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Flashcards in Ch 4 Deck (38):
1

what is a nucleotide?

a monomer including a sugar, phosphate, and base

2

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

3

what type of replication does DNA structure allow for?

semiconservative replication

4

what is the main stabilizing force for the double helix?

stacking of bases (base stacking)

5

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

6

what is the melting temperature TM of a double helix?

temperature at which half of the helical structure is lost

7

what is annealing:

when the 2 strands come back together

8

what is the secondary structure of nucleic acids?

single stranded DNA and RNA can form stem loops

9

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

10

How big is a ribosome, and what is it an example of?

has a mas of 3 megadaltons, example of rna tertiary structure

11

what reaction does DNA Polymerase catalyze?

phosphidester bond formation:

(DNA)n + dNTP ---> (DNA)n+1 + Ppi

12

what is required for DNA synthesis?

dNTPs, DNA template, DNA polymerase requires a primer

13

what direction does elongation of DNA proceed in?

5'--> 3' direction

14

how do viruses with RNA genomes convert genomes to DNA?

reverse transcriptase

15

what does rna syntehsis require?

teplate: double stranded dna template
activated precursors: ribonucleoside triphosphates - ATP, GTP, CTP, UTP
divalent metal ion - Mg2+ or Mn2+

16

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

17

differences between DNA and RNA synthesis?

rna pol does not require a starting primer to initiation elongation
rna polymerase cannot proofread for errors

18

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

19

where is the promotor located?

upstream (5') of the transcription start site

20

what is the consensus sequence?

the most common nucleotide or amino acid at a particular sequence after multiple sequences are aligned

21

how is transcription terminated in bacteria?

transcription can be terminated by an RNA stem loop called the terminator

22

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

23

what is an adapter molecule?

a molecule that caries an amino acid to the RNA and fits onto the RNA

24

what is the adapter molecule?

tRNA

25

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

26

what is each tRNA unit called? and what catalyzes its formation?

aminoacyl-tRNA...aminoacyl-tRNA synthestase

27

what is an anticodon?

sequence of 3 bases that recognizes a complementary sequence of bases on the mRNA

28

what does it mean by the code is nonoverlapping?

one DNA sequece cannot encode multiple proteins through frameshifting

29

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

30

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

31

why is the genetic code degenerate?

1. allows for resistance against fatal mutations

32

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

33

how does translation start in eukaryotes?

first aug closest to 5' end serves as start signal

34

what are the stop codons?

UAA, UAG, UGA

35

how does termination of translation occur?

relase factor proteins recognize stop codons that release protein

36

what is splicing?

the removal of introns and joining of exons

37

what is the catalytic component of the spliceosome?

RNA.

38

how can a premrna produce different proteins?

alternative splicing