Micro Exam 2

What do you call the collection of all genetic material in a cell?

Genome

Describe the difference between genotype and phenotype and give an example.

Genotype- the full collection of genes that a cell contains within its genome.

Phenotype- the expression of the genotype creates observable traits/physical characteristics. Phenotype is the result of the genotype. EX: S. marcescins has a genotype that causes red appearance. When grown at 37 C, the red is not expressed.

Compare and contrast prokaryotic and eukaryotic superhelices.

Prokaryotic- DNA is supercoiled by DNA gyrase. 

Eukaryotic- DNA is wrapped around histones, condenses into chromatin, supercoils to a chromosome.

What are the components of a DNA nucleotide? 

1. 5 carbon sugar

2. phosphate group

3. nitrogenous base

Which components make up the backbone of DNA?

Phosphate and sugar

What type of bond is formed between adjacent nucleotides?

Covalent

What type of bond holds two strands of DNA together?

Hydrogen

Which pairs of nitrogenous DNA bases matchup, and which pair is more stable?

The C-G bond is more stable than the A-T bond. 

What part of the nucleotide is on the 5’ end? 3’ end?

5’ phosphate group

3’ hydroxyl group

Name 3 ways RNA is different from DNA

1. DNA is double stranded; RNA is single stranded.

2. DNA has deoxyribose sugar and RNA has ribose.

3. DNA has Thymine and RNA has Uracil

Explain why DNA is more stable than RNA

DNA is double stranded.

Messenger RNA (mRNA)

carries the gene from DNA master code to the ribosome

Transfer RNA (tRNA)

carries amino acids to ribosome during translation

Ribosomal RNA (rRNA)

forms the major part of a ribosome and participates protein synthesis

Primer

primes DNA for processes

Micro, antisense, riboswitch, and small interfering RNA

regulation of gene expression

Spliceosomes and ribozymes

remove introns from eukaryotic RNA, catalyze reactions

Why are tRNA and rRNA more stable than mRNA?

They bond to themselves to stabilize

Why is DNA replication a semiconservative process?

The two new complementary strands are synthesized by using each single-stranded template as the pattern.

Why is the origin of replication AT-rich?

Requires less energy to separate the two strands.

Describe the events that occur during DNA replication.

1. Helicase binds to DNA and beings to separate the two strands.

2. primase binds to the DNA and synthesizes a small RNA primer

3. DNA Polymerase 3 synthesizes new DNA strands using the original DNA as a template.

4. DNA polymerase 1 removes the RNA nucleotides that make up the primer and replaces them with the corresponding DNA nucleotides.

5. Ligase seals the gap between the Okazaki fragments

What purpose do primers serve and why is primase necessary during DNA replication?

The primer acts as a cushion since DNA poly 3 requires a double strand to attach. Primase lays down the primers. 

Why must the lagging strand be replicated in fragments instead of one continuous motion?

The polymerase must replicate in a 5’-3’ direction

What is different about the function of DNA polymerase 3 and DNA polymerase 1?

3 extends the primer, 1 replaces the primer.

Why is ligase needed for the lagging strand?

It seals the gaps between the Okazaki fragments.

What is the complementary strand for: 5’ -CGATCGGAT -3”

3’- GCTGCCTA -5'

What is the central dogma?

he pathway from DNA to RNA to protein that results in expression of genes.

What does gene expression mean?

Process in which a gene is used to produce a protein or non-coding RNA to affect the phenotype.

What is the role of DNA in protein production?

Used as a template to make an RNA copy through the process of transcription

What is transcription? What is the purpose of transcription?

the process of making a RNA strand from a DNA strand. Important to create a RNA strand that can be used to make proteins. 

Describe the general events that occur during transcription.

1. Initiation- RNA polymerase binds to promoter region upstream of the gene

2. Elongation- RNA polymerase adds nucleotides complementary to the DNA template strand in the 5’-3’ direction

3. Termination- RNA polymerase recognizes a stop sign in the DNA and releases the transcript

What purpose does the sigma factor have during transcription?

binds to promoter region upstream of gene to recruit polymerase to bind to the DNA at the leader sequence.

What direction does RNA polymerase elongate the mRNA strand?

5’-3’

What is Translation, what is its purpose?

The information in the mRNA strand is read to create proteins.

What is the start codon and what is special about the start codon on bacteria?

The start codon (AUG) is recognized by the ribosome and it begins to translate at that point.

Some amino acids are recruited by more than one codon, why is this helpful?

Helps prevent mutations that change the amino acid sequence

Describe the general events that occur during translation

1. Initiation- ribosome assembles on the 5’end of the mRNA strand and scans for start codon. tRNA molecules with complementary anticodon enter the P site of the ribosome and bind to the mRNA. A second tRNA with the complementary anticodon fills the A site.

2. Elongation- A peptide bond is formed between the amino acids on the neighboring tRNAs. The first tRNA is released and the ribosome slides down to the next codon.

3. Termination- the process stops when the stop codon is reached.

What purpose do tRNAs serve in translation, how do their structures make this possible?

Act as a translator of the mRNA code into a protein. They are bent into hairpin loops to form a cloverleaf. Bottom loop holds anticodon, 

What is a polyribosome complex? Whay are they useful? Why are polyribosomal complexes essential for bacteria?

Assembly line for protein production, allows bacteria to respond to stimuli rapidly.

Explain why prokaryotes can perform transcription and translation simultaneously but eukaryotes cannot.

Eukaryotes store their DNA in the nucleus and their ribosomes in the cytoplasm. So, mRNA has be transferred from the nucleus to the cytoplasm for translation.

Name 3 differences between the eukaryotic and prokaryotic gene expression processes.

Prokaryotic:

• occur simultaneously

• first amino acid is formyl-methionine

• single mRNA which encodes multiple proteins

• no introns

Eukaryotic:

• occurs separately

• first amino acid is methionine

• single mRNA encodes for a single protein

• eukaryotic mRNA has 5’ cap and 3’ polyadenylated tail

• DNA contains introns that must be spliced out of the final mRNA transcript

What are introns and exons? What type of organisms have them?

Eukaryotes have introns that are sections of DNA that are transcribed but not translated. Exons are transcribed and translated.

What is special about the arrangement of genes in prokaryotes? What is the purpose of this arrangement?

Organized into operons that allows them to all be turned on/off at once. Meaning they are expressed (transcribed and translated) all at once. Bacteria must be able to respond to certain stimuli rapidly.

What are two types of operons?

1. Inducible: Turned ON by substrate. produced when needed.

2. Repressible: turned OFF by the product synthesized.

Describe how the presence of lactose changes the expression of the genes in the lac operon

Lac Operon is an inducible operon, so the presence of lactose turns the operon on by acting as the inducer. 

If an operon’s repressor in in its inactive form, would transcription of the operon occur?

No, repressor repress the operon when active.

What is a mutation? In what two ways can they form?

A permanent change in the nucleotide sequence of DNA.

1. Spontaneous- random change in the DNA due to errors in replication that occur with no known cause.

2. Induced- result from exposure to known mutagens, physical or chemical, that interact with DNA in a disruptive manner

What is the difference between a wild-type strain and a mutant strain?

Wild type- a natural, nonmutated characteristic

Mutant strain- an organism that has a mutation, could show variance in morphology, nutritional characteristics, genetic control mechanisms, resistance to chemical, etc.

Point mutation

addition, deletion, or substitution of a single base

Silent, missense, nonsense, truncated, or frameshift

Silent mutation

alters a base but does not change the amino acid

Missense mutation

causes change in a single amino acid

nonsense mutation

changes a normal codon into a stop codon, results in a truncated amino acid chain

Frameshift mutation

when the reading frame of the mRNA is altered due to an insertion or deletion of one or more base. usually results in many errors or a premature stop codon. 

How does auxotroph detection help to determine if a chemical is carcinogenic? What test does this?

Auxotrophs are mutants that lost the ability to synthesize certain substances required for their growth because of mutations. The ames test is used to measure the mutation rate associated with exposure to the carcinogenic compounds.

Describe the types of mutation repair mechanisms that some cells have.

1. DNA polymerase proofreads nucleotides during replication

2. Mismatch repair- locates and repairs mismatched N bases that were not repaired by DNA polymerase

3. Light repair using photolyase (UV light damage)

4. excision repair- locates and repairs incorrect sequence by removing a segment of the DNA and then adding the correct nucleotide

Are all mutations bad?

No, mutations can be beneficial to certain environments and are the basis of change in populations.

What is Genetic Recombination?

The process in which a donor DNA molecule replaces a segment of a host genome or is inserted into a host genome

What are the four possible fates of donor DNA once it has been given to a recipient cell?

1. Integration of donor DNA

2. Donor DNA self-replicates

3. Donor DNA cannot self-replicate

4. Host restriction

Describe the 3 processes in which genetic recombination occurs in bacteria.

1. Conjunction- transfer of a plasmid or chromosomal fragment from a donor cell to a recipient cell via direct contact.

2. Transformation- Free chromosome fragments from a lysed cell are accepted/taken up by a recipient cell

3. Transduction- bacteriophage serves as a carrier of DNA from a donor cell to a recipient cell.

What does it mean for bacteria to be competent in regard to transformation?

Bacteria that can freely accept DNA from their environment.

The eukaryotic flagella are different from prokaryotic flagella in which two ways?

They are thicker and 

What are the 3 functions of cilia?

Found only on a single group of protozoa and certain animal cells. Function in motility, feeding, and filtering

What two groups of eukaryotes have a cell wall?

Fungi and most algae

What cellular processes are conducted in the Nucleolus?

Ribosomal RNA synthesis and ribosome construction

Compare and contrast the functions of the rough ER and the smooth ER.

Smooth: 

• nutrient processing

• lipid synthesis

• storage of lipids

Rough: 

• essential for secretory pathway

• ribosomes

• protein packaging and transport. 

What type of ribosomes are found in eukaryotic cells and what do they do?

Scattered in cytoplasm or associated with the RER. larger than prokaryotic ribosomes. Site of protein synthesis. 40S and 60S subunits make up the 80S ribosomes.

What is the purpose of a lysosome?

vesicles containing enzymes that originate from Golgi apparatus.

What forms the cytoskeleton of eukaryotic cells?

microfilaments and microtubules 

Compare and contrast the structure of yeasts and molds.

Yeast- Non filamentous and unicellular

Fungi- hyphae filaments

Why are fungi a problem in the food industry?

They grow in high sugar and salt concentrations, can grow in low moisture, can metabolize structural carbohydrates, aerobic

What term is used to describe the type of infection that fungi cause?

Mycoses

Name two benefits that fungi provide to humans.

Sources of antibiotics, alcohol, organic acids, vitamins. Used in making foods and in genetic studies

What group of eukaryotic microorganisms have a cell wall and can photosynthesize?

Algae

Why is red tide dangerous and what causes it?

Caused by red algae. Can produce a lethal toxin

What species is also referred to as brain eating amoeba and how is it contracted?

Amoebozoa- contracted through infected water getting into the mouth, nose, or eyes.

Trypanosoma

African sleeping sickness, chaga’s disease. Transmitted by blood-sucking insects

Giardia lamblia

giardiasis

Trichomonas vaginalis

Trichomoniasis-STI

Plasmodium

Malaria

Taxoplasma gondii

Taxoplasmosis

Cryptosporidium

Cryptosporidiosis

What are neglected tropical diseases?

Diseases caused by parasitic helminths. High number of cases worldwide, but diseases are not a focus because they are not found in high numbers in the US

What are the defining characteristics of cestodes and trematodes? What group are they a part of?

Flatworms

Hookworms

enter through the skin and move to the lungs swallowed infected sputum carries it to the intestines

Heartworms

spread by mosquitos

Threadworms

infect animals and plants. biopesticide applications

Soybean cyst nematode

can damage roots, foliage, seeds

Why are children typically reservoirs for infections diseases?

Because they are gross. 

What are the fundamental difference between viruses and the other acellular infectious agents?

Viruses contain at least protein and nucleic acid

What makes viruses obligate intracellular parasites?

they must enter a host cell and hijack the cellular machinery.

How does the size of viruses compare to the other microbes we have discussed?

Very small 100-200 micrometers

Are viruses capable of producing their own proteins?

No, lack protein-synthesizing machinery (ribosomes) 

What is the proteinaceous structure that protects the nucleic acid of viruses?

Capsid

What is a capsomer?

protein subunits that make up capsids

What makes up the nucleocapsid?

the capsid and the nucleic acid together

Compare and contrast the structures of helical nucleocapsid and icosahedral nucleocapsid

helical- 

• continuous helix of capsomers forming a cylinder

• tight association

• rod-shaped capsomers assemble into hollow disks

• the nucleic acid is inserted into the center of the disc

Icosahedral Capsids

• 3D Symmetrical polygon with 20 sides and 12 evenly spaced corners

What is the envelope of viruses usually from?

Acquired when the virus buds from the host cell

What is it called when a virus does not have an envelope?

naked

What is the specific purpose of spike proteins on viral envelopes or nucleocapsids?

Essential for the attachment of the virus to the host cell

What are the 3 main functions of capsids/envelopes?

1. protection- protects the nucleic acid when virus is outside of a host 

2. Attachment- helps the virus bind to a cell surface

3. entrance/penetration- necessary for the entrance of the viral DNA or RNA into a suitable host cell