You've started learning these terms. Keep it up!