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bbs1001 > Learning goal 1 (case2) > Flashcards

Learning goal 1 (case2) Flashcards

1
Q

nucleic acids

A

DNA, RNA

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2
Q

building blocks of DNA, and nucleic acids

A

Nucleotides.

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3
Q

Nucleotides

A

A,T,G,C,U
Ribose,
Phosphate group

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4
Q

purine

A

adenine (A) and guanine (G).

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5
Q

pyrimidines

A

cytosine (C), thymine (T), and uracil (U).

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6
Q

A, T bonds

A

two hydrogen bonds

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7
Q

G, C bonds

A

three hydrogen bonds

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8
Q

monosaccharide

A

D-ribose. RNA
2-deoxy-D-ribose. DNA

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9
Q

sugar and base

A

nucleoside

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10
Q

bond between the phosphate group and the nucleoside

A

ester bond (-o-)

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11
Q

Primary structure

A

sequence nucleotides

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12
Q

backbone of DNA

A

stability, Monosaccharide and the phosphate group

deoxyribose and phosphate groups that are throug phosphodiester (5’-o-(o=p-oh)-o-3’) bonds connecting through the oxygen on the 5’ carbon of one to the oxygen on the 3’ carbon of another deoxyribose.

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13
Q

Bases function

A

carries information for protein synthesis

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14
Q

the asymmetrical ends of DNA

A

5’ prime (phosphate terminal(end), oh )
3’ prime ( deoxyribose, OH terminal(end) )

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15
Q

twisting of the DNA Alpha-Helix and the geometry of the bases impact on the DNA structure

A

B-DNA form:
creats wide gaps, minor and major grooves, its important binding sites for proteins that maintain DNA and regulate gene activity.

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16
Q

largest rna

A

mRna

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17
Q

secondery structure RNA

A

single stranded, or often single and souble stranded RNA becasue they can fold to peforme there functions, they also contain stem loops like the ones in tRNA

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18
Q

3d structure of DNA

A

in the nuclei, 147 paired bases in a Alpha-Helix DNA(-) (2nm) coiled around 8 Histones proteins core (+) (11nm) = nucleosomes&raquo_space;» Chromatin form when a 30 nm fiber form of 6 nucleosomes pers turn (solenoid) a repeating unit.
chromatine fiber&raquo_space;> loops»» (bands)»» stacked minibands (18 loops flower) matrix in the middle»» ALMIGHTY SUPERSTRUCTURE OF CHROMOSOME!!! with centromere in the middle.
short arm, long arm

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19
Q

when are nucleosomes considered chromatine

A

when a 30 nm fiber form from nucleosomes (solenoid), 6 nucleosomes per turn

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20
Q

where the energy comes from for polymerisation of DNA

A

from the two terminal phosphate group on the deoxynucleotide triphosphate ,that disbond and become Pyrophosphate, and constantly hydrolsed to provide energy for polyrisation.

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21
Q

DNA strands names

A

sense (coding) which has the same sequence as mRNA and antisense (template) which is processed by Polymerases in transcription

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22
Q

what regulate DNA function

A

proteins that bind to the grooves and can alter the DNA structure, regulate replication, transcription.

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23
Q

where the DNA of prokaryotes is located

A

central region called Nucleoid

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24
Q

cell set of DNA (all DNA)

A

genome

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25
Q

octameer

A

the 8 histones core of a nucleosome, consists of two copies of each histone proteins (H2A, H2B, H3, H4), each histone has both C-terminal (COOH free in an amino acid) histone-fold and N-terminal(NH2 free group) tail,when its created from mRNA, its created from N-terminus to C-terminus.

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26
Q

Each loop in chromsome loop’s band, contains 50 turn of chromatine thethered by…..

A

Nonhistone scaffold protein

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27
Q

histones relations to genes

A

determines which genes are active

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28
Q

Dna form in prokaryotes comparing to chromsomes in Eukaryote

A

Supercoiling

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29
Q

forms of DNA

A

A-DNA (dehydrated non-physiolgical), Z-DNA, B-DNA

B-DNA + mtheylation= Z-DNA recognised by a protein binds to it, to regulate transcription.

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30
Q

denaturation

A

breaking the hydrogen bonds between the bases in a DNA helix by eposing it to high temperature

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31
Q

why DNA with more G=C bonds isharder to denaturate

A

more H bonds

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32
Q

vertical gene transfer

A

transmission of DNA info from mother to daughter cell through replication, DNA doesnt serve structural role in cells

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33
Q

Semi- conservative replication

A

two daughter DNA each with one Parental strand and a new daughter strand.

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34
Q

types od replication

A

semi conservative, conservative, dispersive

35
Q

conservative replicatio

A

the re-basepair of the used pair parental DNA strands. and daughter DNA two new pair together

36
Q

dispersive

A

alternating parental and new daughter DNA segments

37
Q

what is a primosome

A

a primosome is a protein complex (DnaG primase, DnaB helicase, DnaC helicase assistant, DnaT, PriA, Pri B, and PriC.) formed by primase enzyme responsible for creating RNA primers, in prokaryotes.

38
Q

why do wwe have two replication forks

A

two helicases bond, goes both directions

39
Q

how are supercoilings resolved

A

through topoismerase, by causing temporary nicks in the DNA helix

40
Q

initiation

A

Helicase opens up Dna helix, breaks hydrogen bonds + activate primase = forms primosome. A replication bubble with its two replications forks forms in the origin of replication nucleotides sequence.

free nucleotides provides energy from breaking two phosphate bonds, from its three phosphate. the energy is used to form phosphatdieseter bond between two nucleotides.

the opening of the helix causes overwinding or suopercoiling, ahead of the replication forks.

41
Q

how many repication origins in both types cells

A

pro, one origins, approximately 245 base pairs long wich with AT sequences.

euk, multiple up to 100,000 origin

42
Q

DNA polymerase lll

A

requiere a template and a primer, 5’ > 3’ synthesize, he moves 3 to 5
proofread ( remove nuleotides that are accedintly added)

43
Q

lagging strand

A

the strand made of okazaki fragments, with each has its own primer

44
Q

single strand binding protein

A

coat the seperated strand causing to not bind again temporary

45
Q

Dna igase

A

Dna ligase, repairs the Okazaki fragments in lagging strand

46
Q

Sliding clamp

A

helps DNA polymerase to stay bonded on the lagging strand

47
Q

topoisomerase

A

prevent the DNA helix from getting to tightly wounded

makes temporary nicks in the helix to release the tension, then sealing the nicks to avoid permanent damage.

48
Q

DNA polymerase l

A

DNA repairing enzyme.

able to catalyse multiple polymerisation before releasing the template DNA.

filliling okazaki fragments with DNA

removes RNA primers from 5 to 3

proof reading from 3 to 5 exonuclease activity

49
Q

exonuclease activity meaning

A

Exonucleases are enzymes that catalyze the removal of nucleotides in either the 5-prime to 3-prime or the 3-prime to 5-prime direction from the ends of single-stranded and/or double-stranded DNA. Removal of nucleotides is achieved by cleavage of phosphodiester bonds via hydrolysis

50
Q

Dna polymerase ll

A

DNA replication

3 to f proofreading exonuclease activity
5 to 3 polymerase activity

interacts with DNA polymerase 3 to maintain the fidelity (accuracy) and processitivity of DNA replication

51
Q

ORC

A

origin recognition copmplex, initiator protein by eukaryotes
ORC binds to two different areas at one end of the replicator durng G1 phase + recruits other replication proteins to foprm prereplicative complexes that get ativated between g phase and S phase

52
Q

Pol ε

A

synthesizes the leading strand

53
Q

Pol δ

A

synthesizes the lagging strand

54
Q

what hapens when the primers are removed from the 5’ end of the new strand

A

overhang of the parental DNA, cant filled with complimentary DNA becasue DNA polymerase needs primer, this why the DNA get shorter after each repliation

55
Q

eukaryote telomerase

A

has a complementary RNA sequence to the 3’ Overhang parental DNA strand after replication,
The RNA sequence s used to SYnthesize the complemantary strand
telomerase shift and the process is repeated
Primase and dna polymerase
continue the synthesize of the strand

56
Q

RNA synthesized in … to … direction

A

5 to 3

57
Q

molecules in replications

A

dNTP’s datp dctp etc…

58
Q

which ion is needed for optimal DNA polymerase activity

A

Mg+ Magnesium

59
Q

Molecules in Transcription

A

ATP GTP CTP UTC

60
Q

Reverse transcriptase

A

DNA polymerase synthesiz double stranded DNA from RNA

61
Q

is RNA polymerase rimer dependent

A

no

62
Q

prokaryote transcription

A

initiation:
promoter sequence, signles the RNA polymerase to start transcription.

RNA- coding sequence, coding region for the RNA polymerase, determines the Amnio acids sequence.

terminator sequence, where the process stops

general transcription factors activate transcription

RNA polymerase has sigma factor to recognize the promoter

holoenzyme in the RNA polymerase contacts the -35 sequence and then binds to the full promoter (closed promoter complex)

untwists DNA in the -10 region (open promoter complex)

63
Q

transcription elongation pro

A

o Transcription bubble

o Transcription factors unzip the double
helix by breaking the hydrogen bonds

o Sigma factor is released and RNA polymerase moves along the DNA

o Core enzyme can complete the transcription of the gene alone
o RNA polymerase continues to untwist the DNA ahead of it (behind the translation bubble the DNA strands reform into double stranded DNA)

o RNA exits the enzyme single stranded

o Two proofreading mechanisms:
1. replacing an incorrect nucleotide for a correct nucleotide (RNA polymerase reverses its synthesis reaction);
2. Enzyme moves back one or more nucleotides and cleaves the RNA at that position

64
Q

termination transcription pro

A

terminator sequence (repetiton of a sequence)
core RNA polymerase terminate the process
RNA polymerase transcribes the terminator sequence > RNA folds into a hairpin loop structure
Rna polymerase dissociate from template

65
Q

termination pro transcription hairpin loop stracture function

A

causes RNA polymerase to slow down and then pause in its catalysis of RNA synthesis

66
Q

types of terminators in Pro transcription

A

Rho-depndent recognised by RNA polymerase and the Rho factor

Rho- independent: only RNA polymerase hairpin loop structure

67
Q

transcription eukaryotes PRODUCT

A

pre-mRNA with introns (NON-CODING FOR AMINO ACIDS) and exons

68
Q

Regions ofthe promotor in euk

A

core promoter , promotor proximal elements

69
Q

core promotor function euk

A

ensure the start of transcription at the correct site

70
Q

promotor proximal elements function

A

Short sequence element called Inr (initiator) which spans the transcription initiation start site;
2. The TATA box at position ca. -30; they determine where transcription will begin

71
Q

TATA boxfunction

A

determines where transcription begin

72
Q

Activators

A

regulate how and when a gene is expressed

73
Q

enhancers

A

modulate the transcription form distance

74
Q

the three mRNA parts

A

5’ UTR, untranslated region or leader sequence at the 5’ end, upstream

protein coding sequence

3’ UTR, trailer sequence, downstream

UTR can regulate gene expression

75
Q

initiation transcript euk

A

RNA Pol ll, and GTF’s (general transcription factors) on the core promoter.
GTF bind and then RNA form complex
with other GTF’s
Preinitiation complex (PIC): GTFs and RNA polymerase 2 bind to promoter elements in a particular order
transcription begins

76
Q

5’ end modification

A

5’ caping after RNApolymerase 2 made 20-30 nuc pre-mRNA
capping enzyme add guanine nucleotide (7-methyl guanosine) to the 5 end

it protects the transcript from being broken down. It also helps the ribosome attach to the mRNA and start reading it to make a protein

77
Q

3 modification

A

poly a tail 50-250
The tail makes the transcript more stable and helps it get exported from the nucleus to the cytosol

78
Q

ribonuclease

A

When a sequence called a polyadenylation signal shows up inan RNA molecule during transcription, an enzyme(ribonuclease) chops the RNA in two at that site.
Another enzyme adds about 100-200 adenine (A) nucleotides to the cut end, forming a poly-A tail.

79
Q

splicing

A

introns chop chop, exons recombination occur occur, boom gigtrilion propapility amino acid sequence from one mRNA

80
Q

are all genes transcriped

A

transcription for each gene is controlled individually
Cells carefully regulate transcription, transcribing just the genes whose products are needed at a particular moment
in prokaryote each group of genes are transcriped together

81
Q

types of RNA

A

tRNA, rRNA

82
Q

tRNA function

A

match mRNA codon and bring its aminoacid
L shape
has anti codon
attachment site of the amino acid
differ slightly in structure, cause each tRNA has its own amino acid

83
Q

rRNA

A

responsible for most of the structure and function of the ribosome

bbs1001 (7 decks)

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