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Biochem Finals Fatima > Gene Expression > Flashcards

Gene Expression Flashcards

0
Q

DNA to RNA

A

Transcription

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1
Q

DNA for the synthesis of another identical DNA.

A

Replication

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2
Q

RNA to protein or AA

A

Translation

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3
Q

RNA to DNA because of retro virus

A

Reverse transcription

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4
Q

Largely dictates the physical observable characteristic of an organism which is known as phenotype

A

Genotype

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5
Q

Characteristic of an organism

A

Phenotype

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6
Q

Refers to a change in the DNA

A

Mutation

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7
Q

Result from different kinds of mutation

A

Disease

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8
Q

DNA structure

A

Double helix

2 anti parallel strand

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9
Q

Bond that keeps the 2 anti parallel strands together

A

H bond

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10
Q

Stacked at the center of the DNA

A

Base

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11
Q

Back bone of DNA

A

Sugar and phosphate

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12
Q

3 form of DNA

A

B
A
Z

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13
Q

Tall and slender
It is where enzymes will attach during replication and transcription
Right handed

A

B form

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14
Q

Form seen in a solution with higher salt concentration or with alcohol added
Short and stout

A

A form

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15
Q

Longer than B form

Seem to zigzag

A

Z form

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16
Q

A molecule made up of repeating sub units

A

Polymer nucleotides

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17
Q

Nucleotides linked by

A

Phophodiester bond

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18
Q

Each nucleotide is made up of?

A

Bases
Deoxyribose
Phosphate

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19
Q

H bonded with each other

Attached to the sugar

A

Bases

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20
Q

Attached to the PO4

A

Deoxyribose

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21
Q

Sugar

Has 5 carbon

A

Deoxyribose

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22
Q

Used to distinguish it from the carbons of the base

A

Primes

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23
Q

Attachment of bases by glycosidic bond

A

C1

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24
Q

Contains a hydroxyl functional group 3’ ends

A

C3

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25
Q

Contains hydroxyl group
Called the 5’ end of the sugar
Always contain a PO4

A

C5

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26
Q

Mitochondria

Prokaryotic DNA bacteria

A

Closed circular

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27
Q

Eukaryotic DNA

A

Linear

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28
Q

Linear DNA ends are referred to as

A

Telomeres

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29
Q

Telomeres shorten after each round of

A

Replication

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30
Q

Linker part of the DNA

A

Linker histone

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31
Q

Associates with the linker part of the DNA

A

H1

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32
Q

Will form the octameric core

A

H2A

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33
Q

Nucleosome

A

H4

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34
Q

Size of DNA that wounds around Histone

A

150 bp

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35
Q

Size of linker DNA

A

50bp

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36
Q

DNA that is further compacted

A

Nucleosome

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37
Q

Is the nucleosome

A

30 nm fiber

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38
Q

30 nm fiber will be packaged into a lampbush or test tube brush appearance

A

700 nm scaffold

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39
Q

Packaging ratio during interphase

A

1000

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40
Q

Packaging ratio during mitosis

A

10,000

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41
Q

The lampbrush in turn will be packaged into a

A

Chromosome

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42
Q

Central part of the chromosome

A

Centromere

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43
Q

Ends of linear chromosome

A

Telomere

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44
Q

1 chromosome =

A

1 DNA molecule

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45
Q

In the nucleus of human cell, it contains how many molecules of DNA

A

46

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46
Q

Refers to all the DNA present in human cell

A

Genome

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47
Q

DNA present in the nucleus

A

Nuclear genome

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48
Q

DNA present in the mitochondria

A

Mitochondrial genome

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49
Q

Portion of the nuclear DNA that can be potentially transcribed into RNA

A

Gene sequences 30%

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50
Q

The remaining 70% of nuclear genome do not code for anything. They are just there as

A

Spacers

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51
Q

Gene sequences 30%

A

10 % codes for protein

90% codes for RNA

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52
Q

Apparent when the chromosome is stained

A

Extragenic DNA

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53
Q

Usually contain active genes

Referred as euchromatin

A

Light staining areas

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54
Q

Usually contain junk DNA

Referred as heterochromatin

A

Dark staining areas

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55
Q

DNA polymerization proceeds in

A

5’ to3’ direction

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56
Q

DNA polymerization, complementary DNA acts as

A

Template

57
Q

DNA polymerization, acts as co factor

A

Magnesium

58
Q

Enzyme that catalyze the synthesis of phosphodiester bond

A

DNA polymerase

59
Q

It will determine the sequence of the new strand

A

Template

60
Q

Bond formation between P and OH and cleavage of the diphosphate

A

Nucleophillic attack

61
Q

The oxygen would launch a nucleophillic attack as a result there is formation of

A

Phosphodiester bond

62
Q

Why do we say that the DNA grows in the 5’ to 3’ direction?

A

You can always add only in the 3’ end

63
Q

Synthesize primers?

A

Primase

64
Q

To provide 3’OH to initiate DNA synthesis

A

Primers

65
Q

Without primers

A

DNA polymerase cant start its activity

66
Q

Responsible for removal of primers

Take over DNAsynthesis by inserting 5’ to 3’ polymerase function

A

DNA polymerase 1

67
Q

Utilizes energy from ATP

Synthesize a phosphodiesterbond to make it a one continous strand without breaks

A

Ligase

136
Q

Unwinding and primer formation

A

Initiation

137
Q

Formation of daughter DNA strands

A

Elongation

138
Q

Will separate the 2 strands

A

Helicase

139
Q

Keeps the 2 strand apart from each other

A

Single strand binding protein

140
Q

Primary responsible for the synthesis of leading strand

A

DNA polymerase 3

141
Q

Synthesis of leading strand

A

Requires primers
5’to3’ direction
Synthesis is continous
DNA grows towards the direction of the replication pork

142
Q

Synthesis of the lagging strand

A

Requires multiple primers
5’ to 3’
Discontinuous resulting to the formation of okazaki fragments
DNA goes away from the replication fork

143
Q

Enzyme responsible for initial synthesis of the okazaki fragment

A

DNA polymerase 3

144
Q

Remove primers

A

DNA polymerase 1

145
Q

Connect adjacent okazaki fragments after the primers have been taken out

A

Ligase

146
Q

Mechanism that make sure that the replication porks meet at the other end simultaneously

A

Termination utilization substance

147
Q

Difference between eukaryotic and prokaryotic DNA replication

A

Prokaryotic- single origin

  • DNA polymerase 2 creates both strands
  • supercoiling

Eukaryotic- multiple origin

  • DNA polymerase alpha for leading strand and delta for lagging strand
  • supercoiling and telomere shortening
148
Q

Problem associated primarily with prokaryotic replication

A

Supercoiling

149
Q

Solution for supercoiling

A

Topoisomerase

150
Q

Problem associated with linear DNA replication

A

Telomere shortening

Because there is no 3’ for OH no attachment site

151
Q

Solution for telomere shortening

A

Telomerase

152
Q

How do we solved that 3 overhand

A

T loop, dahil sa telomerase

153
Q

It synthesize DNA utilizing an RNA template

A

hTRT human telomerase

154
Q

New strand is longer than the original one. Extra sequences have been introduced.

A

Replication slippage example huntingtons disease

155
Q

Change in nucleotide sequence

A

Mutation by UV light

156
Q

Happens on the 3rd base of the codon
Usually codes for the same amino acid
Least dangerous

A

Silent mutation

157
Q

Change in the base, change in the amino acid

A

Missense mutation

Sickle cell anemia

158
Q

Amino acids become stop codon

A

Nonsense mutation

Most severe

159
Q

Opposite of nonsense mutation

Stop codon to an amino acid

A

Readthrough mutation

160
Q

Type of mutation

A

Substitution
Deletion
Insertion

161
Q

A deletion mutation can result to frameshift with removal of

A

1,2 or 4 amino acids

No frameshift if the removal of 3 bases or any multiples of 3

162
Q

Consequences of mutation

A

Disease
Silent- if mutation happen in the spacer DNA
Evolution

163
Q

DNA repair system

A

Base excision
Nucleotide excision
Mismatch repair

164
Q

Damage base

A

AP site

165
Q

Recognize AP site and remove its base

A

DNA glycosylase

166
Q

Removes AP site and neighboring nucleotides

A

AP endonuclease

167
Q

Involved in removing damaged nucleotides

A

UvrA
UvrB
UvrC

168
Q

Mismatch repair is very expensive. Enzyme involve

A

Helicase 2
SSB protein
DNa polymerase 3
Ligase

169
Q

Synthesis of RNA utilizing DNA as the template

A

Transcription

170
Q

Not all forms of DNA can be transcribed, only certain stretches and this called

A

Gene

171
Q

Enzyme used in transcription

A

RNA polymerase

172
Q

Synthesis of RNA 3 major steps

A

Initiation
Elongation
Termination

173
Q

Works to inhibit the RNA polymerase

A

Rifampisin

174
Q

Initial binding site for RNA polymerase

A

Promoter region

175
Q

Parts of the gene that being transcribed

A

Promoter region
Informative sequence
Terminator sequence

176
Q

Other name for promoter region

A

Tata box
Pribnow box
GC box
Hogness box

177
Q

This is the actual transcription site, ito talaga yung itatranscribe

A

Informative region

178
Q

2 strand from DNA

A

Template

Coding strand

179
Q

When the RNA polymerase has reached this region of the gene, transcription has to end

A

Terminator sequence

180
Q

Allows hairpin loop formation on mRNA

A

GC rich region

181
Q

RNA polymerase with sigma factor locate promoter region

A

Closed promoter complex

182
Q

RNA polymerase will also act as helicase, the 2 strand separated is now called

A

Open promoter complex

183
Q

When RNA polymerase locate the first base it will now

A

Start synthesize RNA

184
Q

While the polymerase unwinds the DNA, after the DNA has been used as template, there is an

A

Automatic rewinding

185
Q

In the RNA, the sequence will be CG,CG,CG which has what is known as

A

Self complimentarity

186
Q

Remember, in the terminator sequence, the sequence is

A

GC,GC,GC

187
Q

There will be hair pin loop formation

A

Poly A for DNA

Poly U for RNA

188
Q

Alternative ending, a protein which comes in and separates the RNA from DNA template

A

Rho Factor

189
Q

Transcription in eukaryote

A

3 types of RNA polymerase
Not just promoter region
RNA Is not ready for use
Transcription and translation not coupled together

190
Q

Eukaryotic transcription

Code for RNA and protein as well
These are sequence that are transcribe and translate

A

Exons

191
Q

Eukaryotic transcription

Code for RNA but do not code for protein.
Transcribe but not translate

A

Introns

192
Q

Eukaryotic transcription

Types of RNA polymerase

A

RNAP 1,2,3

193
Q

Eukaryotic transcription

Transcribe all ribosomal RNA with the exception of 5S

A

RNAP 1

194
Q

Eukaryotic transcription

Transcribes mRNA

A

RNAP 2

195
Q

Eukaryotic transcription

Transcribe tRNA including 5S

A

RNAP 3

196
Q

This will render the gene silent and cannot be expressed

A

Methylation of CpG islands

197
Q

Example of how activators and repressors work together to control expression of the lactase gene

A

Lac operon

198
Q

DNA is released so that it is not anymore lightly packed

A

Acetylation of nucleosome

199
Q

Smallest
Adaptor molecule
T loop

A

tRNA

200
Q

Complimentary to the codon in mRNA

A

Anti codon loop

201
Q

Where amino acids are artached

A

Acceptor arm

202
Q

Largest
Most abundant
Found in ribosome
Ginger like

A

rRNA

203
Q

Has P site, A site and mRNA bunding site

A

Small ribosomal sub unit

204
Q

The one where it has the enzyme peptidyl tranferase

A

Large ribosomal sub unit

205
Q

tRNA
RNA
AA

A

P site
M ribosomal binding site
A site

206
Q

The synthesis of protein utilizing as mRNA as template

Begins at the start codon and ends when the stop codon reached

A

Translation

207
Q

Template that determines the sequence of the amino acids

A

mRNA

208
Q

The one that brings the amino acid there

A

tRNA

209
Q

It is where it will all.

It is ribosomes catalyzes peptide bond formation

A

rRNA

Biochem Finals Fatima (6 decks)

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