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final for LS2 > LS3 week 1 > Flashcards

LS3 week 1 Flashcards

1
Q

what is molecular biology?

A

molecular biology is the study of biochemistry and genetics.

study of the formation, structure and the function of essential macromolecules.

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2
Q

what are the macromolecules that we are going to discuss in this class?

A

DNA

RNA

PROTEINS

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3
Q

What are some of the models that are used to research to study in order to discover things ?

A

1) bacteriophages ( bacterial viruses )

the viruses eat the bacterias.

2) bacteria ( virus)
3) yeast ( eukaryotic single celled organism)
4) other eukaryotic model organisms.

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4
Q

what are some of the similarities and differences between the prokaryotes and the eukaryotes?

A

differences :

prokaryotes: smaller

no membrane bound organelles

unidirectional transfer of dna

translation and transcription are both in the same place so those processes are coupled.

eukaryotes :

are larger

have membrane bound organelles

have mitochondria

multicelluar

transcription: nucleus

translation : cytoplasm.

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5
Q

what are the four most important macromolecules?

A

DNA : Genetic materials of the cell.

deoxyribonuclease and ribonucleotides

2) proteins
- workforce of the cell.

3 lipids

  • energy storage and structure
    4) carbohydrates or polysaccharides
  • structure and energy materials of the cell.
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6
Q

how can an organism have different cell types even though they contain the same DNA?

A

Organisms can have different cell types even if their DNA is the same because of gene expression. some of the genes are turned on and some are turned off .

different cells express different genes at different times at different levels.

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7
Q

explain the central dogma of molecular biology?

A

the central dogma of molecular biology basically states that the flow of genetic information starts from the DNA and goes to the RNA via transcription and then to Proteins via translation.

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8
Q

what are the four criterias for genetic material.

A

1) information
- the genetic material must contain the information necessary to make the whole organism.
2) replication
- must be accurately replicated
3) transmission
- must be transmitted from parent to the offspring otherwise the information wont be maintained.
4) variation
- differences in the genetic material must account for the variation within the organism.

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9
Q

what did archbold Garrod propose

A

relationship between enzymes and genes

studied alkaptonuria. ( metabolic defects)

disease due to missing enzymes.

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10
Q

george beadle and edward tatum

A

studied neospora( bread mold)

one gene-one enzyme hypothessis

each gene controlled a single protein.

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11
Q

what are genes and how do they participate in the synthesis of proteins?

A

Researchers believed that chromosomes carried the genetic information .

chromosome had both DNA and protein.

they thought protein was the genetic material because it was more complex.

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12
Q

explain what F. Griffith did

A

F. Griffith did an experiment on the R strain and the S strain.

he found out that the non-virulent genes become virulent when they are mixed in the heat killed virulent gene.

R-strain does not have a capsule and thus is not harmful.

S-strain is harmful with a capsule.

when heat killed S-strain was mixed with R strain, the rat died which showed that somehow the R strain had been converted to S-strain through transformation.

demonstrated transformation by genetic material.

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13
Q

O.Avery , C.Macleod and M.McCarty

A

they extracted DNA from virulent bacteria.

purified DNA from other macromolecules.

pure DNA was able to transform the non virulent strain into virulent one.

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14
Q

what did Avery, and his colleagues do to confirm it

A

Avery and his colleagues treated the extract with different enzymes to identify the chemical nature of the transforming agent.

whichever was able to change the strains was the genetic material.

DNase = degrades DNA

RNase = degrades RNA

Protease = Degrades proteins.

when the tubes were mixed with everything. only the ones that contained the DNA was able to transform into a virulent strain.

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15
Q

what conclusion did avery make?

A

It was concluded that DNA is the genetic material .

DNase destroys ability of heat extract transform R strain into S strain. ( if DNA is degraded then it cant transform)

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16
Q

what did hershey and chase do?

A

hershey and chase wasnted to confimr averys work so their experiment consisted of blending with radioisotopes and bacteriophages.

they used 32P for DNA

35 S for Protein

studied T2 virus that infects E.Colie

T2 only consists of DNA so it was a good candidate.

E.coli cells were infected with 35S labeled phage and blended. if the bacterial cell contains the radioisoptopes then that means that genetic information has been transformed or passed down. NOT THE CASE .

infected E.Coli with 32 P and found out that the radioisotope was in fact in the bacterial cell so therefore it confirmed that DNA is the genetic material.

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17
Q

what is the structure of DNA

A

DNA has a double stranded helix.

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18
Q

other important properties of DNA.

A

It can denature and renature.

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19
Q

requirements for denaturation

A

1) high Temperature
2) lower salt concentration
3) high pH

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20
Q

Requirement for renaturation

A

1) low temperature
2) high salt concentration
3) low pH

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21
Q

What is the monomer of nucleic acids

A

DNA and RNA are the monomers of nucleic acids.

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22
Q

what are the components of the nucleotides

A

1) nitrogenous bases

purines

pyrimidines

2) pentose sugars

ribose

deoxyribose

3) phosphate groups.

accounts for the negative charge of the DNA.

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23
Q

What is the difference between thymine and uracil?

A

the main difference is that thymine has a methyl group and uracil doesnt.

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24
Q

what is the difference between a nucleoside and a nucleotide?

A

nucleoside = base + sugar

nucleotide = base + sugar + phostphate.

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25
Q

what links the nucleotides together?

A

nucleotides are held together by phosphodiester bonds between the 3’ and the 5’ carbon on the next nucleotide.

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26
Q

what is the direction of the DNA?

A

DNA moves from 5
‘ to 3’ because of its polarity.

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27
Q

what was Linus Paulings method of working out the proteins?

A

Linus Pauling used the balls and stick model.

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28
Q

what did chargaff use

A

chargaff studied the bases and suggested that A goes with T and C with G .

29
Q

What did Rosalind Franklins X-ray diffusion reveal?

A

it revealed that DNA was helical with uniform diameter.

30
Q

what did chargaff suggest about the base content?

A

he suggested that the amount of A=T and G=C

31
Q

How many hydrogens does GC and AT have?

A

GC has three H bonds and it maintains the stability of DNA .

AT has only two H bonds.

32
Q

what did watson and crick propose

A

watson and crick proposed that DNA was helical and there were two stands that were wounds around an imaginary axis.

strands are anti paralles

the sugar phosphate is the backbone of the DNA and the bases are inside the double strands.

33
Q

explain the polarity of the DNA structure

A

The phosphate group is hydrophilic and the bases are hydrophobic.

this explains their position .

34
Q

what are the three conformations of the DNA.

A

DNA exists as A form with 11 bp per turn

B form= 10.5 bp/turn

Z-form= 12 bp / turn.

35
Q

what holds the double strands together?

A

the DNA double strands are held together by hydrogen bonding between base pairs on opposite strands.

there is also hydrophobic stacking interactions between base pairs on the same stands.

large number of weak strands such as the GC base pairing with many H bonding contributes to stability

36
Q

when does base pairing occur?

A

base pairing occurs rarely and it is not energetically favorable.

occurs during the enzymes that is responsible for base methylation, removal of damaged bases.

base flipping enables the base to sit in the active site which is not good because it disrupts the enzymatic reaction.

37
Q

what are major and minor grooves?

A

DNA contains Major and minor grooves. Major grooves are better than minor groove s because it provides more information. it can tell you if it is GC OR CG and AT or TA.

Minor groove cannot give a lot of information and can only tell you whether it is gc or at.

38
Q

what does AADH stand for?

A

AADH stands for GC base pairs in the major groove .

39
Q

what does ADAM STAND FOR?

A

ADAM is for the AT base pairn in the major groove.

40
Q

why are patterns important?

A

patterns are important because it allows proteins to recognize the sequences without disrupting the double helix.

41
Q

explain the mica experiment

A

Mica is a gel that absorbs the DNA .

DNA can only be cleaved if it is far away from the gel and it will get cleaved every 10th base pair.

reason: phosphate is bulky so when they tried to degrade it , it did not go down so they had to start from the top.

42
Q

describe the process of gel electrophoresis for DNA?

A

DNA separation by gel electropheresis

DNA is negatively charged , so when electric field is added, it migrates towards the positive end.

dependent and inversely proportional to size. the smallest fragment will go down the fastest.

43
Q

what are the two types of gel that can be used for gel electrophoresis?

A

1) polyacrylamide
- high resolution
- can separate base pair with a single base pair difference.
2) agarose
- low resolution
- can separate DNA molecules hundreds of kilobases in size.

44
Q

what can be used to visualize the dna molecules and why is that the choice?

A

Ethidium can be used to visualize the DNA molecules

  • intercalates between the base pairs
  • once intercalation takes place, the fluorescnece level increases and when it is under the UV light we can see the DNA molecules.

DNA markers are used to estimate the size of the unknown DNA molecules.

45
Q

characteristics of a DNA strand

A

DNA strand can be

1) denatured
2) renatured

46
Q

requirements for Denaturing

and Renaturing

A

Denaturing: ( melting)

1) high pH
2) Low salt concentration
3) high temeperature

H-bond breaking

once cooling takes place

Renaturing occurs

1) low Temperature
2) low pH
3) high salt concentration.

H-bond formation .

47
Q

what are holoenzymes?

A

in Prokaryotes the RNA polymerase consists of the core enzymes, alpha, beta and omega. so when these core enzymes interact with the sigma factor ,Holoenzyme is created.

48
Q

does holoenzyme bind specifically or non specifically?

A

The binding of holoenzyme is non-specific. It also scans for the promoter region .

49
Q

what does the sigma factor do ?

A

in Prokaryotes there are two main promoters at -35 and -10 . sigma 2 binds to the -10 and sigma 4 binds to the -35.

50
Q

is the sigma interaction specific or non specific?

A

the sigma interaction or binding is specific. and the active site is stated to be +1.

51
Q

what substrates are involved in transcription of the RNA

A

rNTP

52
Q

When is the sigma factor released?

A

once about 8-10 ribonucleotides are produced the sigma factor gets released, and the RNA polymerase core enzymes move away from the promoter and synthesizes the mRNA as it goes along.

53
Q

what are the two types of termination factors involved in prokaryotic transcription

A

Rho independent and Rho dependent.

54
Q

Process of the 5’Cap

A

1) removal of the gamma phosphate
2) linkage of GMP with 5’-5’
3) methylation of the 7th position on the G.

4 ) all the mrnas are capped.

55
Q

Process of Poly A tail

A

1) two factors are needed
i) CPSF
ii) CstF
2) Transcription of poly A signal causes transger of those factors
3) RNA cleavage and release of CstF
4) poly A polymerase is added on the 3’ end of the mrna.

approximatel 200 As are added to RNA.

Poly A binding proteins then bind to A RESIDUES.

56
Q

WHAT ARE THE TWO MODELS THAT HELPS TO EXPLAIN TERMINATION OF THE EUKARYOTIC ORGANISMS.

A

The two models are

1) torpedo model.
i) RNAse attaches to the uncapped end and rapidly degrades the remaining RNA , destabilizing the RNA polymerase and it leaves.

2 ) Allosteric model

i) once Poly A is passed, RNA polymerase becomes unstable due to conformational change and it leaves on its own.

57
Q

what are the additional proteins required in transcription of the in vivo organisms.

A

the additional proteins that are required are

1) the mediator complex
2) the nucleosome modifying enzymes
3) transcriptional regualtory proteins.

58
Q

what is the main function of the mediator complex.

A

the mediator complex mediates between the activator and the RNA polymerase.

59
Q

what happens as the number of genes increases

A

number of genes goes up, complexity goes up.

60
Q

what is the difference in the bacterial RNA splicing and eukaryotic RNA splicing?

A

bacterias dont have a lot of introns but eukaryotes have a lot of introns.

61
Q

difference between exons and introns?

A

exons: coding region and they are present in the final produt of the mature RNA.

Introns: non coding and they are spiced out by the spiceosomes .

62
Q

what is the experimental evidence of RNA splicing?

A

the experimental evidence of RNA splicing is that before it was believed that RNA was synthesized as a longer precursor.

hnRNA WAS LONGER however, the mRNA that was found associated with the polyribosomes were much smaller.

there was a test that was done called the Pulse Chase experiment which used the retro zonal cnetrifucgation that was based on the size gradient. it showed that the HnRNA was longer , and the size changed later.

63
Q

what is required in the splicing reaction?

A

two esterification .

1) destroy the old phosphate and create a new one.

cleavage at 5’ intron / exon junction , lariat is created via 5’-2’ bond.

2) cleavage of 3’ intron / exon junction and 5’ exon=> 3’ exon splicing.
3) separated

64
Q

what are the steps of the Spliceosome- mediated splicing reaction?

A

1) E complex
- U1 binds to the 5’ end and recognizes the 5’ splice site
- BBP binds to the branch point

U2AF binds Py tract and 3’ splice site.

  • A complex

U2 switches with BBP

-b COMPLEX

binding of u4, u5, u6

U1 is released

and then the U4 gets released allowing U6 and U2 to interact.

C complex.

  • U6 and u2 CATALYZE THE FIRST ESTERIFICATION

U5 assists in the second esterificaiton.

65
Q

what is the rare case of RNA splicing?

A

self splicing.

group I and group II

1) group II spliceosome does not require a spliceosome but it is the same as the regualr splicing .
2) group I IS WHERE THERE IS A CONFORMATIONAL CHANGE
- instead of A being the branch site , it is G

does not form a lariat.

66
Q

Alternative splicing .

A

alternative splicing produces more than one polypeptide. it can pick and choose which ones are going to make it to thefinal mrna Product.

some of the results of Alternative splicing includes

1) normal exons
2) extended exons
3) exon skipped
4) intron retained
5) alternative exons.

the change in the results can result in differnent funciton.

67
Q

why do prokaryotes do not have introns and eukaryotes do?

A

there are two models to explain this

1) Introns early model
- Originally prokaryotes had introns but they lost them over time to be more efficient in terms of replicaiton
2) Introns late model
- introns were inserted into genes that originally did not have introns.

68
Q

exon shufflin

A

introns are more likely to be involved in recombination than exons since they are larger.

  • exons often encode functional protein function and the different domains can interact with one another.

related exons are soemtimes found in unrelated genes.

69
Q

what are the requirements for mRNAs transports

A

final for LS2 (3 decks)

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