Exam Information and Microbiology Presentation

• The first exam will be 50 minutes.
• It involves multiple-choice questions and a bonus question.
• Use a pencil or pen and write answers on a separate sheet, explaining the bonus clearly.
• Final answers should be checked, as the final sheet is final.
• Maintain distance from classmates and keep desks free of items; only a pen/pencil is allowed.
• The short presentation of Black Microbiologists will be from Feb 1 to March 1.
• 5–7 people should present per day, with each presentation lasting 2–5 minutes.
• Presentations should summarize the microbiologist's bio (name, area of focus) and why they were chosen.
• Revise Brightspace frequently.
• Revise the syllabus.
• Quizzes are always due by the next lecture and lateness point deduction applies.
• Tutoring is available for select biology courses such as BIO 1101, BIO 1201, and BIO 3302.
• Tutoring is on Monday, Wednesday, and Friday from 10:00 AM-1:00 PM.
• Tutors are available to assist with lecture and lab questions.
• Contact the Atrium Learning Center for further information.
• Chapter 8 covers Microbial Genetics and Genetic Engineering.
• Learning outcomes for Section 8.1 are defining genome and gene, differentiating genotype and phenotype, drawing DNA segments, summarizing bacterial DNA replication, and comparing leading/lagging strand synthesis.
• Humans share more than 50% of their genes with bananas.
• Genetics is the study of inheritance/heredity in living things.
• Genetics explores biological traits' transmission from parent to offspring, their expression in organisms, the structure/function of genetic material, and how this material changes.
• The genome is the total genetic material in an organism.
• Most of the genome exists as chromosomes, while some appear as plasmids or reside in organelles of eukaryotes like mitochondria/chloroplasts.
• Genomes of cells are composed exclusively of DNA.
• Genomes of viruses can contain either DNA or RNA.
• A chromosome is a distinct structure of a neatly packaged DNA molecule.

Eukaryotic Chromosomes

• DNA winds around histone proteins, is located in the nucleus, are diploid or haploid, and have a linear appearance.

Bacterial Chromosomes

• DNA condenses into a packed by histone-like proteins and contains one, two, or sometimes several chromosomes.
• Three categories of genes structural genes, RNA machinery genes, and regulatory genes.
• A structural gene codes for proteins.
• Genes code for RNA machinery in protein production.
• Regulatory genes control gene expression.
• Genotype is the sum of all gene types and an organism's distinct genetic makeup.
• Phenotype is the expression of the genotype, creating traits (structures or functions).
• Nucleotides are the basic unit of DNA structure.
• The three parts of a nucleotide are phosphate, deoxyribose, and a nitrogenous base.
• Nucleotides are covalently bonded with a sugar-phosphate linkage.
• Each sugar binds repetitively to two phosphates.
• One bond in sugar is to the number 5' carbon on deoxyribose, and the other is to the 3' carbon.
• The antiparallel arrangement means one side of the helix runs in the opposite direction of the other.
• The order of the bond between carbon on deoxyribose and the phosphates tracks the direction of both sides.
• One side goes from 5’ to 3’ and the other side goes from 3’ to 5’.
• This is a factor in DNA synthesis and protein production.
• Nitrogenous bases attach by covalent bonds at the 1' position of the sugar.
• Purines (A, T) and pyrimidines (C, G) join with complementary bases using weak hydrogen bonds.
• Molecules unzip to access the information encoded in the bases.
• Adenine always pairs with thymine (T).
• Guanine (G) always pairs with cytosine (C).
• The overall DNA replication process is semiconservative.
• The replication process requires the orchestration of 30 different enzymes.
• Enzymes separate the strands of the existing DNA molecule, copying one strand and producing two complete daughter molecules.
• Each daughter molecule is identical to the parent in composition.
• One original parent DNA strand serves as the template.
• Helicase unzips the DNA helix.
• Gyrase untangles DNA supercoils.
• Primase synthesizes an RNA primer.
• DNA polymerase III adds bases to the new DNA chain and proofreads.
• DNA polymerase I removes the primer, closing gaps and repairing mismatches.
• Ligase binds nicks in DNA during synthesis and repair.
• Topoisomerase supercoils and untangles.
• DNA replication origin is a sequence rich in adenine/thymine, held by two hydrogen bonds rather than three.
• Topoisomerases unwind the DNA helix, giving helicases access to bind to dsDNA at the initiation site.
• Helicases break hydrogen bonds, separating the two strands.
• Single-strand binding proteins keep the strands apart.
• DNA polymerase III adds nucleotides according to the template.
• RNA primase has already added a short RNA length.
• DNA polymerase is oriented for synthesis in the 5' to 3' direction on the new molecule (blue).
• The leading strand is synthesized as a continuous, complete strand.
• The lagging strand is in the opposite orientation (3' to 5').
• Polymerase adds nucleotides a few at a time, direction away from the fork (5' to 3').
• The next segment is synthesized backward to the previous one, repeated until complete.
• This enables DNA polymerase to synthesize both new strands simultaneously.
• Producing one strand with short DNA fragments (100-1,000 bases long) produces Okazaki fragments.
• DNA ligase attaches these fragments to the growing lagging strand.
• Some bacteria can add nucleotides at 750 bases per second at each fork.
• DNA polymerase I removes RNA primers and replaces them with DNA.
• Ligases link fragments on the lagging strand, completing synthesis and separating daughter molecules, and mistakes can still occur.
• When DNA is replicated, two brand-new nucleotide strands are produced (False, it results in semiconservative replication).
• Learning outcomes for Section 8.2 are providing an overview of the relationship among DNA, RNA, and proteins, identifying differences between RNA and DNA, drawing a picture of transcription, and listing the three types of RNA directly involved in translation, as well as defining codon/anticodon and eukaryotic vs bacteria transcription.
• Transcription first uses DNA to synthesize an RNA molecule known as the master code.
• Transcription is followed by translation when transcribed RNA is used to produce proteins.

Exceptions to DNA->RNA->Protein

• RNA viruses convert RNA to other RNA.
• Retroviruses convert RNA to DNA.
• A wide variety of RNAs are used to regulate gene function.
• Only one strand is used for instruction; the template strand dictates why.
• RNA is similar to DNA in terms of its general properties, but its structure is different in several ways.

Structure Variations between DNA and RNA

• A single-stranded molecule exists in helical form.
• It can form secondary and tertiary complexity, leading to specialized forms of RNA like tRNA and rRNA.
• Contains uracil (U) rather than thymine (T).
• Contains ribose rather than deoxyribose.

Other RNA Varieties (Regulators of Gene Expression)

• Regulatory RNAs such as Micro RNAs, Anti-sense RNAs, Riboswitches, and Small interfering RNAs.
• Primer RNAs are operative in bacterial and eukaryotic cells.
• Ribozymes are enzymes made of RNA and remove other RNAs.
• The three RNAs involved in translation are ribosomal RNA (rRNA), transfer RNA (tRNA) , and messenger RNA (mRNA).
• Transfer RNA carries amino acids.
• Messenger RNA creates transcripts.
• Ribosomal RNA helps mediate translation.
• Transcription products used in translation are characterized as prokaryotes and eukaryotes in being different sizes.
• Ribosomes in bacteria, mitochondria and chloroplasts are 70S size, made of 50S and 30S subunits.
• The eukaryotic ribosomes are 80S, made of 60S and 40S subunits.
• The small subunit binds to the 5' end of mRNA.
• The large subunit supplies enzymes for making peptide bonds.
• The genetic codes: RNA to protein (translation).
• Codons are groups of three nucleotides dictating which amino acid is added to the growing peptide chain.
• It consists of 64 different triplet codes and 20 amino acids.
• Redundancy: some amino acids are represented by several codons insertion.
• Wobble is important to note as only the first two nucleotides are required to encode the correct amino acid, and the third nucleotide does not usually change its sense.
• Coupling transcription with translation speeds up the protein assembly line in bacteria.
• Bacteria couple transcription and translation, but eukaryotes don't.
• Characteristic is its start codon for bacteria it is always AUG while the same mRNA in Eukaryote codes only for one protein.
• Transcription and translation of Bacteria exist simultaneously in the cytoplasm while in Eukaryotes, transcription occurs in the nucleus; translation occurs in the cytoplasm.
• Genes in transcription and translation are important to highlight where bacteria exist as an uninterrupted set of triplets coding for a protein and transcript.
• Regulatory RNAs are operative in both bacterial and eukaryotic cells.
• Ribozymes are enzymes made of RNA and remove unneeded sequences from other RNAs.
• Transfer RNA contains hairpin loops and is involved in carrying amino acids to the ribosome during translation.
• Learning Outcomes Section 8.3 covers definition of operon while highlighting the main points of lac operon operation.
• Control mechanisms ensuring genes are active only when needed and their regulation occurs in bacteria and archaea.
• Operons are only found in bacteria and archaea.
• They consist of a coordinated set of genes regulated as a single unit, and are inducible or repressible.

Catabolic operons examples Lactose Operon

• Induce Structural genes that substrate enzyme for.
• They only produce when that substrate is present.

Repressible Operons

• Anabolic enzymes that are turned off.

Three (3) Features of Lac Operon

• Composed of the gene and protein
• Capable of repressing the operon (a repressor)
• Control locus-recongized by RNA
• Polymerase (on/off switch)
• Made up of three genes of enzymes
• needed for the catabolize of of lactose

The lac operon is on when glucose levels are low and lactose levels are high.

• Learning Outcomes Section 8.4 Covers defining recombinant organisms.
• Highlight three transfer events in bacteria as in

Horizontal Gene Transfer in Bacteria

• Is to transfer DNA that has resulted in organism acquiring new genes.

Plasmids

• Small and circular Contain replicated traits.
• Chromosal with bacteria integrates for replication.

Horizontal Gene Transfer Mode Examples

• Conjugation - donor transfers DNA
• Transformation - free donor to live cell
• Transduction bacterial carrier.
• Mode of genetic exchange in which material is transferred .
• Transfer from a to cell as to to pili with fertile factors and receptors .
• Is the resistance plasmids.

Transformation

• A chromosome released by the cell small .
• By facilitating DNA to the cell wall for genetic material.
• Learning 8.5, to define the term mutation one postive and negative examples.
• Point ( base pairing ) can cause to the phenotype and to an effect.
• From it we can gain an understanding in the following

1. Point (addition , deletion ,or substitution of sing bases)
2. Missense ( a change amino or functions differently)
3. Nonsense ( mutatios astop codon) 4.silent( affect base to to)
4. Back - when gene is back base.
5. Frameshit is inserted

• UV Damage - visible lights small cell for mutations. Mutations Permanent ,spontaneous change that is not a gene .
• Most frameshifts point . 8 .