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Biochem K > Molecular bio. Chapter 35. > Flashcards

Molecular bio. Chapter 35. Flashcards

1
Q

What is the whatson and crick rule?

A

The concentration of A=T

And the concentration of G=C

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2
Q

How many DNA forms are there?

How do they differ?

A

At least six forms which differ in intra- and inter- strand interactions and structural rearragements within the monomeric units of DNA.

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3
Q

Which DNA form is Left handed?

A

Z-form of DNA (aniclockwise)

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4
Q

Which form is a dehydrated form of DNA?

A

A-form is a dehydrated, condensed form of DNA.

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5
Q

H- Form of DNA has…?

A

A tripple helix.
Possible binding forms are:

  • AAT
  • TAT
  • CGC
  • GGC
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6
Q

what kind of bonds hold the nucleic acid backbone together?

A

3’-5’ Phosphodiesterbonds

between the 2’deoxyribosyl moities which are attached to their respective bases by N glycosidic bonds

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7
Q

B- DNA

A

-Most common form of DNA, and most favored under physiological conditions.
-Is right handed (spirals go in a clockwise direction)
1 turn= 10 Bp 34Å (3,4 nm) => with 20Å/2nm

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8
Q

How does the rotation around the phosphodiester bond effect the base pairing?

what else effects base pairing?

A
  • the rotation causes restrictions on the DNA chain which helps base pairing to occur properly.
  • The favored anti-configuration of the glycosidic bond and the predominant tautomers allow base pairing.
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9
Q

How are the adjacent bases held together?

A

Hydrophobic interactions and wan der waals interactions.

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10
Q

Which DNA strand is copied during transcription?

A

Template strand, also known as non-coding strand.

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11
Q

Which strand is the coding strand?

A

The one that isn’t being copied.

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12
Q

How can separation of the strands be done?

A
  • By increasing the temperature

- By decreasing the salt concentration.

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13
Q

What is Hyperchromisity of denaturation?

A

An increase of optical absorbance of the bases as a result of denaturation, which results in stacking.
=> results from the stacking of bases and the hydrogen bonding between the stacks when denatured.

ss-> higher curve.

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14
Q

How is DNA’s “consistency”in solution effected upon denaturation?

A

Is normally a viscous material in solution, but looses its viscosity upon denaturation.

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15
Q

What is the Tm?

A

Melting teperature.

it is the midpoint of the temperature range in which a given DNA moleculeseparates.

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16
Q

What influences the Tm?

A
  • Base composition : A-T only has 2 hydrogen bond, thus are easier to break that C-G bonds which have 3.
  • monovalent cation concentration: increasing the monovalent cation concentration by 10-fold, increases the Tm by 16,6 degrees by neutralizing the intrinsic interchain repulsion between the highly negatively charged phosphates of the phosphodiester bonds.
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17
Q

What is Formamide?

-What is its advantage?

A

An organinc solvent which destabilizes hydrogen bonding and allows separation of DNA strands at much lower temperature.
- It minimizes the phospodiesterbond brakeage.

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18
Q

What is Hybridization?

A

is the reassociation of DNA strand after denaturation when temperature and salt concentration have gone back to normal physiological conditions.
-An example is the reassociation of the DNA of the chromosome after replication

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19
Q

What does the rate of reassociation depend on?

A

The concentarion of the complimentary strands.

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20
Q

What are hybrid molecules?

A

DNA can form hybrids with complimentary DNA (cDNA) or with a cognate complimentary RNA eg.mRNA.
Förklara!!!!

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21
Q

what kind of DNA does the bacteria, bacteriophages, some DNA-containing animal viruses and mitochondria have?

A

Circular DNA

  • doesnt destroy the polarity of the molecule but it has no free3’ &5’ hydroxyl&phosphate ends.
  • can exsist in relaxed or supercoiled form.
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22
Q

How are supercoils introduced?

A

When a circular DNA (or linear DNA which has fixed ends) is twisted around its own axis.

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23
Q

Negative supercoils

A

Are formed when a molecule is twisted in the direction opposite to the clockwise right-handed helical turns of the B-DNA.
-Such DNA is said to be “underwound”

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24
Q

What are topoisomerases?

A

Enzymes that catalyze topologic changes in DNA.

-They can both relax or insert super coils, using ATP.

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25
Q

Under which conditions is linear DNA also supercoiled?

A

When particular DNA segments are constrained by interacting tightly with nuclear proteins that estanblish 2 boundary sites defining topological domain.

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26
Q

The two functions of DNA?

A
  • Providing the cell with genetic information for protein synthesis (transcription)
  • Reproduction
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27
Q

Why can RNA be alkali treated and not DNA?

A

The sugar in DNA lacks a 2’ Hydroxyl group.

-Rna however can be hydrolyzed by alkali to2’,3’ cyclic diesters of the nucleotides.

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28
Q

can RNA achieve double strand characteristics?

A

Yes, given the proper complementary base sequence with opposite polarity, the single strand RNA may fold back on itself and achieve a hairpin structure, thus acquiring double strand characteristics.

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29
Q

What is the role of peptidyl transferase?

A

It is a ribozyme with catalytic acticity. It catalyses the peptide bond formation on the ribosome.

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30
Q

What are Ribozymes?

A

RNA’s with catalytic activity. some are involved in protein synthesis or RNA splicing.

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31
Q

What are snRNA’s?

What is their function?

A 
Small nuclear RNA.
Can be found in eukaryotes and archea.
-size: 90-300nt long.
-They play role in RNA processing, particularly mRNA processing but also rRNA  processing and gene regulation. (thus indirect regulation of protein synthesis)
-Pre mRNA ripening and splicing.
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32
Q

which snRNA’s are involved in inton removal and processing of pre-mRNA into a mature mRNA?

A

U1, U2, U4, U5 & U6

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33
Q

which snRNA is involved in production of proper 3’end of the mRNA’s which lack a poly-A-tail, like histones?

A

U7

34
Q

What is the role of the snRNA 7s?

A

It associates with several proteins to form a ribonuclear protein complex called P-TEFb, which modulates gene transcription elongatio n by Pol II

35
Q

which snRNA’s are found in the nucleoplasm

A

U1, U2, U4, U5.

36
Q

which snRNA is found in the nucleolus?

A

U3

37
Q

which snRNA’s are found in the nucleolus and cytoplasm?

A

7s and 4,5s

38
Q

Which organisms have RNA as their genetic material?

A

some animal and plant viruses.

39
Q

What enzyme transcribes retroviruses such as HIV?

A

Reversed transcriptase

=> to produce a double stranded DNA copy of the initial RNA genome.

40
Q

What happens if the viral DNA (retrovirus) is integrated into the human DNA of the host cell?

A

if, as in many cases the viral DNA is integrated into the hostgenome it will serve as a template for gene expression from which new viral RNA can be transcribed.

  • This kind of genomic insertion can, depending on the site of insertion be:
  • Mutagenic: inactivating an other hene or disregulating its expression.
41
Q

What causes the mRNA to be so heterogeneous in size and function?

A

posttranscriptional modifications.

42
Q

What is the function of mRNA?

A 
All rna's in this class function as messengers, conveying information from the gene to the translation machinery. 
Each mRNA serves as a template for thr translation process.
43
Q

What does it mean that the Eukaryotic mRNA is “capped”?

A

The all have a 7-methyl Guanosinetriphosphate attached to their 5’ end phosphate. its a posttranscriptional modification.

44
Q

What kind of sugar is at the 5’terminal end which is capped?

A

It’s a 2’-O-methyl ribonucleotide.

45
Q

In cap formation which molecule looses what molecules.

A

Both the gamma and beta phosphate groups of the guanidine triphosphate (GTP) are lost, whilst only the gamma phosphate of the mRNA is lost upon the bond formation.

46
Q

In which RNA molecule frequently contains 6-methyladenine and other 2’-O-ribonucleotides?

A

mRNA

47
Q

What is the function of the Cap?

A

To stabilize thr mRNA by prevention of nucleophilic attack by 5’-exonucleoases.
- the cap is also involved in recognition of the mRNA by the translation machinery.

48
Q

Which molecule is A-tailed and what does it mean?

A

Adinosine tail of about 20-250 nucleotides is also added on the 3’end of the mRNA to maintain intracellular stability and protect the mRNA from nucleophilic attack by 3’-exonucleases.

  • It’s a non-genetically encoded polymer of adenine residues.-also functions to facilitate the translation process
  • OBS. not all mRNA have A-tails, eg. histones remain without.
49
Q

When and where is the A-tail and the Cap added?

A

Right after transcription by non-template dependent enzymes within the nucleus before “shipping”
ints a non-genetically encoded polymer of adenine residues.

50
Q

Whad did the Meselson-stahl experiment show.

A

The semiconservative behavior if DNA replication using nitrogen isotopes and weighing the DNA before and after.
(- By second cell div. an intermediate weight of all)

51
Q

In what direction is the mRNA read by the translation machinery?

A

5’ to 3’ direction

=> aniparallel reading.

52
Q

What does the anticodon arm of the tRNA consist of?

A

It consists of 7 nucleotides and is able to recognize the 3letter codons of the mRNA.
=> 3’- N-Pu-X-X-X-Py-Py-5’
N= a variable base
Pu= A modified Purine base
X-X-X = The 3 letter anticodon specific for that t-RNA
Py= pyramidine

53
Q

What is the Function of the TyC-arm?

A

Its involved in the binding of amino acetyl residues to the ribosomal surface on the site of translation.
-Together with the D-arm it helps define a specific t-RNA.

54
Q

What is the function of the D-arm of the t-RNA molecule?

A

It’s important in recognition of thw given t-RNA species to its proper aminoacetyl tRNA synthase enzyme.
The enzyme and the amino acyl residue forms an AMP enzyme complex in order to recognize the D-arm of the specific tRNA.

55
Q

Where is the amino acyl residue attached on the tRNA?

How is it attached?

A

on to the acceptor arm, which gets “charged” with the help of the aminoacetyl-tRNA synthase enzyme.
-through an ester linkage.

56
Q

When is the CCA termination on the 3’end of the tRNA added and by what?

A
  • Posttranscriptionally

- By the nuceotidyl transferase enzyme.

57
Q

Which RNA is a cytoplasmic nucleoprotein?

A

rRNA

58
Q

Which are the two main subunits of the ribosome and which subunits does each of them consist of?

A
  • 60s subunit: mW=2,6x10’6
    - Consists of : -5s subunit
    - 5,8s -“-
    - 28s
    - 50 specific polypeptides.
  • 40s subunit: smaller and consists of:
    - 18s subunit
    - 30 polypeptide chains.
59
Q

Where does all the rRNA (subunits of the ribosome) come from? Eukaryotes.

A

They are all processed from a single 45s precursor rRNA (which is highly methylated) aside from the 5s subunit.
(They’re all ncRNA’s)

60
Q

Wich are the types of rRNA’s found in prokaryotic Ribosomes?

A
  • 23s
  • 16s
  • 5s
61
Q

Where can sRNA’s be found and what are their characteristics and functions?

A

small RNA’s are highly conserved and can be found in eukaryotic cells.
Most of them are complexed withproteins to form ribonucleoproteins.
-sRNA’s are constituents of the signal-recognition particle which binds onto the protein synthesis to direct the newly synthesiszed P.P to its inta or extra cellular destination.
-Are about 20-1000 nt long.
-there are different kinds of sRNA, eg. snRNA is a kind of sRNA.

62
Q

snRNA’s are..?

A

A subset of sRNA, which are involved in rRNA and mRNA processing and gene regulation.

63
Q

Which class does the miRNA belong to?

A 
microRNA belongs to small noncoding RNA's  which also is a subclass of sRNA's. 
they're 20-22nt long.
64
Q

How are the miRNA’s processed?

A

Their precursors are noth 5’capped and 3’-polyadenylated and about 500-1000 nucleotides large.

65
Q

Where are the miRNA’s found an d what is their primary function?

A
  • In eukaryotic cells
  • Inhibition of mRNA translation (by binding to its complementary mRNA)

-Both mi- and si-RNA are capable of inhibition of gene expression through production of specific proteins that target the mRNA through one of several mechanisms.

66
Q

How are siRNA’s produced?

And where r they found?

A

They’re produced by specific nucleolytic processing of double stranded RNA’s either from endogenous RNA’s or dsRNA’s introduced to the cell from the external by RNA viruses.
-Found in Eukaryotes.

67
Q

What is the function of siRNA’s?

A

Their main role is to degrade RNA molecules

  • they typically inhibit gene expression through production of specific protein which target mRNA’s.
  • siRNA is used to “knock down” specific protein levels via “siRNA Homology-directed mRNA degradation”

Simply: they stimulate the breakdown of mRNA when not needed.

68
Q

Which sRNA’s are able to hybridize via formation of RNA-RNA hybridization to their target/complementary mRNA’s?

A

siRNA and miRNA.

69
Q

what is siRNA short for?

A

small interfering RNA (or silencing RNA)

70
Q

Which are the two general classes or ncRNA’s (non coding RNA’s)?

A

Large: 50-1000 nt long
Small: 20-22 nt long

71
Q

What is the size of Long non-coding RNA’s (lnRNA) and where are they transcribed from?

A

300-thousands of nt long.

-Typically transcribed from large regions of non - protein coding gonome.

72
Q

In general, what are the roles of all ncRNA’s?

A

They all have roles ranging from contribution of chromatin structures to regulation of gene expression of mRNA by pol II.

73
Q

Bacterial sRNA’s:

A
  • Size: 50-500 nt.
  • are small heterogeneous regulatory rna’s which also controls gene errors.
  • Their role is often to repress, but also to activate gene expression/protein synthesis by binding to mRNA’s.
74
Q

What are Deoxynucleases?

A

Enzymes which digest nucleic acids and have specificity for DNA.

75
Q

What are Ribonucleoases?

A

Enzymes which digest nucleic acids and have specificity for RNA.

76
Q

What are endonucleoases?

A

can be either deoxynucleases or ribonucleoases which are able to cleave INTERNAL Phosphodiester bonds to produce either 5’phosphoryl terminal+ 3’hydroxyterminal or 3’Phosphoryl terminal + 5’hydroxyl terminal.

77
Q

which different functions do the endonucleoases have?

A
  • Some are able to cleave/hydrolyze both strands of a double stranded molecule, -some only one of the strands.
  • Some are only capable of hydrolyzing single stranded nucleic acids.
78
Q

What are Exonucleases?

In what process are they involved?

A
  • The are nucleases that are able to hydrolyze (only) the nucleotides found at the terminal ends of the nucleic acid.
  • They play part in the DNA replication process , where they have a proofreading function. (in bacteria?)
79
Q

what are restriction nucleases?

A

They are a class of Endonucleases that are capable of recognition of the DNA sequences in need of hydrolyzing.

80
Q

Which direction does the Exonucleases work in?

A

3’-5’ or 5’-3’ (Both)

Biochem K (10 decks)

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