Bio 313 Test 3

fully assembled virus particle

• 1. carry all genes necessary to replicate a virus
• 2. ss, ds, RNA or DNA
• 3. only a few genes....WHY?
• a. needs a gene to encode protein coat and _____? rest comes from host

• 1. protect nucleic acid
• 2. aids in transfer of host
• 3. Structure: capsomere can be helical, polyhedral, complex, etc.

virus has SURFACE MARKER, host has a receptor site

• 1. Infect BACTERIA
• 2. variety of sizes andshapes
• 3. TYPES:
• A. Virulent bact.: use lytic cycle
• B. Temperate bact.: uses lysogenic cycle for reproduction

• 1. adpsorption: phage binds to bacterium
• 2. phage dna enters host cell
• 3. host dna is digested
• 4. phage dna replicates
• 5. host cell transcribes and translates the phage dna, producing phage proteins
• 6. phage encoded enzyme causes cell to break releasing fully developed new phage

• 1.adsorption
• 2. phage enters cell
• 3. phage dna integrates into bacterial chromosome and becomes a prophage
• 4. prophage replicates (so cell with dna that has viral dna embedded in its own)
• 5. prophage(viral dna) will separate and lysis of original cell

• bacterial genes transmitted without contact
• (transfer agent is bacteriophage)

• 1. bacteriophage and dna both separate inside cell
• 2. bacterial dna breaks, viral dna breaks, but and bacteriophage now either take viral or original dna fragments
• 3. this is injected into new cell

• 1. genes located closer to one another are more likely to be co-transduced
• 2.

• animal virus 5 step life cycle:
• 1. attachment
• 2. penetration and uncoating 
• 3. nucleic acid replication and protein synthesis
• 4. assembly /maturation
• 5. release

• 1. 3 enzymes: transcriptase, protease, integrase
• A. Transcriptase:RNA reverse transcription to dsDNA 
• B. remove viral code and above is released
• C. integrase; w/host chromosome

• Drift: constant accumulation of point mutations
• (constant mutations due to enzyme that copies RNA)
• Shift: when genetic material of different strains ar combined in a process called reassortment

• DNA polymerase add nucleotides only to the 3' end of growing strand 
• the replication can only go from 5' -> 3'
• continuous and discontinuous replication

Phosphodiester: between 2 nucleotides in backbone

• 1. initiation
• 2. unwinding
• 3. elongation
• 4. termination

• 1. initiator proteins (dnaA ) bind to oriC, the origin of replication
• 2. causing short stretch of DNA to unwind , which causes negative coil
• . helicase and other binding proteins help stabilize the previous step
• A. DNA helicase binds on lagging strand template and moves in 5' to 3' direction along this strand. 
• B. single strain proteins stabilize, gyrase relieves strain ahead of the replication fork
• 3. Elongation: existing group of RNA nucleotides with 3' OH group to which a new nucleotide can be added (RNA Primers)
• a. dna polymerase III: carries out dna polymerization
• b. dna polymerization I: removes RNA primer
• c. dna ligase: connects nicks after RNA primers are removed

• 1. DNA helicase binds to lagging strand template at each replication end, on lagging
• 2. lagging strand loops around so that both strands can replicate simultaneously

• 1.DNA polymerase III: exonuclease activity removes incorrect paired nucleotide
• 2. DNA polymerase I:
• 3'->5': removes incorrectly paired nucleotide
• 5'->3': exonuclease activity removes RNA primers

• seals nick w/ phosphodiester bond between the 5'-P gorup of the initial nucleotide added by DNA polymerase III and the 3'-OH group of the final nucleotide added by DNA Polymerase 
• this nick is between the 5' end of original DNA nucleotides of new strand and replaced RNA to DNA

• 1. euk. replication IN NUCLEUS
• 2. larger size of euk genome= many origins of replication
• 3. linear structure of euk. chromosomes= problem with replication at ends of chromosomes (telomeres and telomerases)

• 1. origin-recognition complex binds to origin to initiate replication
• 2. licensing of DNA replication by the replication licensing factor
• 3.

1. end-of-the-replication problem: everytime a cell replicates, will lose terminal end of DNA (for somatic cells)

• 1. telomere: has protruding G rich section at end
• 2. telomerase: telomerase presents complementary RNA section of the G rich section. However, this section is LONGER than the telomere
• 3. then the original creates more DNA in order to match the extended template, kinda like a reverse process
• 4. RNA template of telomerase moves along DNA , so that the original template grows
• 5. TELOMERASE: extends DNA, filling in gap due to removal of RNA primer

• "christmas tree" 
• Rna polymerase attaches to end whre it is small

• 1. promoter
• a. if this deleted, no gene expressed
• 2. RNA-coding sequence, the beginning of this is considered the transcription start site
• 3. terminator

• 1. Full name: ribonucleoside triphosphates- rNTPs added to the end of the RNA molecule
• 2.

• 1. Holoenzyme: 5 subunits + sigma facotr
• A. 5 ubunits: (core enzyme)
• B. sigma factor: controls binding of rna polymerase to the promoter
• i. confers specificity to promoter

• 1. binding of RNA polymerase holoenzyme to the promoter region
• a. 35 and pribnow sequence, are in the promoter. Sigma factor responsible for polymerase binding to these 2 sequences
• b. holoenzyme:  unwinds dna strand
• 2. promoter is NOT transcribed
• 3.

• 1. uses rho factor, which is an enzyme?
• a. r.f. binds to rut site (which is on NEW strand), and moves toward 3' end
• b. when rna polymerase encounters terminator sequence, it pauses,
• c. and rho catches up
• d. using helicase activity, rho unwinds the DNA-RNA hybrid and brings an end to transcription

• uses hairpin structure formed by inverted repeats, followed by a string of uracils
• 1. rho-independent terminator contains an inverted repeat followed by a string of approximately six adenine nucleotides
• 2. inverted repeats transcribed into RNA
• 3. string of U's cause polymerase to pause
• 4. destabilizes rna/dna pairing
• 5. rna transcript separates with last set of nucs as U's

Shine -Dalgarno sequence:

# of nucleotides in a gene should be proportional to the number of amino acids in the encoded protein

• 1. NOT colinear
• A. demonstrated through hybridization experiment,
• B. above determined that coding sequences in a gene may be interrupted by non-coding sequences.
• C.

• 1. transcriptional activator binds to: enhancer
• 2.

• 1. RNA polymerase II transcribes well past coding sequences of most genes
• 2. cleavage is near the 3' end of RNA
• 3. while RNA polymerase continues to transcribe
• 4. Rat1 endonuclease attaches to the 5' end of the trailing RNA
• 5. moves toward the RNA polymerase , degrading RNA as it goes
• 6. when Rat1 reaches the polymerase, transcription

• called pre-mrna or 1 degree transcript
• 1. introns, exons, and a long 3' end are all transcribed into pre-mRNA
• 2. a 5' cap is added
• 3. cleavagee at the 3' end is approximately 10 nucelotides downstream of the consensus sequence.
• 4. polyadenylation at the cleavage siteproduces the poly(A)tail.
• 5. introns removed
• 6. producing the mature mRNA
• 7. now ready to be translated!

• 1. nucleotide w/ 7-methylguanine
• 2. 5'-5' bond is attached to the 5' end of the RNA
• 3. additional 2' methyl groups maybe present

• 1. 50 to 250 adenine (A) nucelotides are added to the 3' end of the mRNA
• HOW THIS HAPPENS:
• 1. pre-Mrna cleaved, at position from 11 to 30 nucleotides downstream of the consensus sequence, in the 3' untranslated region.
• 2. addition of adenine nucleotides (polyA)right after the cleavage side mentioned before
• CONCLUSION: polyA added thru: cleavage and polyadenylation

• 3 consensus sequences are required for splicing:
• 1. 5' consensus seq. :GU A/G AGU: (5' splice site)
• 2. 3' consensus seq. CAGG
• 3. Branch point adenine "A": 18-40 nucleotides upstream of 3' -splicing site
• 4. 4. intron released as lariat 
• 5. and the 2 exons are spliced together
• 6. bond holding lariat is broken, linear intron is degraded 
• 7. spliced mRNA is exported to the cytoplasm and translated

• 1. transcription
• 2. 3' cleavage and polyadenylation
• 3. alternate RNA splicing
• a. either 2 introns are removed to yield one mRNA
• b. or 2 introns and exon 2 are removed to yield a different mRNA

• 1. tRNA
• 2. rRNA
• 3. Regulatory RNAs (small interfering & microRNAs)

• 1. an adaptor molecule, 76 to 90 nt in length
• 2. link between the mRNA and the amino acid sequence of protein 
• 3. heavily modified after the transcription : ribothymine and  pseudouridine
• 4. tRNA 2° structure elements

• 1. is the RNA component of the ribosome 
• 2. three forms of rRNA
• 3. ribosome (the site of protein synthesis): large ribosome subunit and small ribosome subunit

• 1. RNA small interfering (siRNA) & microRNAs (miRNA)
• 2. RNA interference (RNAi)

• 1. polymers of amino acids
• 2. joined together by peptide bonds
• 3. 20 common amino acids

biological catalysts

fight off infection

• 1. primary structure: amino acids
• 2. 2ndary structure: interactions between amino acids cause the primary structure to fold into a secondary structure, such as this alpha helix
• 3. tertiary structure: 2ndary folds further  into a tertiary structure
• 4. two or more polypeptide chains may associate to create a quaternary structure

basic units of genetic code

1. triplet RNA code: 64 possible codons

grp of 3 nucleotides specify which amino acid?

AUG

• 1. UAA
• 2. UAG
• 3. UGA

• 1. 20 amino acids
• 2. 61 sense codons
• 3. tRNA adapts the RNA codon to a particular amino acid via its anticodon
• 4. SOLUTION: different tRNAs will accept same amino acid, isoaccepting tRNAs but will have different anticodons

on tRNA

• 1. takes place on ribosome
• 2. prokaryotic 70s ribosome
• 3. eukaryotic 80s ribosome

• 1. binding of amino acids to tRNA
• 2. initiation of translation
• 3. elongation
• 4. termination

• in charge of charging end of tRNA with amino acid
• 20 different synthetases

• 1. ribosome has two parts, small 30s and large 50s
• 2. "If -3" binds to the smaller r part, therefore mrna attaches.
• 3. tRNA charged with N-formylmethythionine attaches to initiation codon
• CONCLUSION:
• 1. ribosome assembled on mRNA
• 2. first tRNA is attached to initiation codon