Capsid – protein coat surrounding nucleic acid;

key role in attachment sometimes;

made of capsomeres

Virion – complete virus particle, with envelope (if there is one)

Envelope – bilayer membrane outside capsids; acquired from host cells (can “hide” virus); naked viruses don’t have an envelope

What the fuck are the 5 steps of viral replication for both animal viruses and bacteriophages?

1. Adsorption – Phage is adsorbed onto bacterial cell wall

2. Penetration – Phage penetrates bacterial cell wall and cell membrane. Phage DNA injected

3. Biosynthesis – The phage DNA directs the cell’s metabolism to produce viral components – proteins and copies of phage DNA

4. Maturation – Collar, sheaths, and base plates have been attached to heads. Tail fibers are added last.

5. Release – Bacterial cell lyses, releasing mature phages.

What are the two fucking ways a enveloped virus can enter a human host cell?

Fuse their envelope with the host’s plasma membrane or enter by endocytosis (fuses with the vesicle membrane)

Replication fork – the points at which the 2 strands of DNA separate to allow replication of DNA

Leading DNA strand

Leading DNA strand – template for synthesis of continuous new strand, 5’ to 3’

Lagging DNA strand- The other strand going in the 3’ to 5’ direction, discontinuous synthesis of new DNA that involves RNA primers that are replaced later on with DNA nucleotides

Okazaki fragments

Okazaki fragments- series of short DNA segments 100-1,000bp long

5-prime to 3-prime direction?

5-prime to 3-prime direction- the 3’ end is a free deoxyribose end while the 5’ end is attached to a phosphate. Think of the 5’ end as the end car in a train, while the 3’ end is the engine cart

Semi-conservative replication?

Anti-parallel strands?

Anti-parallel strands- When 2 strands of a double helix combine by base pairing, they do so in a head to tail or anti-parallel fashion.

How does reverse transcription differ from transcription?

mRNA  cDNA

instead of DNA  mRNA

Codons?

Codons are the words in the language of nucleic acids (sequence of 3 bases)

Nonsense codons?

Nonsense codons do not code for amino acids. They code for stop codons

Genetic code?

Genetic code is the relationship between each codon and a specific amino acid constitutes the genetic code

Start codon?

Start codon is ATG and AUG, which denote sequences of DNA and RNA respectively that are the start codon or initiation codon encoding the amino acid methionine (Met) in eukaryotes and a modified Met (fMet) in prokaryotes.

What 2 chemical features make a single strand of DNA different from a single strand of RNA?

1. The repeating units of RNA are ribonucleotide monophosphates and of DNA are 2'-deoxyribonucleotide monophosphates. The 2' deoxyribose allows the sugar to assume a lower energy conformation in the backbone. This helps to increase the stability of DNA polynucleotides.

1. Also the pyrimidine U is specific to RNA, while T is specific to DNA.

Ribosomal RNA

mRNA

tRNA - contains a three-base anti-codon

Ribosomal RNA (pg 185 direct verbatim)– this binds closely to certain proteins to form two kinds of ribsomoe subunits. A subunit of each kind combines to form a ribosome. Recall that ribosomes are sites of protein synthesis in a cell. They serve as binding sites for transfer RNA and some of their proteins act as enzymes that control protein synthesis. Prokaryotic ribosomes are made of a small (30S) and a large (50S) subunit (Eukaryotic ribosomes are formed from a 40S and a 60S subunit).) After the two subunits join together around the strand of mRNA, the synthesis of a peptide beings. The newly formed polypeptide chain grows out through a tunnel in the 50S subunit.

mRNA – mRNA is synthesized in units that contain sufficient information to direct the synthesis of one or more polypeptide chains. One mRNA molecules corresponds to one or more genes, the functional units of DNA. Each mRNA molecules becomes associated with one or more ribosomes. At the ribosome, the information coded in mRNA acts during translation to dictate the sequence of amino acids in the protein.

tRNA – The function of tRNA is to transfer amino acids from the cytoplasm to the ribosomes for placement in a protein molecule. Many different kinds of tRNAs have been isolated from the cytoplasm of cells. A tRNA molecules consists of 75 to 80 nucleotides and is folded back on itself to form several loops that are stabilized by complementary ase pairing. Each tRNA has a three-base anticodon that is ocmplementary to a particular mRNA codon. It also has a binding site for an amino acid—the particular maino acid specified by the mRNA codon. (The mRNA codon, of course, got its information directly from DNA.) Thus the tRNAs are the link between the codons and the corresponding amino acids. Amino acid attachement to specific tRNA molecules is achieved by the actioin of amino-acid-activating enzymes and energy derived from ATP.

The codon attaches by complementary base pairing to the appropriate mRNA codon so that its amino acid is aligned for incorporation into a protein. The accuracy of amino acid placement in protein synthesi depends on this precise pairing of codons and anticodons.

??it is because it can give way to genetic variability and thus diversity. It allows for mutations to not have a catastrophic effect on transcription/translation when these occur in the introns which are spliced out.??

typically regulates anabolism. When tryp is available, the aa binding activates repressor proteins, which then binds to the promoter and represses tryp synthesis (which is usually a product).

controls the breakdown of nutrients as they become available in the growth medium (catabolism). Such a system is turned on when a nutrient is available and turned off when it is depleted. The nutrient itself acts as an inducer of enzyme production.

is also called end-product inhibition; the end product of a biosynthetic pathway directly inhibits the first enzyme in the pathway.

UV light causes pyrimidine dimer formation in DNA. What can cells do to remove them?

There are two mechanisms, light and dark repair, that are known to repair damage caused by dimmers.

Light repair or photoreactivation <-Explain

ccurs in the presence of visible light in bacteria previously exposed to ultraviolet light. When organisms containing dimmers are kept in visible light, the light activates an enzyme that breaks the bonds between the pyrimidines of a dimmer. Thus, mutations that might have been passed along to daughter cells are corrected, and the DNA is returned to its normal state. This mechanism contributes to the survival of the bacteria but creates problem for microbiologists. Cultures that are irradiated with ultra violet light to induce mutations must be kept in the dark for the mutations to be retained.

UV light causes pyrimidine dimer formation in DNA. What can cells do to remove them?

There are two mechanisms, light and dark repair, that are known to repair damage caused by dimmers. Explain

Dark repair, which occurs in some bacteria, and can take place in the presence or absence of light, requires several enzme-controlled reactions. First, an endonuclease breaks the defective DNA strand near the dimmer. Second, a DNA polymerase synthesizes new DNA to replace the defective segment, using the normal complementary strand as a template. Third, an exonuclease removes the defective DNA segment. Third, an exonuclease removes the defective DNA segment. Finally, a ligase connects the repaired segment to the remainder of the NDA strand. These reactions were identified in E Coli but are now known to occur in many other bacteria. Human cells have similar mechanisms; some human skin cancers, such as xeroderma pigmentosum are caused by a defect in the cellular DNA repair mechanism

The Ames Test is used to screen for potential mutagenic properties of substances. How does the test work?

The Ames test is used to test whether substances induce mutations in certain strains of Salmonella (Auxotrophs) that have lost their ability to synthesize the amino acid histidine. These strains easily undergo another mutation that restores their ability to synthesize histidine. The Ames test is based on the hypothesis that if a substance is a mutagen, it will increase the rate at which these organisms revert to being histidine synthesizers. Furthermore, the more powerful a substance’s mutagenic capacity, the greater the number of revered organisms it causes to appear. In practice, the organism is grown in the presence of a test substance. If any organisms regain the ability to synthesize histidine, the substance is suspected of being a mutagen. The larger the number of organisms that regain the synthetic ability, the stronger the substance’s mutagenic capacity is likely to be.

• Gene Transfer

  • in most eukaryotes it is an essential part of the life cycle and is through sexual reproduction

  • male and female parents produce sex cells known as gametes

  • gametes join together to form a zygote

• Lateral gene transfer (Horizontal gene transfer)

  • when genes are passed to other organisms in their same generation.

  • when microorganisms come together and exchange DNA

    • ex: a virus introducing a new trait to a host cell

• Vertical gene transfer

  • When genes are passed from parents to offspring

  • Bacteria reproduce asexually by binary fission

When gene transfer occurs the DNA from a donor cell is taken up by a recipient cell.  A recombination event occurs on the recipient chromosome which allows the incoming DNA to get incorporated into the recipient chromosome. Explain recombination...

• Recombination: The combining of genes (DNA) from two different cells

  • Once DNA is introduced into a cell it doesn’t just ‘sit’ there it has to get incorporated into the DNA of the cell it entered

  • The resulting cell is known as the recombinant

The 3 types of lateral transfer that occur in bacteria 

• Transformation:

  • A change in an organism’s characteristics because of the transfer of genetic information

  • Think of ‘naked’ or ‘free DNA’ coming in from the outside

    • Naked DNA is DNA released from an organism often after the cell has been lysed

  • DNA uptake can only occur at a certain stage of a cell’s growth cycle and competence factor is released

    • Competence factor: a protein release into the medium that helps facilitate the entry of DNA

    • When competent factor is used in one culture to treat a culture that doesn’t have it, the cells in the culture being treated become competent and they can now take up DNA fragments

      • NOT ALL bacteria can become competent so not all bacteria can be transformed

  • DNA entry depends on factors such as:

    • Modifications of the cell wall

    • Formation of specific receptor sites on the plasma membrane that can bind DNA

    • DNA exonuclease and DNA transport proteins are also needed

  • DNA can be taken up from almost any source as long as they are ‘close relatives’ and competent

• Transduction:

  • Method of transferring genetic material from one bacterium to another using bacteriophages

    • Bacteriophage: a virus that can infect bacteria and overtakes the host bacteria to replicate its DNA inside the host cell.

    • Phages: composed of a core of nucleic acid covered by a protein coat

    • A page is capable of infecting the bacterium by attaching to a receptor site on the cell wall because they have high specificity

    • The phage enzyme weakens the cell wall and the phage nucleic acid then enters the cell

    • Once the nucleic acid is in the cell, there are two pathways that further describe the phage

      • Virulent phage: capable to causing the infection and then destruction and death of a bacterial cell

        • It infects the cell, then ‘kills’ the cell releasing the new formed phages

        • Because this cycle results in lysis or rupture it is called a lytic cycle

      • Temperate phage: capable of causing the infection but DOES NOT ‘kill’ the host

        • The phage’s DNA is incorporated into a bacterium’s DNA and is replicated with it.

        • Phage produces a repressor substance that prevents the destruction of bacterial DNA and the Phage’s DNA does not direct the synthesis of the ‘new phages’

        • Prophage: Phage DNA that is incorporated into the host DNA

        • Lysogeny: persistence of a prophage without phage replication and destruction of the bacterial cell

        • Lysogenic: cells containing a prophage

• Conjugation:

  • Method of transferring genetic information from one bacterial cell to another BUT

1. it requires contact between the donor and the recipient

2. it transfers much larger quantities of DNA (occasionally whole chromosomes but they usually break apart because there’s too much motion involved in the transfer)

Conjugation requires cell to cell contact to transfer a F+ (Fertility plasmid) to a F- cell. Why does a successful conjugation event convert a F- strain to a F+ strain?

1.  

   • F plasmid carries information for the synthesis of proteins that form F pili

   • F⁺ cells make an F pilus (sex pilus or conjugation pilus) which functions as a bridge to attach to the F^- cell when F⁺ and F^- cells conjugate

   • A copy of the F plasmid is then transferred from the F⁺ cell to the F^-

   • DNA is transferred as a single strand over the conjugation bridge (a.k.a. mating bridge)

   • The pilus contacts the F^- cell and a pore forms, the pilus is pulled into the F^- cell which brings the two cells closer together and the DNA is transferred

   • Each cell makes a complementary strand of DNA so they BOTH have a complete F plasmid.

   • When F⁺ cells are present, all cells become F⁺ because they all receive the F plasmid

   • If a culture is only F^- no DNA transfer occurs so the cells all stay F^-

   • Donor: F⁺

   • Recipient: F^-

   • Molecules Transferred: F plasmid

   • Product: F⁺ cells

How do Hfr and F' cells transfer their DNA to a F- strain?

1. High frequency recombinations (cannot become F⁺ because not all F plasmid is transferred)

   • Literally meaning that the number of recombinations occurs very fast at a very high rate

   • Clone: a group of identical cells from a single parent cell from an F⁺ strain that could more than 1000 times the number of genetic recombinations in ‘regular conjugations.

   • Hfr (High Frequency of recombination strain): type of donor strain

   • With an Hfr cell, the F plasmid only initiates the transfer (gets it going) but isn’t fully invested in the process

   • Initiating segment: the only part of the F plasmid is transferred

   • Recipient cell does not become F⁺ because only a portion of the F plasmid is transferred

   • Donor: Hfr

   • Recipient: F^-

   • Molecules Transferred: Initiating segment of F plasmid and some chromosomal DNA

   • Product: F^- with some variability ‘cause it took in some chromosomal DNA

Plasmids are circular, extra chromosomal, double stranded DNA molecules. Plasmids can provide new traits to an organism through the genes they carry in their DNA. What are some of these new traits that an organism may acquire from a plasmid?

1. F plasmids (fertility factors) can directly make proteins that self-assemble into a conjugation pili

2. Resistance (R) plasmid carry genes that provide resistance to things like antibiotics (tetracycline or chloramphenicol) or heavy metals (arsenic or mercury)

3. Bacteriocins: plasmids can make these proteins that directly kill bacteria

4. Virulence plasmids cause disease signs and symptoms (ex: Salmonella ot neurotoxin genes on plasmids in Clostridium tetani)

5. Tumor-inducing (Ti) plasmids cause tumor formation in plants

Why can transposable elements cause mutations?  How do they contribute to the spread of drug resistance?

• A transposable element is a genetic sequence that is mobile

• Transposition: the ability of a genetic sequence to move from one location to another

• Insertion sequence: the simplest type of transposable element, contains a gene for the enzyme transposase

• Transposon: a transposable element that contains the genes for transposition, and one or more other genes as well

• Transposable elements ONLY REPLICATE when in a plasmid or a chromosome

• The insertion sequence is copied

• The copy RANDOMLY inserts itself into the bacterial chromosome or into another plasmid

• The original copy stays in the same place, but the ability to move around plasmids or chromosomes affects the genetic makeup of a cell

• This random shuffling can disrupt the cell’s replication and cause spontaneous mutations

• Because viruses can mutate so readily and in so many different combinations, a slight alteration can cause a drug to be ineffective

Rhinovirus

Parainfluenza

Croup (obstruxtion of larynx, causing a barking cough)

no vaccine.