micro exam three

How can bacteria cultures be preserved?

Deep-freezing: -50° to -95°C Lyophilization (freeze-drying): frozen (-54° to -72°C) and dehydrated in a vacuum

Know in detail the structure of DNA. Which bases form H-bonds with each other and how many? What is the orientation of the strands? Which are pyrimidines? Purines?

Double helix, 1 strand runs 5'à 3', the other 3'à 5' Purinesà A, G pyrimidines C, T A-T, 2 H bonds C-G, 3 H bonds These are base pairs Order of nucleotides = genetic code

Role of Trace Elements

K-protein synthesis, membrane formation Na-cell transport Ca-stabilizes cell walls and endospores Mg-component of chlorophyll, stabilizes membranes, ribosomes Fe-component of cytochromes (ETS)

What is the Ames test? What organisms are used? What does it test for? What is bacterial recombination? What are plasmids? What are the 3 types of recombination that can occur in bacteria? What are transposons?

Use bacteria as an indicator organism Salmonella typhimurium cannot synthesize histidine ( dies) Spontaneous reversion to wild type( normal) is low If chemical is a mutagen, it will enhance the rate of reversion beyond normal rate of mutation

Importance of Growth Curves

Used to inhibit growth using heat and disinfectants Exponential growth phase more susceptible Exponential growth phase produces the most and virulent cells Growing cells in culture/lab

Be able to interpret and read a population growth curve, pointing out the lag, exponential growth, stationary and death phases.

Used to track bacterial growth Predictable pattern: 4 phases Lag-low cell count, adjustment Log (Exponential growth)-maximum rate of division Stationary-survival mode, slow/no growth Death-exponential death, slower than growth rate

How does transcription start? Which molecules and enzymes are involved? In which direction is the RNA made?

add finished chart from board

What is an autotroph? How many different types are there?

autotroph-inorganic carbon (CO2)

describe bacterial adaptations to temperature? Know the temperatures they grow at and the organism name. which are the pathogens? which are spore/ cysts formers?

bacteria have there own optimal temperature that they grow best at Psychrotrophs- can grow at freezing tempt spoilage in refrigerator Cooling warm food in the fridge will depend on the type of container

Why is cell metabolism called amphibolic?

because it involves both catabolism and anabolism.

What is leading and lagging strand synthesis? What are Okazaki fragments?

2 replication forks are formed Primase synthesizes a short RNA primer DNA pol attaches and begins to add nucleotides in the 5'à3' direction only (elongation) Leading and lagging strand synthesis Leading strand à continuous Replication is bidirectional

what is a stop codon?

3rd amino acid à A site Peptide bond à 2nd + 3rd amino acid Second tRNA à E site Growing peptide à P site This cycle continues until a stop codon (tRNA) is reached UGA ( stop codon)

What is the Lac operon? Know its parts and how it's controlled.

operon( gene/DNA Regulates lactose metabolism in E. coli ( in gut) 3 DNA regions (loci) Regulator à codes for repressor protein Promoter à where RNA pol binds Operator à where repressor binds 3 genes that code for enzymes that catabolize lactose:

Translation: elongation which goes into A site?

peptide bond covelent

where is it easier to open DNA?

A, T

What is the origin of replication? What is a replicon? Which enzymes are involved in replication?

Bacterial chromosome is circular Origin of replication (AT rich), replication fork ( less hydrogen) Helicases ( bacteria, gyrase (protazoan) , topoisomerase unwind/uncoil the DNABacterial chromosome is circular

How are mutations repaired? Do mutations have a role in evolution?

Cells use nucleotide excision repair Enzymes break bonds between bases at site of error, remove incorrect bases Gap is filled in by DNA pol I and ligase Methylases add methyl group to bases on newly synthesized strand No methylation à nucleotides removed

chem vs complex

Chemically defined media: exact chemical composition is known Complex media: extracts and digests of yeasts, meat, or plants Nutrient broth Nutrient agar

structure of DNA

Composed of nucleotides Deoxyribose sugar, phosphate, base Adenine, Guanine, Thymine, Cytosine

Bacterial Recombination

Conjugation-occurs between 2 related species, formation of bridge for DNA transport Transformation-transfer of naked DNA Transduction-transfer of DNA by virus Horizontal vs vertical gene transfer

How are genes regulated?

Constitutive genes are expressed at a fixed rate Other genes are expressed only as needed Inducible genes Repressible genes Catabolite repression

How are bacteria grown? What types of media are used to culture bacteria?

Culture medium: nutrients prepared for microbial growth Sterile: no living microbes Inoculum: introduction of microbes into medium ( inoculations) Culture: microbes growing in/on culture medium Can grow bacteria on Agar Complex polysaccharide Used as solidifying agent for culture media in Petri plates, slants, and deeps Generally not metabolized by microbes Liquefies at 100°C Solidifies at ~40°C

How does replication end? How are mistakes during replication corrected?

DNA pol proofreads new DNA, low error rate Check for mismatched bases Excising out incorrect bases Replacing correct base Topoisomerase (gyrase) supercoils DNA (nucleosome packaging) The following DNA sequence is to be replicated: ATGGCCCATGCCG Give the correct complementary strand

What is the total ATP yield after all 3 stages of aerobic respiration?

Total yield= 38 ATPs per glucose

What is anaerobic respiration? What are the different types?

Fermentation Goes through glycolysis in absence of oxygen, low ATP yield Pyruvic acid à ethanol, acetic, lactic, formic acids depending on bacteria species Lactic acid fermentation-breakdown of pyruvic acid à lactic acid, bacteria Alcoholic fermentation-pyruvic acid à ethanol, yeast

What is genetics? How is genetic information passed in the cell? Which are the key molecules involved?

Flow of genetic information instructions translator worker DNA RNA Proteins transcription translation nucleus Ribosomes (cytoplasm) 1 gene (DNA sequence) = 1 protein (amino acid sequence) = 1 specific function Proteins dictate the phenotype, DNA dictate the genotype of a cell (organism)

Genome, chromosomes, gene

Genome-all genetic information in a cell, includes STRs Chromosome-structures that contain/package DNA Organized using histone proteins Gene-segments of DNA that code for proteins

Atmospheric pressure? Know the range they grow at, concentration of salt, pressure

Growth prevented by high osmotic pressure Osmophile-high osmotic pressure Osmotolerant-tolerate wide range of solute concentrations, S. aureus Plasmolysis à occurs in a hypertonic solution (water leaves)

What is an heterotroph? How many types are there?

Heterotroph-organic carbon source

Growth Calculation Problem

How many bacteria cells would you have after 5 generations, if your initial population is 400 cells? How many cells would you have started with if after 3 hours you have 16,000? The bacteria doubles every hour.

What are the light dependent and light independent reactions? Compare and contrast them.

In the light-dependent reactions, energy from sunlight is absorbed by chlorophyll and that energy is converted into stored chemical energy. In the light-independent reactions, the chemical energy harvested during the light-dependent reactions drives the assembly of sugar molecules from carbon dioxide.

What are the terms used to describe a bacteria's oxygen requirement? Know terms, amount of O2 required, organism type based on oxygen requirements

Intracellular oxygen is converted to toxic intermediates: singlet oxygen, superoxide anion radicals, peroxide anion, hydroxyl radical Cells require superoxide dismutase (SOD), catalase, peroxidase to make H2O + O2 (live longer if they have this) If cell doesn't have these enzymes, must live in oxygen free environment Aerobe-requires O2 Anaerobe-does not require O2 Microaerophile-low O2 requirements Facultative vs. obligate Capnophiles-grow at higher CO2 levels, Neisseria, Brucella, S. pneumoniae

What is metabolism? What is catabolism? Anabolism?

Metabolism-all the processes within a cell Anabolism-biosynthesis, processes that synthesize molecules/structures, energy requiring (endergonic) Catabolism-degradation, breakdown of macromolecules into smaller ones, energy releasing (exergonic) Metabolism is a cycle of biosynthetic and degradative pathways that make/release energy (ATP)

What is the genetic code? What are codons? How many are there? What do they specify? Be able to take a DNA sequence convert it to RNA and determine the amino acid sequence using the genetic code

Newly synthesized mRNA is used to make proteins mRNA is read 3 nucleotides at a time called codons 1 codon = 1 amino acid There are 64 codons 61 specify amino acids (sense codons) 1 is also a start 3 are stops (antisense codons)

How are RNAs processed before translation? What are exons and introns?

Newly synthesized transcripts are not ready to make a protein Genes (mRNA) à exons and introns Exons à coding sequences that make a protein Introns à noncoding (junk) sequences Introns are cut out by "Splicing"

are stop codes counted as amino acids?

No

Chapter 6 What is a nutrient? Macronutrient? Micronutrient? Give examples of each that are required for bacteria growth. Bacteria cells are composed of what types of molecules?

Nutrients-elements required for metabolism and growth CHNOPS, Ca, Mg, Fe, Na, Cl, K, Mn Macronutrients à proteins, carbs Micronutrients à trace elements such as Mn, Zn, Ni Inorganicà not C based, gases, metals, salts, non living Organic à C based, from living things

What is binary fission? What is generation (doubling time)? Be able to calculate the number of cells after a given generation time

Practice calculations !!!!!!!

What are biofilms and why are they important?

Prevalent in most natural environments Happens through quorum sensing and inducer molecules Important in medical setting, resistant to microbicides Pseudomonas infections in lung S aureus colonizing medical devices Streptococcus in dental plaques

Anaerobic Growth Media

Reducing media Contain chemicals (thioglycolate or oxyrase) that combine O2 Heated to drive off O2 Capnophiles Microbes that require high CO2 conditions CO2 packet Candle jar

What is translation and who are the key players involved? What is the role of each? How are ribosomes assembled and how are tRNAs arranged inside? Know the 3 stages: initiation, elongation, termination

Ribosomes mRNA (codons) tRNAs (mRNA/anticodon and amino acid binding site) Amino acids à peptide

What are enzymes? What is the role of enzymes in metabolism? What are their properties?

Role of Enzymes in Metabolism Metabolic processes inside cells involve chemical reactions Collision Theory Activation energy and reaction rate These reactions are directed by protein catalysts à enzymes Properties of Enzymes Proteins (exception: ribozymes) Speed up chemical reactions by lowering the energy of activation Reaction/substrate specific Recyclable, do not change during reaction Do not change the reaction

Selective and Differential Media

Selective Media à Suppress unwanted microbes and encourage desired microbes, bismuth sulfite agar Differential Media à make it easy to distinguish colonies of different microbes, Blood Agar MSA is both a selective and differential media Enrichment Media à encourages growth of desired microbe

Why is DNA replication called semi-conservative? What do enzymes do?

Semiconservative-new DNA strands are composed of 1 parental strand each Parental DNA is used as template using base pair rules 30+ enzymes are required to separate DNA, add correct nucleotides, close any gaps, proofread

What is substrate level phosphorylation? Oxidative phosphorylation? Photophosphorylation?

Substrate-level phosphorylation refers to the formation of ATP from ADP and a phosphorylated intermediate, rather than from ADP and inorganic phosphate, Pi, as is done in oxidative phosphorylation.

Define: substrate, holoenzyme, apoenzyme, cofactors, coenzyme

Substrate-reactant, changes during course of reaction Holoenzyme-apoenzyme + cofactors Apoenzyme-protein portion of enzyme Cofactors-required for enzyme activity, can be organic=coenzyme (vitamin) or metallic = Fe, Ca, Mg, Zn Cofactors activate enzymes, bring substrates to active site, transfer functional groups between substrates