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biochem exam 4 > nucleic acid transcription/translation > Flashcards

nucleic acid transcription/translation Flashcards

1
Q

what is a primary structure?

A

covalent structure and nucleotide sequence

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2
Q

what is a secondary structure?

A

regular, stable structure taken up by some or all nucleotides

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3
Q

what is a tertiary structure?

A

complex folding of large chromosomes or the elaborate folding of tRNA or rRNA structures

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4
Q

What is a phosphodiester linkage?

A

Covalent bond that joins successive nucleotides of both NDA and RNA

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5
Q

What is a parallel strand?

A

3’ , 5’-phosphodiester bonds run in the same direction

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6
Q

What is an antiparallel strand?

A

3’ , 5’-phosphodiester bonds run in the opposite directions

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7
Q

How was antiparallel strands confirmed?

A

x-ray analysis

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8
Q

What is Chargaff’s Rules:

A

A + G = T + C
A = T
G = C

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9
Q

How many hydrogen bonds between G & C

A

3 H bonds

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10
Q

How many hydrogen bonds between A & T

A

2 H bonds

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11
Q

What is a palindrome sequence?

A

has the potential to form a hairpin (single strand) of cruciform (double stranded)

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12
Q

What is a mirror repeat?

A

no possibility of self-complementarity (does not lead to secondary structure)

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13
Q

A form DNA

A

right handed helix
more common in solutions lacking water
usually outside physiological conditions

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14
Q

B form DNA

A

Watson-Crick
most stable
most common in physiological conditions

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15
Q

Z form DNA

A

left handed helix
common when C-G pairs are alternating
can be found in physiological conditions but not common

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16
Q

Hoogsteen pairing forms a:

A

triplex DNA

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17
Q

Tetraplex DNA is formed when:

A

four DNA strands pair
occur readily only for DNA sequences with a very high proportion of G residues

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18
Q

Is a G tetraplex stable?

A

very stable

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19
Q

mRNA structure:

A

always single stranded
right handed
can base pair with complementary regions of DNA or RNA

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20
Q

Structure of complementary RNA strands is:

A

an A-form right handed double helix

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21
Q

breaks caused by mismatched or unmatched bases result in:

A

bulges or internal loops

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22
Q

internal loops form between:

A

palindromic sequences

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23
Q

what is the most common RNA secondary structure?

A

hairpin

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24
Q

DNA cellular locations:

A

Nucleus
Mitochondria
Chloroplast

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25
Q

Nucleus DNA:

A

primary location, containing all genetic material
organized in chromosomes

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26
Q

Mitochondria DNA (mtDNA):

A

much smaller than nuclear chromosomes
codes for mitochondrial tRNA, rRNA, and some mitochondrial proteins

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27
Q

Chloroplast DNA (cpDNA):

A

even smaller than mtDNA
provide chloroplast specific things

28
Q

New gene definition:

A

all the DNA that encodes the primary sequence of some final gene product

29
Q

What is a gene product?

A

polypeptide or RNA with a structural/catalytic function

30
Q

one gene-one polypeptide hypothesis:

A

one protein is produced from one gene (not 100% true)

31
Q

What are introns?

A

nontranslated DNA

32
Q

What are exons?

A

translated DNA (coding DNA)

33
Q

What is a codon?

A

3 consecutive nucleotides in a single strand of DNA that codes for a specific amino acids

34
Q

In Bacteria DNA is present as a:

A

Plasmid compacted in the nucleoid

35
Q

What is a plasmid?

A

small, circular DNA molecule that are in the cytosol of many bacteria

36
Q

What are viruses?

A

a single RNA or DNA molecule and a protein coat
not technically living

37
Q

Genomes are variable across species and the association between number of chromosomes and protein coding genes is:

A

not associated with more DNA equaling more proteins coded

38
Q

What is chromatin?

A

eukaryotic chromosomal material composed of DNA, RNA, and proteins

39
Q

What are chromosomes?

A

tertiary packaging of DNA

40
Q

DNA has regions that are ____ and ____?

A

underwound and supercoiled

41
Q

enzymes that increase or decrease the extent of DNA underwinding?

A

topoisomerases

42
Q

What is a centromere?

A

A DNA sequence that functions during cell division as an attachment point for proteins that link the chromosome to the mitotic spindle

43
Q

What are telomeres

A

sequences at the ends of eukaryotic chromosomes that help stabilize the chromosome

44
Q

What are histones?

A

Proteins that are tightly associated with chromatin and function to package and order the DNA

45
Q

What base pairs do histones attend to associate with?

A

regions rich in A/T

46
Q

What is a nucleosome?

A

the fundamental structural unit of chromatin
composed of a “bead” plus DNA connecting next to the bead

47
Q

DNA replication occurs during this phase?

A

Interphase

48
Q

DNA polymerase reads in what direction and synthesizes in what direction?

A

reads 3’ to 5’ and synthesizes 5’ to 3’

49
Q

What is an Okazaki Fragment?

A

result of lagging strand of DNA

50
Q

5’ end is the end where 5’ C is only bound to:

A

phosphate, not another base pair

51
Q

3’ end is the end where 3’C is:

A

free

52
Q

What are the 3 main functions of DNA Polymerase?

A

Incorporate dNTPs
Proofread (exonuclease activity)
Replaces RNA primers with DNA

53
Q

What is the template strand?

A

3’ to 5’ strand only the way that the polymerase moves
DNA strand that serves as template for RNA synthesis

54
Q

What is the non template strand?

A

DNA strand that is identical in base sequences to the transcribed RNA, with U in RNA in place of T in DNA

55
Q

Bacterial RNA Polymerase sigma subunit does what:

A

Directs the enzyme to specific DNA binding site

56
Q

Eukaryotic RNA Polymerases functions:
I
II
III

A

I - pre-ribosomal RNA, matures to rRNA
II - mRNA
ncRNA (non-coding RNA)
III - tRNA
5S rRNA
ncRNA

57
Q

Eukaryotic Transcription has what that binds promoter sequences to regulate transcription?

A

Transcription Factors

58
Q

What is the CTD?

A

carboxyl-terminal domain of RNA pol II

59
Q

What is a-amanitin?

A

compound produced by the death cap mushroom Amanita phalloides

60
Q

What does a-amanitin do?

A

disrupts transcription in animal cells by blocking Pol II and, at higher concentrations, Pol III

61
Q

mRNA processing has what 3 features:

A

5’ cap
Intron splicing
Poly A tail

62
Q

What is the 5’ cap?

A

addition of a 7-methylguanosine to the 5’ end for blocking of degradation by RNAses

63
Q

What is Intron Splicing?

A

an intron can code for noncoding mRNA
Facilitated by a spliceosome congregation of proteins
most common intron removal
can be spontaneous though

64
Q

What is the polyadenylation enzyme?

A

Polyadenylate polymerase catalyzes the synthesis of the poly A tail
Serves as the buffer from degradation at the 3’ end

65
Q

mRNA processing leaves a smaller or larger length

A

The final mature mRNA is smaller in length than the full gene coded in DNA

66
Q

With mRNA processing how does it work in different locations?

A

Different cell locations, cell types, or different environmental factors can process differently

67
Q

What is alternative splicing?

A

Some genes go through alternative splicing depending on specific conditions or different cell types to produce different proteins.

biochem exam 4 (3 decks)

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