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345 Cards in this Set
- Front
- Back
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Question
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Answer
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What is the composition of nucleosides?
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base + pentose
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What is the composition of nucleotides?
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base + pentose + phosphate
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What is pentose?
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5 member sugar (ribose or deoxyribose)
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What is the nucleotide base group?
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either purine or pyrimidine
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What distinguishes structurally speaking the purines from the pyrimidines?
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purine = 2 rings pyrimidines = 1 ring
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Name the purines
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Adenine and guanine
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Name the pyrimidines?
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cytosine
thymine uracil |
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Which nucleotide base is in DNA but not RNA?
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Thymine
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Which nucleotide is in RNA but not DNA?
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Uracil
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4 (abbr.) nucleotides in DNA?
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AGCT
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4 (abbr.) nucleotides in RNA?
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AGCU
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The 2 pentoses?
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ribose (RNA) and deoxy-ribose (DNA)
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Both ribose and deoxy-ribose are what kind of rings?
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beta furanose rings
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Each sugar in DNA has one less what then RNA?
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one less -OH group (see slides
very clear)...you will see H group in RNA where you see an OH group in DNA |
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The nucleoside of adenine associated with RNA?
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adenosine
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The nucleoside of adenine assoc. with DNA?
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deoxyadenosine
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The nucleoside of guanine assoc. with RNA?
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guanosine
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The nucleoside of guanine assoc. with DNA?
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deoxyguanosine
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The nucleoside of cytosine associated with RNA?
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cytidine
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The nucleoside of cytosine associated with DNA?
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deoxycytidine
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The nucleoside of thymine associated with DNA?
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thymidine or deoxythymidine (thymine is not associated with RNA)
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The nucleoside of uracil associated with RNA?
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uridine (uracil not associated with DNA)
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How many bonds between G and C pairs?
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three
H-bonds |
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How many bonds between A and T or A and U?
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2 H-bonds (A=T or A=U)
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Are A
G C T and U the only bases? |
No
the are other minor bases in both DNA and tRNA |
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What kind of linkage do you see in RNA and DNA polymers?
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phosphodiester linkage with 5' to 3' directionality...alternating sugar and phosphate groups form the backbone...in a chain there is usually a phosphate at the 5' end but not the 3'
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Which carbon is the phosphate usually attached to?
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5'...but it can also be attached to 2' or 3'...and there are cyclic nucleotides with phosphate attached to C carbons
forming a ring (ex cAMP) |
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Why is the backbone of DNA and RNA polymers considered hydrophilic?
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a) because at physiological pH
each phosphate group is negatively charged b) because of the free -OH groups in RNA |
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Explain the hydrolysis of the covalent backbone?
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the covalent backbone is subject to hydrolysis...though this is a slow process...But under alkaline conditions (high pH) RNA is rapidly hydrolyzed...BUT DNA is not
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What is the convention in writing DNA and RNA sequences?
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with 5' (phosphorylated end) on left and 3' (not phosphorylated end) on right
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The 3 levels of nucleic acid structure?
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1. primary = sequence (just order) 2. secondary = local interactions and patterns (helix is most common) 3. tertiary = 3-dimensional
longer-range possibly involving other mol.s |
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The predominant conformation of DNA? (secondary structure)
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3-D Watson-Crick model of DNA 1. Right handed double helix 2. H-bonds between bases 3. Major and Minor grooves alternate 4. 2 anti-parallel strands
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Relative distance per turn A vs B vs Z?
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A = 28 B = 36 Z = 44
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In vivo what probably plays a role in determining whether a given segment of DNA exists in the B or the Z form?
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the sequence of nucleotides
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What secondary structure can palindromes form?
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1. hairpins (stemloops) for single stranded 2. Cruciform for Double strand (looks like 2 hairpins)
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Prokaryotes can have what type of mRNA?
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mono- or polycistronic
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eukaryotes mostly have what type of mRNA?
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monocystronic (this includes humans)
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Since mRNA synthesized from DNA what can you say about it's structure?
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right handed helix with base stacking
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Describe tRNA?
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transfer RNA....links mRNA and amino acids
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Describe rRNA?
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ribosomal RNA...the core of ribosomes (enzymatic role within RNA although they usually make new proteins)
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What are some "other RNAs"?
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viruses
ribozymes |
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The RNA is usually what structurally?
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single stranded with hairpins
bulges internal loops and single strands...so folds back on self...imperfect regions....energetically favorable....looped and bulged regions are not part of the paired regions always |
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What can RNA from base pairs with?
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self...or with other RNA or DNA...G(triple bond)C
A=U and sometimes G=U |
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In it's double stranded regions what form does RNA most commonly exist in?
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A form (in secondary structure)(RH helix
with base stacking)...B form not observed...Z form made in lab |
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in RNA their can be extensive what? What else is important?
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can be extensive secondary structures...and tertiary structure is important (very specific)
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What are ribozymes?
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RNA enzymes
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What is the denaturation of nucleic acids?
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unfolding
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What is annealing of nucleic acids?
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renaturation...tells us that the propensity to come together is inherent within each strand
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How can you monitor denaturation and renaturation? Why?
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UV absorption...because it varies as a function of base stacking and pairing
and so can be used to determine whether DNA is paired or denatured |
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When denaturation occurs which bonds break and which do not?
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H-bonds break...covalent breaks do not
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Where is the tm (melting point) for denatured DNA?
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mid-point of a melting curve...different for different DNAs because they have different base concentrations
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The more G + C DNA has the higher the what?
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melting point because of H bonds...so harder to pull apart...remember these have 3 h-bonds...you would just look at a graph to figure it out
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Which is more tightly bound RNA:RNA hybrids or RNA:DNA hybrids or DNA:DNA hybrids?
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RNA:RNA > RNA:DNA > DNA:DNA
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Describe chemical transformations of nucleotides and nucleic acids?
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1. nonenzymatic so very slow/rare 2. cause of mutations 3. 3 types of spontaneous rxns a. Removal of exocyclic amine (deamination) b. Breaking the sugar-base bond c. UV irradiation (dimer formation)
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Which chemical formations is caused by chemicals such as nitrites and nitrates (nitrosamines
HNO2) and bisulfites? |
deamination : removal of exocyclic amines...replace it with O2
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Which chem. transformation involves the breaking of a sugar-base bond?
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depurination...mostly happens in cells where it doesn't matter
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Which chm. transformation is caused by UV radiation?
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dimer formation...mutates DNA
cancer...induced (not chemical)(light) |
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What are alkylating agents? ex.
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reactive chm. that may cause nucleotide or NA transformations...disrupts base pairing...dimethylsulfate...add alkyl (-CH3)
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How are nucleotides important in their own right? (stand alone functions)
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1. energy carriers: ATP->ADP->AMP->adenosine 2. component of enzyme cofactors (coenzyme A
NAD and FAD) 3. regulatory molecules (cAMP cGMP ppGpp) |
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Answer
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What's a single ring base called?
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pyrimidine
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What are important nucleotides?
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ATP
NADP+ FAD+ |
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Which carbon does the phosphate attach to on the other nucleotide?
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3' C
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What is the name of the bonds between the nucleotides?
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phosphodiester bonds
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What sugar does ATP use?
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ribose
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What type of bond joins phenylalanine and leucine?
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peptide bond
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What's the formula for ribose?
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C5H10O5
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What does RNA act as?
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a messenger from DNA to the ribosomes
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If all the DNA in one somatic cell were lined up end to end how long would it be?
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6 feet
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How many base pairs are in one pitch of DNA?
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10 base pairs
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What is one DNA molecule+histones called?
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a chromosome
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What percent of DNA is coding DNA?
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5%
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How did your junk DNA come to be?
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Genes that didn't work well were turned off
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What does dogma mean?
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basic core truth
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What are the 2 purposes of DNA?
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1) Hereditary information 2) Daily protein recipe card box
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Where do ribosomes make protein?
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In the cytoplasm on rough ER
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What is it called when the left+ right strands of DNA are fliped?
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anti-parallelism
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How do antibiotics work?
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The chop the hydroxyl on the 3' C on DNA of bacteria so it can't replicate
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What is a virus made up of?
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nuleic acid and protein coat (capsid)
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What is a retrovirus?
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a genome made of RNA but is not an RNA virus that affects RNA going back into DNA
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What is the enzyme that retroviruses use?
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reverse transcriptase
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How do retroviruses work?
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They use an enzyme to make a DNA copy of their genome
open eukaryotic chromosomes and the dna copy of themselves in it |
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What is an example of a retrovirus that mutates faster than any other virus?
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HIV
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What are the 4 types of RNA?
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mRNA (messenger) tRNA (transfer) rRNA (ribosomal) snRNA (small nuclear)
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What is the name of the enzyme that travels up and down DNA looking for a promoter sequence?
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RNA polymerase
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How long is a promoter sequence
what is the most common one called where is it located and what is it made up of? |
8-12 base pairs
tata box 5' end of gene strand rich in T's and A's |
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Why are T's and A's used in the promoter sequence?
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Because only 2 H bonds connect them
so it costs less energy to break them |
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What is a codon?
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3 bases that code for one particular AA
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What are 3 names for the gene strand of DNA?
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coding strand
inactive strand sense strand |
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What are 3 words for the strand of DNA that is read?
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active strand
template stand non-sense strand |
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What end of RNA hangs down?
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5'
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What is the bubble called that RNA polymerase makes?
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open promoter complex
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In what direction does RNA polymerase read the DNA?
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3' --> 5'
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What does complex mean?
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more than 1 part
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How is mRNA built?
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complimentary
anti-parallel 5'-->3' |
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Where does RNA polymerase get its energy?
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Each incoming nucleotide has a triphosphate
2 are removed and donated for energy for polymerization (pyrophosphate) |
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Why can't mRNA be translated by ribosomes as soon as its done being built in eukaryotes?
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Because it is made in the nucleus
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Why can bacteria replicate so fast?
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Because it has polyribosomes that can translate it (many ribosomes reading mRNA)
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What are the protein blobs that sit on the promoter sequence called?
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transcription factors
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How is a gene expressed?
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It makes a protein
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What is the recipe for a ribosome?
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2/3 rRNA 1/3 protein and 50s+30s=70s
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What is the primary structure of tRNA?
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the order of nucleotides
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What is the secondary structure of tRNA?
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cloverleaf
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What is the tertiary structure of tRNA?
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L-shaped
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What is the name for the bottom loop on tRNA?
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anticodon loop
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What is the name for the 3 bottom nucleotides?
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anticodon
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What parts on tRNA stay the same and what parts vary?
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the stems stay the same
the loops change |
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How would you name a tRNA that carries glutamine?
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glutaminyl-tRNA
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How is the secondary structure formed?
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H bonds
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Where does the AA attach on tRNA?
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3' end
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What are the two quaternary structures of proteins?
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globular and fibrous
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What is the generic name for a tRNA with its respective amino acid?
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Aminoacyl-tRNA
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How would you name the enzyme that loads the proper AA in the tRNA truck?
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glutaminyl-tRNA synthetase
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What powers aminoacyl-tRNA synthetase to attach the AA to the tRNA?
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ATP
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Whats the name for the hereditary disease where youre urine is black?
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alkoptonuria
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What is neurosporra crassa?
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bread mold
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What are the 3 stop codons?
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UAA
UAG UGA |
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What is the start codon?
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AUG
formyl-methionine |
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What is the name of the sequence of nucleotides on mRNA that is complementary to the rRNA in the 30S subunit?
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Shine Dalgarno sequence
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What does formyl mean?
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extra aldehyde group
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What are the 3 steps of translation?
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initiation
elongation termination |
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What is the initiation complex composed of?
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30 S 50 S mRNA tRNA w/ f-met joined to 3'
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Whats the name of the enzyme that breaks the bond between the AA and tRNA and makes a peptide bond?
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peptidyl transferase
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What powers peptidyl transferase?
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GTP (glutamine triphosphate)
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What is a release factor?
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A protein blob that frees the polypeptide chain because there is no tRNA for the stop codons
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What are enhancer sequences?
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In eukaryotes
they promote strong transcription. They bend the DNA so the RNA polymerase stays in place. |
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What are the 3 types of RNA polymerase?
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I and II make rRNA and tRNA III makes regular mRNA
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What is the difference between ribose and deoxyribose?
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Ribose has an OH on the 2' C
deoxyribose has an H |
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What is the micromolecule for nucleic acids?
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nucleotides
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What are the 3 parts to a nucleotide?
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a phosphate group
a 5 carbon sugar and a nitrogen containing base |
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What is the name for a base with a 2 ring structure?
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a purine
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What C does the phosphate join to in a nucleotide?
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5' C
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What C does the base join to in a nucleotide?
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1' C
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What are the pyrimidine bases?
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cytosine
thymine and uracil |
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What are the purine bases?
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adenine and guanine
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How many H bonds connect T and A?
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2 H bonds
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How many H bonds connect G and C?
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3 H bonds
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What reaction links nucleotides?
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dehydration synthesis
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How does mitochondria work?
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It is a battery recharger that puts the P back on ATP
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What gets added to the 3' end of mRNA before it can leave the nucleus?
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a poly-A tail (150-200 bases depending on how many times it will be read)
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What are the purposes of a poly-A tail?
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1)prevents mRNA from being 'eaten' by nucleases 2)lets mRNA out of the nucleus
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What is added to the 5' end of mRNA?
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a methylated guanine cap
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What is the purpose of a methylated guanine cap?
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1) lets mRNA bond to small ribosome subunit by working like a shine-dargarno) 2)keeps 5' end from being eaten by nucleases
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What is an intron?
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garbage parts within a gene
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How is the garbarge cut out of mRNA?
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mRNA (primary transcript) must have it cut out so snRNPs made out of snRNA and protein do the snipping
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What is the name of the small subunit in a eukaryotic cell?
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40S
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How is the first amino acid in a eukaryote different from that in a prokaryote?
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It is f-met in bacteria and regular met in eukaryotes
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What are the first 20 AA called in a polypeptide chain?
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the signal peptides
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What happens to signal peptides in the ER?
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they are cut off
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In what is a polypeptide chain transferred from the ER to the Golgi in?
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a transport vesicle
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What is the name of the vesicle through which proteins meant to go out of the cell travel in?
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secretory vesicle
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If a protein is to be used inside of the cell
what type of packaging is it in? |
a vacuole
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What goes inside of a lysosome?
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hydrolyzing enzyme proteins used to digest food or old organelles
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What role do lysosomes have in cellular suicide?
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apoptosis occurs when lysosomes explode so that messed up DNA cannot spread
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What is the name for anything that performs phosphoralization?
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a kinase
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What is the name for any enzyme that uses a condensation reaction to hook micromolecules together?
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a polymerase Question
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What is the basic unit of DNA?
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The nucleotide
which is composed of deoxyribose (a sugar) bonded to both a phosphate group and a nitrogenous base |
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What are the two types of bases?
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Purines
which are double-ringed and the single-ringed pyrimidines |
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What are the purines in DNA?
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Adenine and Guanine
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What are the pyrimidines?
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Cytosine and Thymine
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What do nucleotides bond together to form?
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Polynucleotides
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What is the 3’ hydroxyl group of the sugar on one nucleotide is joined to what?
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The 5’ hydroxyl group of the adjacent sugar by a phosphodiester bond
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How many bonds does T always form with A?
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Two hydrogen bonds
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G always forms how many hydrogen bonds with C?
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Three hydrogen bonds
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What does this base-pairing form?
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It forms rungs on the interior of the double helix that link the two polynucleotide chains together
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The strands are positioned how to each other?
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They are positioned antiparallel to each other, i.e. one strand has a 5’ ‡ 3’ polarity
and its complementary strand has a 3’ ‡ 5’ polarity |
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What does this mean?
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It means one strand has a 5’ ‡ 3’ polarity
and its complementary strand has a 3’ ‡ 5’ polarity |
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What is the 5’ end designated as?
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It is designated as the end with a free hydroxyl group bonded to the 5’ carbon of the terminal sugar
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What is the 3’ end designated as?
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The one with a free hydroxyl group attached to the 3’ carbon of the terminal sugar
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What is semiconservative replication?
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During replication the helix unwinds and each strand acts as a template for complementary base-pairing in the synthesis of two new daughter helices
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What dos each daughter helix contain?
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It contains an intact strand from the parent helix and a newly synthesized strand, this means it's semi conservative
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Where does replication begin?
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It begins at specific sites along the DNA called origins of replication and proceeds in both directions simultaneously
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What forms as replication proceeds in a given direction?
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A replication fork
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What does the enzyme helicase do?
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It unwinds the helix
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What does single-strand binding protein do?
|
SSB binds to the single strands and stabilizes them
preventing them from recoiling and forming a double helix |
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What does DNA gyrase do?
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It is a type of topoisomerase that enhances the action of helicase by the introduction of negative supercoils into the DNA molecule
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What is a primer chain?
|
It is usually several nucleotides long and composed of RNA
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What does it do?
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It is necessary for the initiation of DNA synthesis
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What does the RNA polymerase
primase do? |
It synthesizes the primer
which binds to a segment of DNA to which it is complementary and serves as the site for nucleotide addition |
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What does the first nucleotide bind to?
|
It binds to the 3’ end of the primer chain
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Which direction does DNA synthesis proceed in?
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It proceeds in the 5’ ‡ 3’ direction and is catalyzed by a group of enzymes collectively known as DNA polymerases
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What is the double-stranded DNA ahead of the DNA polymerase unwound by?
|
A helicase
and SSB again keeps the unwound DNA in a single-stranded form so that both strands can serve as templates |
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What does DNA gyrase do?
|
It concurrently introduces negative supercoils to relieve the tension created during unwinding
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What is the leading strand?
|
One of the daughter strands
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What is the other strand called?
|
It is called the lagging strand
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What happens to the leading strand?
|
It is continuously synthesized by DNA polymerase in the 5’ ‡ 3’ direction
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How is the lagging strand synthesized?
|
It is synthesized discontinuously in the 5’ ‡ 3’ direction as a series of short segments known as Okazaki fragments
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What is the overall direction of growth of the lagging strand?
|
It occurs in the 3’ ‡ 5’ direction
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What covalently links the fragments?
|
DNA ligase
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How many strands is RNA usually?
|
It is usually single stranded
|
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What are the several types of RNA?
|
mRNA
tRNA rRNA and hnRNA |
|
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What is messenger RNA?
|
mRNA carries the complement of a DNA sequence and transports it from the nucleus to the ribosomes
where protein synthesis |
|
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What is monocistronic?
|
mRNA= one mRNA strand codes for one polypeptide
|
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What does this mean?
|
It means one mRNA strand codes for one polypeptide
|
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What is tRNA?
|
It is found in the cytoplasm and aids in the translation of mRNA’s nucleotide code into a sequence of amino acids
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What does tRNA bring amino acids to?
|
It brings them to the ribosomes during protein synthesis
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How many types of tRNA are there?
|
Approximately one type of tRNA for each amino acid
so about 40 |
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What is rRNA?
|
It is a structural component of ribosomes and is the most abundant of all RNA types
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Where is rRNA synthesized?
|
In the nucleolus
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What is hnRNA?
|
It is a large ribonucleoprotein complex that is the precursor of mRNA
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What is transcription?
|
It is the process whereby information coded in the base sequence of DNA is transcribed into a strand of mRNA
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What is mRNA synthesized from?
|
A DNA template in a process similar to DNA replication
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Where does DNA helix unwind?
|
It unwinds at the point of transcription
and synthesis occurs in the 5’ ‡ 3’ direction using only one DNA strand as a template. Template known as The antisense strand |
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What is mRNA synthesized by?
|
The enzyme RNA polymerase
which must bind to sites on the DNA called promoters to begin RNA synthesis |
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What stops mRNA synthesis?
|
It continues until the polymerase encounters a termination sequence
which signals RNA polymerase to stop transcription thus allowing the DNA helix to reform |
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What are exons?
|
They are coding sequences
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What are introns?
|
Noncoding sequences
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What is RNA initially transcribed by?
|
A precursor molecule hnRNA
which contains both introns and exons |
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What happens during hnRNA processing, where does it occur
|
--The introns are cleaved and removed
while the exons are spliced to form a mRNA molecule coding for a single polypeptide. --Within the nucleus and is also necessary for tRNA and rRNA production |
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Where does post transcriptional processing occur?
|
Within the nucleus
and is also necessary for tRNA and rRNA production |
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What is the triplet code?
|
The base sequence of mRNA is translated as a series of triplets
otherwise known as codons |
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How many different codons are possible?
|
64 codons
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What is the fact that most amino acids have more than one codon specifying them?
|
This property is referred to as the degeneracy or redundancy of the genetic code
|
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What is translation?
|
The process whereby mRNA codons are transplated into a sequence of amino acids
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Where does translation occur?
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In the cytoplasm and involves tRNA
ribosomes mRNA amino acids enzymes and other proteins |
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tRNA:
1. Contribution to translation 2. what does it recognize? 3. relationship of structure/function |
1.It brings amino acids to the ribosomes in the correct sequence for polypeptide synthesis
2. It recognizes both the amino acid the mRNA codon Its three-dimensional structure: one end contains a three-nucleotide sequence, the anticodon, which is complementary to one of the mRNA codons |
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What does each amino have?
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It has its own aminoacyl-tRNA synthetase
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What are ribosomes?
|
They are composed of two subunits
consisting of proteins and rRNA |
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How many binding sites to ribosomes have?
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They have three binding sites: one for mRNA
and two for tRNA |
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What are the two sites for tRNA called?
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The P site
and the A site |
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What does the P site do?
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It binds to the tRNA attached to the growing polypeptide chain
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What does the A site do?
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It binds to the incoming aminoacyl-tRNA complex
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Do they require energy?
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All three do
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What are they mediated by?
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Enzymes
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What happens with initiation?
transcription |
Synthesis begins when the small ribosomal subunit binds to the mRNA near its 5’ end in the presence of proteins called initiation factors
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What does the ribosome scan?
|
It scans the mRNA until it bonds to a start codon (AUG)
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What does the initiator aminoacyl-tRNA complex do?
|
Methionine-tRNA
the initiator complex base pairs with the start codon |
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What does the large ribosomal unit do?
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It binds to the small one
creating a complete ribosome with the met-tRNA complex sitting in the P site |
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How does transcription elongation work?
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Hydrogen bonds form between the mRNA codon in the A site and its complementary anticodon on the incoming aminoacyl-tRNA complex
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What does the enzyme peptidyl transferase do?
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It catalyzes the formation of a peptide bond between the amino acid attached to the tRNA in the A site and the met attached to the tRNA in the P site
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What happens following peptide bond formation?
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1. A ribosome carries uncharged tRNA in the P site and peptidyl-tRNA in the A site
2. translocation= The ribosome advances 3 nucleotides along the mRNA in the 5’ ‡ 3’ direction |
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What happens to the empty A site?
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It is ready for entry of the aminoacyl-tRNA corresponding to the next codon
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How does termination work?
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It terminates when one of three special mRNA termination codons (UAA
UAG UGA) arrives in the A site ---codons signal for ribosome to terminate translation --A protein called release factor binds to the termination codon causing a water molecule to be added to the polypeptide chain |
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What happens during and after polypeptide release?
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It assumes the characteristic conformation determined by the primary sequence of amino acids
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What happens with disulfide bonds?
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They can form within or between polypeptide chains
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What is mutation?
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A change in the base sequence of DNA that may be inherited by offspring
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What are the three common types of mutations?
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Base-pair substitutions
base-pair insertions and base-pair deletions |
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What happens with point mutations?
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It occurs when a single nucleotide base is substituted by another
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What happens if the substitution occurs in a noncoding region
or if the substitution is transcribed into a codon that codes for the same amino acid? |
There will be no change in the amino acid sequence; silent mutation
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What is an example of a single base-pair substitution?
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Sickle cell anemia
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What about base-pair insertions and deletions?
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They involve the addition or loss of nucleotides
respectively, They usually have more serious effects on the protein coded for since nucleotides are read as a series of triplets |
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What does the addition or loss of a nucleotide cause?
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It changes the reading frame of the mRNA
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What can it be caused by?
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Internal genetic mistakes or by external cancer-causing agents called mutagens
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How do internal mistakes occur?
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They occur during DNA replication
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What does this result in?
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It results in gene mutations and dysfunctional proteins
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What are physical mutagens?
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They are things such as X rays and ultraviolet radiation
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What are chemical mutagens?
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Base analogs
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How can DNA act as a mutagen?
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Mobile pieces of DNA called transposons can insert themselves in genes and cause mutation
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What does a viral genome contain?
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Anywhere from several to several hundred genes
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What does it consist of?
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Either double stranded or single stranded DNA or RNA
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Are viruses specific?
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They are highly specific with respect to host selection and can be generally grouped into plant viruses
animal viruses and bacteriophages |
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How can a virus infect a host cell?
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It can only infect one that has a surface receptor for the virus’ capsid (protein coat)
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How does it enter the host cell?
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Via a variety of mechanisms
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How do some enter?
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Some introduce only their nucleic acid into the host cell’s cytoplasm
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What about others?
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Other enter the host cell entirely
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What are DNA containing viruses?
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Viral DNA is replicated and viral mRNA transcribed inside the host cell’s nucleus
using the host’s DNA polymerases RNA polymerases and nucleotide pool |
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Do any DNA viruses replicate and transcribe in the cytoplasm?
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A few do
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How do they work?
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They must bring their own DNA and RNA polymerases with them
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How is Viral RNA replicated and transcribed?
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In the host cell’s cytoplasm
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What does RNA replicase do?
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It transcribes new RNA from an RNA template
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What do some viruses do with RNA replicase?
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Some bring it with them into the host
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Otherwise?
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A portion of viral RNA functions as mRNA
which is translated into RNA replicase immediately after entering the hose cell |
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What are retroviruses?
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They are a special group of RNA viruses that use their genome as a template for DNA synthesis rather than for RNA synthesis
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How is DNA synthesized?
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By the enzyme reverse transcriptase
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What happens to retroviral DNA?
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It becomes integrated into the host DNA
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What happens when viral DNA becomes integrated into host DNA?
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It is called a provirus or prophage after that
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What happens to the proviral DNA later?
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It is transcribed into mRNA needed for prophage assembly
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What happens to viral mRNA transcribed from viral nucleic acid?
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It is translated into the polypeptide chains that compose the viral protein coats with the aid of the host cell’s tRNA
amino acids ribosomes and enzymes |
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How do viral progeny assemble?
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They self-assemble
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What happens to the protein-nucleic acid configuration?
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It forms either spontaneously or with the aid of viral enzymes
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What does this mean?
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It means a single virus is capable of producing hundreds of progeny
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What happens once viral progeny are assembled?
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They may be released either by lysis of the host cell
or by extrusion a process similar to budding |
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What happens in extrusion?
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The progeny are enclosed in vesicles derived from the host cell membrane
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What does this permit?
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It permits viral replication without killing the host cell
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What is the process of viral replication and extrusion in animal viruses called?
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A productive cycle
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What is a bacteriophage?
|
It infects its host bacterium by attaching to it
boring a hole through the bacterial cell wall and injecting its DNA while its protein coat remains attached to the cell wall |
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What happens within the host?
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Within the host
the bacteriophage enters either a lytic cycle or a lysogenic cycle |
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What happens in the lytic cycle?
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The phage DNA takes control of the bacterium’s genetic machinery and manufactures numerous progeny
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What happens to the bacterial cell then?
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It bursts (lyses)
releasing new virions |
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What are each capable of?
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Each is capable of infecting other bacteria
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What are bacteriophages that replicate by the lytic cycle
killing their host cells called? |
Virulent
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What happens if the bacteriophage does not lyse its host cell?
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It becomes integrated into the bacterial genome in a harmless form (provirus)
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What happens to it then?
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It lies dormant for one or more generations
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Then what?
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It may stay integrated indefinitely
replicating along with the bacterial genome |
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What can cause the provirus to reemerge and enter a lytic cycle?
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It can be spontaneously
or as a result of environmental circumstances such as radiation ultraviolet light or chemicals |
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What are bacteria containing proviruses resistant to?
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Further infection (super infection) by similar phages
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What does the bacterial genome consist of?
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It consists of a single circular chromosome located in the nucleoid region of the cell
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What are plasmids?
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They are what many bacteria also contain
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What are they?
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They are smaller circular rings of DNA
which contain accessory genes |
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What are episomes?
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They are plasmids that are capable of integration into the bacterial genome
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What does this mean?
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Since the bacterial chromosome is not separated from the cytoplasm by a nuclear membrane
transcription and translation occur almost simultaneously |
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What happens as soon as a small portion of newly synthesized mRNA separates from its DNA template?
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Translation begins
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What is polycistronic?
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It is what a strand of prokaryotic mRNA may be
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Where does replication of the bacterial chromosome begin?
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At a unique origin of replication and proceeds in both directions simultaneously
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What direction is DNA synthesized?
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In the 5’ ‡ 3’ direction
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What is the rate of replication?
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It occurs at approximately 500 nucleotide additions per second
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How do bacterial cells reproduce?
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By binary fission and proliferate very rapidly under favorable conditions
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What type of process is binary fission?
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Asexual
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What are the three mechanisms for increasing genetic variance of a bacterial population?
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Transformation
conjugation and transduction |
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What is transformation?
|
It is the process by which a foreign chromosome fragment (plasmid) is incorporated into the bacterial chromosome via recombination
creating new inheritable genetic combinations |
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What is conjugation?
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It can be described as sexual mating in bacteria
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What is a cytoplasmic conjugation bridge?
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It is formed between two cells and genetic material is transferred from the donor male (+) type to the recipient female (-) type
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How is the bridge formed?
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Through appendages called sex pili
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Where are they found?
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On the donor male
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What are sex factors?
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They are plasmids that allow bacteria to be capable of forming pili and conjugating
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What is the best sex factor known?
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The F factor in E. coli
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How does it work?
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Bacteria possessing the plasmid are termed F+ cells
those without it are called F- cells |
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What happens during conjugation between an F+ and F- cell?
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The F+ cell replicates it F factor and donates the copy to the recipient
converting it to an F+ cell |
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What about plasmids that do not induce pili formation?
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They may transfer into the recipient cell along with the sex factor
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What happens sometimes to the sex factor?
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It can become integrated into the bacterial genome
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What happens during conjugation to the entire bacterial chromosome?
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It replicates and begins to move from the donor cell into the recipient cell
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When does the conjugation bridge break?
|
It usually breaks before the entire chromosome is transferred
but the bacterial genes that enter the recipient cell can easily recombine with the bacterial genes already present to form novel genetic combinations |
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What are these bacteria called?
|
Hfr cells
meaning that they have a high frequency of recombination |
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What is transduction?
|
It is when fragments of the bacterial chromosome accidentally become packaged into viral progeny produced during a viral infection
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What do these virions do?
|
They may infect other bacteria and introduce new genetic arrangements through recombination with the new host cell’s DNA
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What is this process similar to?
|
It is similar to conjugation
and may reflect an evolutionary relationship between viruses and plasmids |
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How does the regulation of gene expression enable prokaryotes to control their metabolism?
|
Regulation of transcription is based on the accessibility of RNA polymerase to the genes being transcribed
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What is it directed by?
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An operon
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What does an operon consist of?
|
It consists of structural genes
an operator gene and a promoter gene |
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What do structural genes contain?
|
They contain sequences of DNA that code for proteins
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What is the operator gene?
|
It is the sequence of nontranscribiable DNA that is the repressor binding site
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What is the promoter gene?
|
It is the noncoding sequence of DNA that serves as the initial binding site for RNA polymerase
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What is the regulator gene?
|
It codes for the synthesis of a repressor molecule that binds to the operator and blocks RNA polymerase from transcribing structural genes
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How may regulation take place?
|
Via inducible systems or repressible systems
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What are inducible systems?
|
They are systems that require the presence of a substance
called an inducer for transcription to occur |
|
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What are repressible systems?
|
They are in constant state of transcription unless a corepressor is present to inhibit transcription
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What happens in an inducible system?
|
The repressor binds to the operator
forming a barrier that prevents RNA polymerase from transcribing the structural genes |
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How long is the repressor active?
|
It is active until it binds to the inducer
|
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What is needed for transcription to occur?
|
An inducer must bind to the repressor
forming an inducer-repressor complex |
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What is this complex?
|
It cannot bind to the operator
thus permitting transcription |
|
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What are the proteins synthesized?
|
They are thus said to be inducible
|
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What do structural genes code for?
|
They typically code for an enzyme
|
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What is the inducer?
|
It is usually the substrate
or a derivative of the substrate upon which the enzyme normally acts |
|
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What happens when the substrate (inducer) is present?
|
Enzymes are synthesized
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What about when it’s not present?
|
Enzyme synthesis is negligible
|
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In this manner
what occurs? |
Enzymes are transcribed only when they are actually needed
|
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What is an example of an inducible system?
|
The lac operon is one
|
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What about repressible systems?
|
The repressor is inactive until it combines with the corepressor
|
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What does the repressor bind to?
|
The operator
|
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What does this prevent?
|
It prevents transcription only when it has formed a repressor-corepressor complex
|
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What are corepressors often?
|
They are often the end-products of the biosynthetic pathways they control
|
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What does this mean?
|
The proteins produced (usually enzymes) are said to be repressible since they are normally being synthesized
|
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How long does transcription and translation occur?
|
Until the corepressor is synthesized
|
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What is an example of a repressible system?
|
The trp operon
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