Flashcards in Ch 4 Deck (38):
what is a nucleotide?
a monomer including a sugar, phosphate, and base
how does the A form helix differ from the B form, and which form does rna and dna take on usually?
a form is wider than the b form. RNA is usually in the A-form while DNA is usually in the B-form
what type of replication does DNA structure allow for?
what is the main stabilizing force for the double helix?
stacking of bases (base stacking)
what is hypochromism?
stacked bases absorb less UV Light at 260nm than unstacked ones as in single stranded DNA.
implications: separation of the 2 strands can be monitored by looking at absorbance at 260nm
what is the melting temperature TM of a double helix?
temperature at which half of the helical structure is lost
what is annealing:
when the 2 strands come back together
what is the secondary structure of nucleic acids?
single stranded DNA and RNA can form stem loops
what kind of structural versatility does RNA have?
it can form complicated tertiary structures
has many base paring possiblities for RNA: base triples, quadruples
2' hydroxyl of the ribose sugar engages in intramolecular interactions
How big is a ribosome, and what is it an example of?
has a mas of 3 megadaltons, example of rna tertiary structure
what reaction does DNA Polymerase catalyze?
phosphidester bond formation:
(DNA)n + dNTP ---> (DNA)n+1 + Ppi
what is required for DNA synthesis?
dNTPs, DNA template, DNA polymerase requires a primer
what direction does elongation of DNA proceed in?
5'--> 3' direction
how do viruses with RNA genomes convert genomes to DNA?
what does rna syntehsis require?
teplate: double stranded dna template
activated precursors: ribonucleoside triphosphates - ATP, GTP, CTP, UTP
divalent metal ion - Mg2+ or Mn2+
what are the similarities of DNA and RNA synthesis
elongation proceeds 5' - 3'
mechanism of elogation is similar
synthesis driven forwards by the hydrolysis of pyrophosphate
differences between DNA and RNA synthesis?
rna pol does not require a starting primer to initiation elongation
rna polymerase cannot proofread for errors
How does RNA polymerase know where to start transcribing?
DNA templates contain regions called promotor sites that bind to the RNA polymerase and specify the start site for transcription
where is the promotor located?
upstream (5') of the transcription start site
what is the consensus sequence?
the most common nucleotide or amino acid at a particular sequence after multiple sequences are aligned
how is transcription terminated in bacteria?
transcription can be terminated by an RNA stem loop called the terminator
what kinds of post transcriptional modifications do mRNA undergo in eukaryotes?
7-methylguanosine cap is added to the 5' end
poly-A polymerase adds a string of adenosines to the 3'end
what is an adapter molecule?
a molecule that caries an amino acid to the RNA and fits onto the RNA
what is the adapter molecule?
describe tRNA structure
1. amino acid is covalently attached to the 3' hydroxyl group of last adenosine of tRNA. e
2. ach amino acid has a unique tRNA sequence.
3. tRNA has a cloverleaf secondary structure.
4. anticodon located at the end of stem loop so that it is accessible for base pairing with mRNA
what is each tRNA unit called? and what catalyzes its formation?
what is an anticodon?
sequence of 3 bases that recognizes a complementary sequence of bases on the mRNA
what does it mean by the code is nonoverlapping?
one DNA sequece cannot encode multiple proteins through frameshifting
what does it mean by the code has no punctuation
mRNA is read from a fixed start site as a reference and read sequentially with nothing to identify individual amino acid codons
what does it mean by the genetic code is degenerate?
most amino acids are encoded for by more than one codon. codons that specify the same amino acid are called synonyms: usually differ in the last base of the triplet codon
why is the genetic code degenerate?
1. allows for resistance against fatal mutations
how does translation start in bacteria?
start with modified amino acid formyl-methionine. an initiator tRNA recognizes the codon AUG. AUG is preceded several nuclotides upstream by a ribosome binding site known as the shine-dalgarno sequence
how does translation start in eukaryotes?
first aug closest to 5' end serves as start signal
what are the stop codons?
UAA, UAG, UGA
how does termination of translation occur?
relase factor proteins recognize stop codons that release protein
what is splicing?
the removal of introns and joining of exons
what is the catalytic component of the spliceosome?