MCB2000 Exam 2 (Asghari UF)

Define Central Dogma of Molecular Biology

DNA > mRNA > Protein > Function

This describes how, typically, DNA is transcribed to messenger RNA, which in turn, is translated into proteins that carry out vital functions

"Flow of genetic information"

What are important points discusses in "Big Picture-Genetics"

Genetics are the study of genes: how they are replicated and passed on from one generation to the next.

Mutations introduce changes into this process, which can be frameshift or base substitution. Genes on operons can be inducible "off" with repressor bound to DNA or repressible "on" with repressor NOT bound to DNA.

Alteration of bacterial genes and/or gene expression may cause disease, prevent disease treatment, or be manipulated for human benefit.

Gene

Segments of DNA that encode functional products, usually proteins

Genome

All genetic info in a cell

Chromosome

Structures containing DNA that physically carry hereditary info; chromosomes contain genes

Name and discuss the roles of different RNA molecules.

Which one contains codon, anticodon

RNA - single-stranded nucleotide, 5 carbon ribose sugar, contains uracil instead of thymine

rRNA - integral part of ribosomes

tRNA - transports amino acids during protein synthesis

mRNA - carries coded info from DNA to ribosome

mRNA has codon > read by ribosome > anti-codon carried by tRNA to ribosome > ribosome makes protein

Define transcription and state what is used as a template for this process

The synthesis of a complementary strand of RNA from a DNA template

Begins when RNA polymerase bind to the DNA, resulting in the release of RNA polymerase and RNA

Define translation and state what is used as a template for this process

AKA Protein Synthesis because it involves decoding the "language" of nucleic acids and converting it into the "language" of proteins

Overall goal to produce proteins using mRNAs as the source of biological information

Products of Replication

Because one strand of DNA serves as a template for another, the products are 2 identical copies of DNA

Products of Transcription

RNA

Products of Translation

Proteins

Products of Reverse Transcription

DNA

Difference between DNA polymerase & RNA polymerase

While DNA polymerase is used in DNA replication to synthesize DNA strands, RNA polymerase is used during transcription to synthesize mRNA strands

RNA don't need primers to start their process

What is the source of reverse transcriptase and what does it do

Makes DNA from RNA

Unique to some viruses (HIV)

Complimentary Strands

Strands of DNA that are paired up to AT & CG

Anti-Parallel

Parallel, but moving or oriented in opposite directions (5' -> 3' ; 3' ->5')

Semiconservative Replication

Describes the mechanism by which DNA is replicated in all known cells

One strand is original from parent, one is new

(1/2 new, 1/2 from parent)

Double Helix

Pair of parallel helices intertwined about common axis, especially that in the structure of the DNA molecule

Enzymes involved in DNA replication and their functions

Topoisomerase and gyrase relax the DNA strands

Helicase separate strands

DNA polymerase add nucleotides to the growing DNA strand in 5-3 direction

Fragments are joined together with ligase

Function of DNA Gyrase

Relaxes supercoiling ahead of replication fork

Function of DNA Ligase

Makes covalent bonds to join DNA strands, Okazaki fragments, and new segments in excision repair

Function of DNA Polymerase

Synthesizes DNA

Proofread and facilitate repair of DNA

Function of RNA Polymerase

Synthesizes RNA from DNA

Function of Helicase

Unwinds double-stranded DNA

What is post-transcriptional control

Some regulatory mechanisms that stop protein synthesis after transcription has occurred. This post-transcriptional step can also be regulated to control gene expression in the cell. If the RNA is not processed, shuttled, or translated, no protein will be translated

Function of miRNA

Small, sing-stranded RNA that prevent translation of a complimentary mRNA

Inhibit protein production in eukaryotic cells

Genetic material for viruses

DNA or RNA, either single or double stranded

Where in prokaryotes can DNA be found

In circular or linear chromosomes inside the supercoil in nucleoid

Plasmid

Where in eukaryotes can DNA be found

In linear chromosomes in the nucleus

Mitochondira

Chloroplast in plants

What is pre-transcriptional control

Repression and induction regulate the transcription of mRNA

These mechanisms control the formation and amounts of enzymes in the cell

Operons and their role in gene expression of bacteria

Group of genes transcribed together and controlled by one promoter

Regulation of gene expression

Examples of operons

Inducible operons - (catabolic, control sugar metabolism) usually off unless there is a substrate for them to metabolize

Repressible operons - control genes involved in synthesis (anabolic) tryptophan operon is an example of "on" because they are synthesis processes and are off when amino acids come in from the environment and the need to make them is no longer there

Catabolic Repression

Can override inducible operons

Shows that glucose is the sugar of choice

Cells prefer glucose over lactose, how are genes expressed to facilitate this preference

When lactose and glucose are together, the lactose operon is off. Glucose is used up and then during lag time you turn it back on

What are ribosomes made from

rRNA and proteins

Difference between prokaryotes and eukaryotes ribosomes

Size and compostition

Pros ribosomes are a target for antibiotics and euks ribosomes and bigger and denser

What is the significance of the difference between prokaryotes and eukaryotes ribosomes

Antibiotics (tetracycline and erythromycine) won't kill euks ribosomes, only pros so they kill bacteria inside us

Recombinant DNA technology

Insertion or modification of genes to produce desired proteins

Purpose of Cloning

To have identical cells coming from one cell

Goals: eliminate undesirable phenotypes, combine beneficial traits, and create organisms that can produce human product (insulin)

Explain how a technique known as Restriction Fragment Length Polymorphins (RFLP) works in analyzing DNA

Different legnths of DNA restriction fragments from individuals of same species because of the deletion or adding of DNA between sites where restriction enzyme cuts

Used to determine ancestry of individual and identify DNA from specific individuals, determines location of genes causing genetic diseases, and identifies new inserted genes or DNA sequences

Take DNA, cut into pieces > gel electrophoresis > take sample from father and child, compare

Can be used for forensic science

Scientific Applications of rDNA

Genetic screening (southern blots used to screen parents and fetuses for inherited diseases caused by mutations)

DNA Fingerprinting

Gene therapy: replace defective and missing genes with normal ones

Agricultural Applications of rDNA

Bt toxin - plants have toxin-producing gene, toxin kills insects that eat plants (Bt cotton, Bt corn)

Herbicide resistance

Suppression of genes-antisense DNA (improve shelf life)

Nutrition-human proteins

RoundUp (glyphosate) - plants have bacterial gene; allows use of herbicides on weeds without damaging crops

Tools used to make Recombinant DNA

Restriction enzymes - cut specific sequences of DNA

Vectors - carry new DNA to desired cells (usually plasmids or viruses)

DNA is cut and can be inserted into a cell via...

Transformation - cells take up DNA from the surrounding environment

Electroporation - electrical current forms pores in cell membranes

Protoplast fusion - removing cells walls from two bacteria allowing them to fuse

Gene library

Collections of clones containing different DNA fragments

Gene gun

Way of introducing foreign DNA into plant cells

Microinjection

Technique for introducing a solution of DNA into a cell using a fine microcapillary pipette

How can one amplify DNA fragments in a lab

Polymerase chain reaction - process of increasing small quantities (amplifying) of DNA for analysis

Reverse-transcription PCR uses mRNA as a template

Synthetic DNA

Builds genes using a DNA synthesis

Therapeutic Applications of rDNA technology

Human enzymes and other proteins such as insulin

Subunit vaccines - made from pathogen proteins in genetically modified yeasts. Nonpathogenic viruses carrying genes for pathogen's antigens as DNA vaccines

Gene therapy to replace defective or missing genes

Hep B vaccine

Human growth hormone

Gene silencing (small siRNAs bind to mRNA, which is then destroyed by RNA silencing complex)

RNA interference (inserts DNA encoding siRNA into pasmid and transferred into a cell) could provide treatments for a wide range of diseases

Goal/Purpose of Genome project

Sequenced entire human genome

Nanotechnology

Branch of engineering that deals with things smaller than 100 nanometers (especially with the manipulation of individual molecules)

Describe the use of the human microbiome in a crime scene investigation

DNA fingerprinting (RFLP) used to identify pathogens > can be used to track infectious diseases

Take DNA cut it into pieces > gel electrophoresis > take sample from father and child, compare

You should notice the same pattern in the gel

Spontaneous Mutation

Occurs in the absence of a mutagen

What causes spontaneous mutation/induced mutation

Chemicals and radiation can lead to this

Base analogs

Molecules that can substitute for normal bases in nucleic acids

How might base analogs induce mutation

Usually, substitution of a base analog will result in altered base pairings and structural changes that affect DNA replication and transcription of genes

How different types of radiation may cause mutation

Ionizing radiation (X rays and gamma rays) causes the formation of ions that can oxidize nucleotides and break the deoxyribose-phosphate backbone

UV radiation causes thymine dimers

Repair for UV only - photolyases (separate thymine dimers) and nucleotide excision repair (enzymes cut out incorrect bases and fill in correct bases)

Frame shift mutation

Insertion or deletion of one or more nucleotide pairs

Shifts translational "reading frame"

Missense mutation

Base substitution results in change in amino acid

Nonsense mutation

Base substitution results in a nonsense (stop) codon

Chemical agents that can cause cancer (mutagen) and describe their mechanism of action

Nitrous acid - causes adenine to bind with cytosine instead of thymine

Nucleoside analog - incorporates into DNA in place of a normal base; causes mistakes in base pairings

Difference between two forms of radiation

Ionizing radiation is a more serious mutation where the DNA is broken; you can't repair broken DNA

UV radiation fuses two T together (thymine dimers); you can fix the thymine dimer

Vertical gene transfer

Transfer of genes from an organism to its offspring

(parent to two daughter cells)

Horizontal gene transfer

Transfer of genes between cells of same generation

(sideways from one bacteria to the next)

Examples of vertical and horizontal gene transfer

Transformation - picking up DNA from environment

Transduction - virus pass DNA from one bacteria to the next

Conjugation - plasmids transferred from one bacterium to the next via direct cell to cell contact via sex pill

Role of plasmids in horizontal gene transfer

Plasmids are self-replicating circular pieces of DNA who carry genes that can cause diseases and antibiotic resistant genes

They may code for proteins that enhance the pathogenicity of bacterium

Significance of Ti plasmid

Used as a vector for genetic modification in plants

Compare general features of bacteria, archaea, and eukarya

Bacteria - prokaryotic, has peptidoglycan, has rRNA loop

Archaea - prokaryotic, cell wall varies in composition, no peptidoglycan, lacks rRNA

Eukarya - eukaryotic, cell wall varies in composition, contains carbohydrates, lacks rRNA

General features of protozoa

Catchall kingdom for a variety of organisms

Autotrophic and heterotrophic

(clades based on rRNA)

General features of fungi

Chemoheterotrophic

Unicellular or multicellular

Cell walls of chitin

Develop from spores

(decomposers)

General features of plantae

Multicellular

Cell walls of cellulose

General features of Archaea

Grow in extreme conditions

Very beneficial to planet

General features of viruses

Submicroscopic

Obligate intracellular parasites with host specificity

Can infect plants, fungi, bacteria, archaea

Acellular

General features of prokaryotic cells vs. eukaryotic cells

Prokaryotes - circular DNA, ribosomes, binary fission

Eukaryotes - linear DNA, ribosomes, mitosis

Pros structures lack membrane enclosed organelles and a nucleus, but tend to have a cell wall

Euks structures have membrane enclosed organelles and a nucleus, but lack cell wall

Importance of cyanobacteria/algae

Primary producers that fix CO2 through photosynthesis to produce oxygen

Features of chlamydiae

Obligate intracellular bacteria

Causes eye infections and chlamydia

Have elementary body and small inactive use for transmission of disease

Features of spirochetes

Causes syphilis and Lyme disease

Move via axial filaments

Features of mycoplasm

Bacteria with no cell wall

Causes pneumonia

Forms of fungal disease

Systemic mycoses - deep within the body

Subcutaneous mycoses - beneath the skin

Cutaneous mycoses - affect hair, skin, nails

Superficial mycoses - localized

Opportunistic mycoses - fungi harmless in normal habitat but pathogenic in a compromised host

Mycosis

Fungal infection

Economic impact of fungi

Saccharomyces cerevisiae - bread, wine, heb b vaccine

Trichoderma - cellulase

Taxomyces - Taxol

Entomophaga - biocontrol

Coniothyrium - kills fungi on crops

Corn > alcohol > fuel

General features of protozoa

Unicellular

Eukaryotes

Inhabit water and soil

Complex life cycles

Cysts

For transmission

Inactive

Resistant to elements

Trophozoite

Growing

Multiplying

Inside and grows

Bacteria vs. Viruses

Bacteria have their own reproductive machinery, must have DNA, and have a cell wall

Viruses must use a host to reproduce, can have DNA or RNA, and have a capsid that wraps itself around the nucleic acid

Obligate intracellular pathogens

Require living host cells to multiply

Which group of infectious agents are included in obligate intracellular pathogens

DNA or RNA

Protein coat

No ribosomes

No ATP generating mechanism

Every virus must have a protein capsid and DNA/RNA

Tissue culture/Cell culture

Used for subculturing where cells from an existing culture are transferred to new containers with fresh nutrient media

A lot of separate subcultures can be made from a single tissue sample

Monolayer

Cells from an organism are blended so they separate and then these cells start growing on the bottom of the flask and do NOT grow on top of each other

Stop growing when they get close

Used to make host cells for viruses and be subcultured

Ways viruses are cultivated

You always need a host to grow viruses because they require a host to replicate

Virus life cycle

Attachment - virus attaches to host cell by capsid > Penetration - inject virus genetic material into host cell > Un-coating - releasing capsid inside host cell to outside (not always done bc capsid usually stays outside cell) > Synthesis/Replication - virus makes viral proteins and nucleic acids (takes over host common center for protein and DNA synthesis and makes copies of its own genes), host cell can't divide > Assembly - maturation and packaging, self-assembly of virions > Release - release of viruses out of host cell

One-Step growth cycle for viruses

Attach to the host and then penetrate and go inside the host

The virus then becomes invisible while biosynthesis and maturation is going on and can't be seen (eclipse period)

Virus releases all of the replicated viruses at the same times and kills host by lysis allowing you to see all the new viruses (latent period when till virus releases)

How viruses grow in a lab

Measure viral growth in animal cells by using the plaque assay (dilutions of the virus used to infect a cultured cell monolayer from and organism which has agar in the media to solidify it)

If the virus attacks the monolayer host it will be concentrated in certain areas of cells and you can see black dots that are the plaques

The number of plaque on the medium = number of infectious virus particles present on plate and then multiply by the dilution factor to get total

Different shapes of viruses

Polyhedral - multiple faces

Helical - ex. ebola virus

Complex - bacteriophage

Come have envelope - ex. flu

Role of viruses in cancer

Transforming infection is when the virus has capacity to alter nucleic acid of host, leading to changes in host's DNA which ultimately leads to drastic changes in the chromosome > cancer

Cancers caused by viruses

HPV > cervical cancer

Hep B and C > Liver cancer

Leukemia

Lymphoma

How viruses might transform a normal cell into a tumor cell

Oncogenes transform normal cells into cancerous cells

The organic viruses become integrated into the host cell'c DNA and induce tumors

How viruses may be used to treat cancer by killing cancer cells

Tumor-destroying, or oncolytic viruses, selectively infect and kill tumor cells or cause an immune response against them

Several viruses are known to selectively infect cancer cells, and these are being genetically modified to remove virulence genes and add colony-stimulating factor genes to promote white blood cells

Plaque

A clear area on an otherwise opaque field of bacteria that indicates the inhibition or dissolution of the bacterial cells by some agent, either a virus or an antibiotic