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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
Under which conditions is linear DNA also supercoiled?
When particular DNA segments are constrained by interacting tightly with nuclear proteins that estanblish 2 boundary sites defining topological domain.
26
The two functions of DNA?
- Providing the cell with genetic information for protein synthesis (transcription) - Reproduction
27
Why can RNA be alkali treated and not DNA?
The sugar in DNA lacks a 2' Hydroxyl group. | -Rna however can be hydrolyzed by alkali to2',3' cyclic diesters of the nucleotides.
28
can RNA achieve double strand characteristics?
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.
29
What is the role of peptidyl transferase?
It is a ribozyme with catalytic acticity. It catalyses the peptide bond formation on the ribosome.
30
What are Ribozymes?
RNA's with catalytic activity. some are involved in protein synthesis or RNA splicing.
31
What are snRNA's? | What is their function?
``` 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. ```
32
which snRNA's are involved in inton removal and processing of pre-mRNA into a mature mRNA?
U1, U2, U4, U5 & U6
33
which snRNA is involved in production of proper 3'end of the mRNA's which lack a poly-A-tail, like histones?
U7
34
What is the role of the snRNA 7s?
It associates with several proteins to form a ribonuclear protein complex called P-TEFb, which modulates gene transcription elongatio n by Pol II
35
which snRNA's are found in the nucleoplasm
U1, U2, U4, U5.
36
which snRNA is found in the nucleolus?
U3
37
which snRNA's are found in the nucleolus and cytoplasm?
7s and 4,5s
38
Which organisms have RNA as their genetic material?
some animal and plant viruses.
39
What enzyme transcribes retroviruses such as HIV?
Reversed transcriptase | => to produce a double stranded DNA copy of the initial RNA genome.
40
What happens if the viral DNA (retrovirus) is integrated into the human DNA of the host cell?
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
What causes the mRNA to be so heterogeneous in size and function?
posttranscriptional modifications.
42
What is the function of mRNA?
``` 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
What does it mean that the Eukaryotic mRNA is "capped"?
The all have a 7-methyl Guanosinetriphosphate attached to their 5' end phosphate. its a posttranscriptional modification.
44
What kind of sugar is at the 5'terminal end which is capped?
It's a 2'-O-methyl ribonucleotide.
45
In cap formation which molecule looses what molecules.
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
In which RNA molecule frequently contains 6-methyladenine and other 2'-O-ribonucleotides?
mRNA
47
What is the function of the Cap?
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
Which molecule is A-tailed and what does it mean?
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
When and where is the A-tail and the Cap added?
Right after transcription by non-template dependent enzymes within the nucleus before "shipping" ints a non-genetically encoded polymer of adenine residues.
50
Whad did the Meselson-stahl experiment show.
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
In what direction is the mRNA read by the translation machinery?
5' to 3' direction | => aniparallel reading.
52
What does the anticodon arm of the tRNA consist of?
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
What is the Function of the TyC-arm?
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
What is the function of the D-arm of the t-RNA molecule?
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
Where is the amino acyl residue attached on the tRNA? | How is it attached?
on to the acceptor arm, which gets "charged" with the help of the aminoacetyl-tRNA synthase enzyme. -through an ester linkage.
56
When is the CCA termination on the 3'end of the tRNA added and by what?
- Posttranscriptionally | - By the nuceotidyl transferase enzyme.
57
Which RNA is a cytoplasmic nucleoprotein?
rRNA
58
Which are the two main subunits of the ribosome and which subunits does each of them consist of?
- 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
Where does all the rRNA (subunits of the ribosome) come from? Eukaryotes.
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
Wich are the types of rRNA's found in prokaryotic Ribosomes?
- 23s - 16s - 5s
61
Where can sRNA's be found and what are their characteristics and functions?
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
snRNA's are..?
A subset of sRNA, which are involved in rRNA and mRNA processing and gene regulation.
63
Which class does the miRNA belong to?
``` microRNA belongs to small noncoding RNA's which also is a subclass of sRNA's. they're 20-22nt long. ```
64
How are the miRNA's processed?
Their precursors are noth 5'capped and 3'-polyadenylated and about 500-1000 nucleotides large.
65
Where are the miRNA's found an d what is their primary function?
- 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
How are siRNA's produced? | And where r they found?
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
What is the function of siRNA's?
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
Which sRNA's are able to hybridize via formation of RNA-RNA hybridization to their target/complementary mRNA's?
siRNA and miRNA.
69
what is siRNA short for?
small interfering RNA (or silencing RNA)
70
Which are the two general classes or ncRNA's (non coding RNA's)?
Large: 50-1000 nt long Small: 20-22 nt long
71
What is the size of Long non-coding RNA's (lnRNA) and where are they transcribed from?
300-thousands of nt long. | -Typically transcribed from large regions of non - protein coding gonome.
72
In general, what are the roles of all ncRNA's?
They all have roles ranging from contribution of chromatin structures to regulation of gene expression of mRNA by pol II.
73
Bacterial sRNA's:
- 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
What are Deoxynucleases?
Enzymes which digest nucleic acids and have specificity for DNA.
75
What are Ribonucleoases?
Enzymes which digest nucleic acids and have specificity for RNA.
76
What are endonucleoases?
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
which different functions do the endonucleoases have?
- 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
What are Exonucleases? | In what process are they involved?
- 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
what are restriction nucleases?
They are a class of Endonucleases that are capable of recognition of the DNA sequences in need of hydrolyzing.
80
Which direction does the Exonucleases work in?
3'-5' or 5'-3' (Both)

Biochem K (10 decks)

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