Module 1 - Content

In which type of cells was the central dogma largely discovered in?

Prokaryotic cells

Why are bacteria cells ideal organism to study molecular biology?

They are simple, have minimal living requirements, have short generation times, are quick, easy and cheap to genetically manipulate and share all basic cellular processes and some genes with human

Why is it important that bacterial cells reproduce asexually in regards to trying to understand the genome?

The genome is more stable and doesn’t resort every generation

Why are bacteria helpful for evolution research?

They have very short generation times so population change over time can be seen faster

What does DNA do?

Stores information for protein synthesis

What enzyme performs transcription?

RNA polymerase

What enzyme translates mRNA?

Ribosomes

How does genotype create a phenotype?

The genotype codes for proteins that form enzymes that make up metabolic pathways that make products resulting in a phenotype

True or false: mutations in genotype always result in changes to phenotype

False

How can a mutation effect a phenotype?

Mutation in the genome changes the mRNA which can change the codons and therefore the proteins added to the peptide chain which can change the metabolic activity

How can you use phenotype to understand the function of genes?

You can change a gene and observe what change, if any, that that has on the phenotype

What are the four major macromolecules?

Nucleic acid, proteins, lipids, carbohydrates

How does the genome produce the four major macromolecules?

Genes code for proteins that form enzymes that make up metabolic pathways that synthesize each macromolecule

True or false: the four major macromolecules are building blocks for only eukaryotic cells

False

Why are nucleic acids important?

They encode instructions for enzymes for the cells metabolism and macromolecule synthesis

What is the function of DNA?

To store instructions for the synthesis of RNA and enzymes

What is the function of RNA?

To transfer information from DNA by acting as a template for enzyme synthesis

Why do most proteins have enzymatic activity?

To produce energy and macromolecules for the cell

What are the functions of proteins in a cell?

Transportation of nutrients, to act as enzymatic catalysists of catabolic and anabolic pathways and to provide cellular structure and motility

Why are carbohydrates important to cells?

They are sources of cellular energy and carbon

Why are lipids important?

They contribute to cellular energy, carbon molecules and structure

What do fatty acids do?

Store energy and carbon

True or false: both eukaryotic and prokaryote cells have chromosomes

True

What is the difference between chromosomes in eukaryotic cells and prokaryotic cells?

Eukaryotic cells have multiple chromosomes of linear DNA, tightly packed by proteins while bacterial chromosomes have a small, single chromosome and made up of circular DNA that is loosely organized by proteins

Why is the cytoplasmic/cellular membrane important?

It controls the passage of substances into and out of the cell and maintains the chemical electrical gradient

What is the composition of the cytoplasmic membrane?

Phospholipids and proteins

True or false: both eukaryotic and prokaryotic cells have membrane bound intercellular structures

False

How does transcription and translation occur in eukaryotic cells?

In eukaryotes, transcription and translation are separated by intracellular structures so that DNA is stored in the nucleus where RNA is synthesized through transcription before mRNA is exported to the ER where proteins are synthesized through translation

How does transcription and translation occur in prokaryotic cells?

Transcription and translation are coupled so that they occur simultaneously in the cytoplasm

Why is transcription and translation coupled in prokaryotic cells but not in eukaryotic cells?

Prokaryotic cells do not have membrane bound organelles to separate transcription and translation while eukaryotic cells do

Where is the primary site of aerobic ATP synthesis in Eukaryotic cells?

The inner membrane of the mitochondrion

Where is the primary site of aerobic ATP synthesis in prokaryotic cells?

Cell membrane

True or false: prokaryotic cell membranes contain proteins of the electron transport chain and ATP synthase

True

What are the 3 primary metabolic pathways for bacteria?

Aerobic respiration, fermentation, and anaerobic respiration

O2 is the terminal electron receptor in which metabolic pathway?

Aerobic

An inorganic chemical is the terminal electron receptor in which metabolic pathway?

Anaerobic respiration

An organic molecule is the terminal electron receptor in which metabolic pathway?

Fermentation

Which metabolic pathway produces the most ATP? How much is that?

Aerobic respiration, 38

Which metabolic pathway produces the least ATP? How much is that?

Fermentation, 4

How much ATP does anaerobic respiration produce? What does it depend on?

4-36 depending on the terminal electron accepter

Which metabolic pathways produce similar ATP?

Anaerobic and aerobic respiration

Which metabolic pathways can eukaryotic cells perform?

Aerobic respiration and fermentation

How can you determine which metabolic pathway a bacteria is using?

Measuring population growth as a measure of ATP production

True or false: population growth overtime is a phenotype

True

True or false: the metabolic pathways of a bacteria have no impact on what specific environment it is found in

False

Why are control variables important?

To ensure any change noticed in the response variable is due to the effect of the manipulated variable

Why are control variables necessary?

They provide a standard to ensure that the experiment is working properly and that the results are valid

What happens if a negative control is positive or a positive control is negative?

The experiment is not working correctly and your results are in valid

What are the two most common phenotypes looked for in Growth Assays?

Survival and Growth

What are the two most common phenotype looked for in a molecular assay?

Gene expression and enzyme activity

What does a molecular assay assess for?

The central dogma

What are 3 growth phenotypes?

Survival, growth and antibiotic sensitivity

What are two assays to measure the size of a bacterial population in response to a manipulated variable?

Viability assay and growth curve assay

Why is serial dilution important?

It makes the number of colonies in petri dish countable and prevents overcrowding from giving artificially low counts

Why does turbidity work as a way to measure bacterial populations?

As more bacterial form, the chance a photon of light will hit a sensory and not bounce off a bacteria will decrease resulting in a decrease in light that a spectrophotometer measures as the population increases

True or false: turbidity decreases as bacterial population size increases

False

True or false: CFU is usually measured per ml

True

Why is there a lag phase?

Cells need nutrients before they can replicate and when introduced to a new environment, they need to activate genes to synthesize new enzymes to be able to exploit nutrients in the new growth medium to be used for growth

How do you determine a generation time

Pick 2 points on the axis representing number of cells where 1 number is 2x that of the other and find the difference in the time the population reaches those two numbers

When is the rate of binary fission maximized?

During the log phase

During which phase of a cellular population growth curve should physiology and metabolic activity be studied? Why?

During the log phase because cells are the most physiologically uniform during this phase which maximizes uniformity during the test

Why does exponential population growth not continue forever?

Nutrients are limited, meaning that as more is used there is less available for producing energy, and metabolic waste increases

Should metabolic activity and cellular physiology studies be performed during the stationary phase? Why or why not?

No because the physiology is less uniform, increasing variability in the sample

Does some binary fission still occur during the death phase?

Yes

Why does the death phase occur?

Nutrients become too scares to allow binary fission to equalize death rate and metabolic waste reaches harmful levels

Why does growth curves of populations measured by spectrophotometer decrease slower during the death phase than those measured by visable counts?

Light still reflects off dead cells

True or false: only using one assay to get results without using at least one other assay is good practice

False

What does a disk diffusion assay determine?

Sensitivity to antibiotic

What are the sets of a disk diffusion test

Prepare an overnight culture → uniformly inoculate a petri-dish prepared with agar → impregnate a paper dish with antibiotics of know concentration and put it in the petri dish → incubate it and than measure the zone of inhibition

What is another name for the disk diffusion test?

Kirby-Bauer test

What increases as the sensitivity of a bacteria to an antibiotic increases during a disk diffusion test?

The diameter of the zone of inhibition

How would biologists evaluate the effect of a manipulated variable on proteins and enzymes of a bacteria?

By evaluating enzyme activity

What is measured to determine the effect of the manipulated variable on gene expression?

mRNA

How is mRNA quantitated?

1 strand of mRNA is converted into 1 double strand of cDNA to make it more stable through a process called RT-PCR, the abundance of cDNA is than measured through qPCR

What happens during qPCR?

The properties of fluorescent dye change when it binds to double stranded DNA and we can measure the level of flurescense

What does qPCR stand for?

Quantitative polymerase chain reaction

What dos an enzyme assay measure?

Whether an enzyme is present in a population and, if so, in what amount

What is the morphology of this bacteria?

Spirochete

What is the morphology of this bacteria?

Corkscrew’s form (Borrelia burgdorferi)

What is the morphology of this bacteria?

Vibrio

What is the morphology of this budding and appendaged bacteria?

Stalk

What is the morphology of this budding and appendaged bacteria?

Hypha

What is the morphology of this bacteria?

Streptobacilli

What is the morphology of this bacteria?

Diplobacilli

What is the morphology of this bacteria?

Bacillus

What is the morphology of this bacteria?

Coccobacillus

What is the morphology of this bacteria?

Tetrad

What is the morphology of this bacteria?

Sarcina

What is the morphology of this bacteria?

Streptococci

What is the morphology of this bacteria?

Staphylococci

What is the morphology of this bacteria?

Diplococci encapsulated (pneumococcus)

What is the morphology of this bacteria?

Diplococci

What is the morphology of this bacteria?

Coccus

What type of bacteria morphologies are these?

Cocci

What type of bacteria morphologies are these?

Bacilli

What are the steps of binary fission?

DNA is replicated with each replication attaching itself to a different part of the cell wall → cell elongates, pulling the DNA away from each other → plasma membrane begins to constrict, forming a septum → cross walls form → cell separates into two identical daughter cells

What happens during budding replication>

Bacteria forms a small outgrowth that enlarge until it’s the size of the parent cell and then separates

How do some filamentous bacteria reproduce?

Some produce chains of condiospores carried at the tips of the filament and other fragment to form new cells

What are the advantages of a logerithmic representation of population growth?

Growth is shown linearly, all population sizes at all times are clearer, and larger populations can be represented in less space than if graph arthmetically

When does generation time equal a constant minimum?

During log phase