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Lecture 5 Flashcards

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1
Q

[Year] - [Scientist] concept of hereditary factor
-chemical composition was not yet known and understood

A

1865 - Gregor Mendel

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2
Q

[1930] - [Scientist]
2 view points about genes
1. Gene is just a hypothetical entity
2. Gene could be a chemical compound

A

R.A. Fisher

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3
Q

What are the three components that make up the chemical composition of a chromosome

A

Lipids, Proteins, and Nucleid

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4
Q

A component of chromosome found in interphase chromosomes, metaphase chromosomes, and nucleic matrix

A

Lipids

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5
Q

A type of protein which is responsible for packing the DNA (chromatid-chromosome)

A

Histones or Protamines

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6
Q

a type of protein that make up the scaffold upon which chromatin loops are anchored

A

Non-histone chromosomal protein

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7
Q

2 types of nucleic acid

A

DNA (deoxyribonucleic acid)
RNA (ribonucleic acid)

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8
Q

DNA is the genetic material of all living organisms except for some _____

A

Viruses

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9
Q

genetic material of some viruses

A

RNA

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10
Q

What are the characteristics of a good genetic material according to H.J Miller

A
  1. Contain all the necessary biological information
  2. Mutation is duplicated
  3. Stable molecular structure with low frequency of mutation
  4. Can transmit information from one generation to another
  5. Stored information must be decoded and translated into action
  6. Can duplicate itself with extra fidelity
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11
Q

DNA can duplicate itself with extra fidelity, how many identical copies are produced during 1 round of replication that can be distributed during M phase?

A

2 identical copies

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12
Q

T or F: Mutation is not inherited and is no a source of variation

A

F: Opposite

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13
Q

1830s
Proteins: ___________
Proteios: “______”

A

Proteins: most important molecule
Proteios: “of first importance”

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14
Q

1860s F. Miescher
-Isolated molecule from nucleus: _______ while characterizing proteins from ______

A

nuclein
pus cells

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15
Q

1866 E. Haeckel
Discovered: most obvious cellular component of the cell is the

A

nucleus

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16
Q

1895 E. Wilson
Observed: important nuclear element handed from one cell to another cell is the ________

A

DNA

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17
Q

1928 F. Griffith
Conducted _______ experiment using Streptococcus pneumoniae
Two strains: _______ (R) stain and ______ (S) strain

A

transformation
Avirulent (R) stain and Virulent (S) stain

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18
Q

In 1928 during the transformation experiment of F. Griffith different set up showed that the _____ stain transformed into the _______ stain which declared the presence of the transforming principle

A

R stain transfromed into the S stai

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19
Q

what is transformation?

A

uptake of genetic material from the surroundings

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20
Q

Heat kills virulence of S cells. When injected to the mouse, it cause the mouse to become healthy. However, when mixed with living R cells, what occurs which cause the mouse to die?

A

transformation of R cells into S cells

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21
Q

1944 O. Avery, C. Macleod, and M. McCarty
identified the transforming principle (TP) as ______

A

DNA

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22
Q

1944 O. Avery, C. Macleod, and M. McCarty
When the transforming principle was treated with proteinases and RNAses ______________ retains hence TP is not protein nor RNA

A

transforming ability

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23
Q

1944 O. Avery, C. Macleod, and M. McCarty
When TP was treated to remove protein and RNA, the composition of substance left _________________ of ____________

A

matched composition of DNA

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24
Q

1952 A. Hershey and M. Chase
Proved: DNA is genetic material of ____________ (phages)
DNA is labeled with P32 while the protein coat is labeled with S35

A

bacterial viruses

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25
Q

What is the blender experiment?

A

Blender separates phages from bacteria after infection
P32 label was present in bacteria after phase infection
-Proves that DNA is injected into cell while protein coat remained outside

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26
Q

1952 N. Zinder, J. E. Lederberg
Performed __________ experiment on Salmonella typhimurium

A

transduction

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27
Q

What is transduction?

A

process wherein bacterial cell can take up DNA through recombination that was introduced by phages
-injection of DNA to the bacterial cell through phages

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28
Q

Main contributors of the elucidation of the DNA structure in 1953

A

F. Crick, J. Watson, R. Franklin, M. Wilkins

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29
Q

F. Crick
involved in development of ___________ and ______________
PHD: Xray studies on proteins

A

radar and magnetic mimes

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30
Q

J. Watson
-Child prodigy
-Did labeling of _________

A

phage DNA

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31
Q

M. Wilkins
-Worked on _________ of DNA

A

Xray diffraction

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32
Q

R. Franklin
-Expert on Xray diffraction technique
-Worked on Xray diffarction of DNA
-Captured famous _________ showing xray diffraction - provided essential information for developing a model of DNA

A

photograph 51

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33
Q

who shared the photo 51 and research to Crick and Watson without Franklin Knowing?

A

Wilkins

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34
Q

a process wherein xrays are projected towards a substance and the atoms in the substance would deflect the rays and create an image produced by the DNA molecule

A

Xray Diffraction

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35
Q

1951-1952 R. Franklin, Gosling, & M. Wilkins
-______ DNA structure (orientation)
-Sugar and Phosphate _______ (where)
-Nucleotides ______ (where)

A

helical
outside
inside

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36
Q

1953 J. Watson and F. Crick
________ helix (Single, Double, Triple) - From Pauling
Phosphate in __ (where) Fr

A

Triple
Center

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37
Q

early 1950
L. Pauling
_______ helix DNA (Single, Double, Triple)

A

Triple

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38
Q

J. Griffith
Nucleotides are ______ (shape) and placed _______ of each other
Calculations show possiblity of base pairing between A and T and C and G

A

Flat; atop

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39
Q

E. Chargaff
DNA of all cells contained ____ amounts of A and T and _____ amounts of C and G

A

equal

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40
Q

Chargaff’s Rule: Ratio of purine-pyrimidine is ______
evidence for specific pairing

A

1:1

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41
Q

J. Donohue
-________ in the bases can change its position
-Possibility for ________ bonding

A

H (hydrogen)
Hydrogen

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42
Q

DNA
molecular basis of ________-
_______ of all living organisms
double helix structure composed of a __________ backbone and ________ on the inside

A

heredity
genetic material
sugar-phosphate; base pairs or nitrogenous bases on the inside

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43
Q

DNA is a ____________ polymer with deoxyribonucleotides

A

nucleic acid

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44
Q

what are the monomers of DNA or nucleic acid

A

nucleotides

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45
Q

bonds that connect nucleotides

A

phosphodiester bonds

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46
Q

nucleoside is composed of two which are

A

sugar and nitrogen base

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47
Q

what is the sugar of DNA?

A

2-deoxyribose

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48
Q

Purines nitrogen bases

A

Guanine and Adenine (PUGA)

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49
Q

Pyrimidine Nitrogen Bases

A

Cytosine and Thymine (Not PUGA)

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50
Q

A nucleotide contains three which are

A

Phosphate Group
Sugar
Nitrogen Bases

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51
Q

give the negative charge of the DNA

A

Phosphate Group

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52
Q

Important for coiling into condensed structure; component of the DNA

A

phosphate group

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53
Q

what is the charge of histones?

A

Positive (they are positively charged proteins)

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54
Q

proteins that bind to DNA to coil it

A

histones

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55
Q

the sugar molecule, 2-deoxyribose is connected to the SUGAR molecule through a bond called

A

phosphoester bond

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56
Q

the sugar molecule, 2-deoxyribose is connected to the nitrogenous bases through a bond called

A

Beta-N-glycosidic bond or simply just glycosidic bond

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57
Q

difference between the sugar of DNA and RNA

A

DNA - nucleotide has 2 deoxyribose
RNA - only ribose sugar

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58
Q

no. of rings of
purine: ___________
pyrimidine: ________

A

purine: 1 ring
pyrimidine: 2 rings with the addition of U or Uracil

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59
Q

what is the bond between A and T

A

double bond

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60
Q

bond between C and G

A

triple bond

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61
Q

base pairs have similar structures: T or F?

A

True

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62
Q

Alphabet of DNA - our genes are written by alphabet that are represented by the _________ (component of a nucleotide)

A

nitrogen bases or base pairs

63
Q

bond between sugar and phosphate group and hydroxyl group (C-O-P-O-C)

A

phosphoester group

64
Q

bond between two nucleotides

A

phosphodiester bond

65
Q

bond that joins a carbohydrate (sugar) molecule to another group

A

glycosidic bond

66
Q

components of DNA that is constant in every molecule and found outside

A

sugar and phosphate group

67
Q

components of the DNA that is not constant in every DNA molecule and found inside

A

nitrogen bases

68
Q

who developed the Chargaff Rule

A

Erwin Chargaff

69
Q

Features of the DNA
1. It is composed of ________ polynucleotide stands connected via __________ of bases
2. Sugar:_________
3. Antiparallel - ______, ____
4. Complementary Specific Pairing
A pairs with T and C pairs with G
5. Forms a ______ colil (shape)

A
  1. 2; hydrogen bonding
  2. 2 deoxyribose
  3. 5’-3’, 3’-5’
  4. helical
70
Q

1 nm = ___ armstrong
how many nm are there in 78 armstrongs?

A

7.8

71
Q

Diameter of DNA molecule

A

2nm or 20 A

72
Q

how many base pairs are there in each turn of DNA

A

10 base pairs

73
Q

how many nm and armstrong in each turn of DNA

A

3.4 nm/34A

74
Q

For each base pair in a DNA, how many nm?

A

0.34nm

75
Q

two DNA strand are held together by

A

hydrogen bonds

76
Q

sugar phosphate backbone is held together by

A

phosphodiester bonds

77
Q

base stacking are done through ________

A

hydrophobic interactions

78
Q

are the nitrogen bases of the DNA polar or nonpolar?

A

nonpolar

79
Q

base stackings adds _____ to the entire molecule

A

stability

80
Q

the environment where the DNA can be found is hydrophobic/hydrophilic

A

hydrophilic

81
Q

direction of the DNA sequence

A

5’ to 3’ (parallel)

82
Q

in a DNA carbon 5 has an attachment of _______ and Carbon 3 has _____

A

Carbon 5: Phosphate
Carbon 3: OH

83
Q

Cells read DNA sequences from ____- to ________

A

5’ to 3’

84
Q

the sequence 5’-TGCA-3’ is not the same as5’-ACGT-3’ why is this so?

A

because the base pairs are different

85
Q

Is DNA a static molecule?

A

No, it is dynamic and change according to the needs of the cells

86
Q

most common conformation of the DNA

A

B-DNA
-RIGHT HANDED HELIX

87
Q

a type of conformation of DNA that is
right handed but much more compact
11 base pairs per turn
occurs in dehydrating conditions

A

A-DNA

88
Q

how many base pairs are there in A-DNA?

A

11 base pairs

89
Q

a type of DNA conformation that is
left handed
unstable experience: from when genes are transcribed and disappears through topoisomerase activity after the gene is no longer transribed

A

Z-DNA

90
Q

the left part of the DNA is in the _______ to _______ direction

A

5’ to 3’ (parallel)

91
Q

the right part of the DNA is in the __________ to _________ direction

A

3’ to 5’ (antiparellel)

92
Q

EVIDENCES THAT THE DNA IS THE GENETIC MATERIAL
1. Relative constancy of DNA in all ____ tissues
Starvation = DNA unchanged
2. ____ cells have half amount of DNA in diploid
3. Double of DNA content at ____ phase
4. Cells with extra sets of __l)____ have a propoirtional increase in DNA content
5. Parallelism of ________ absorption with mutation rates
6. ___________ AND _________ in bacteria (two processes discussed before)
7. Production of new ______ particles in bacterial cells
8. RNA content of TMV caused infection and not the ____ (Viruses can either have DNA/RNA as the genetic material)

A
  1. Diploid
  2. Haplod
  3. S phase
  4. chromosomes
  5. UV radiation
  6. Transformation and Transduction
  7. Viral/Virus
  8. protein coat
93
Q

what is the difference between Polyploidy and polyteny

A

Polyploidy - more number of chromosomes
Polyteny - more number of sister chromatids/chromatids

94
Q

All organisms have ____ as genetic material. However some viruses can have _______

A

DNA;RNA

95
Q

an RNA is composed of ________ polynucleotide strand (number)

A

1

96
Q

what is the sugar of RNA?

A

D-Ribose

97
Q

What is the difference between DNA and RNA when it comes to the attachment of oxygen of the ribose?

A

DNA - no oxygen attached in the deoxyribose
RNA -oxygen attached in the ribose

98
Q

flowchart of process for the DNA replication

A

2 strands - unwind/separate - base pair - production of 2 identical DNA

99
Q

What is the model of DNA replication?

A

semiconservative
-each daughter DNA contains one new strand and one old strand from parental template

100
Q

Grew E.coli: nitrogen source consisted of only 15NH4CL.
- 15N-containing cells were transferred to growth media
containing 14N isotopes
- After 1 cell division only one band was observed to
occur between where 15N-DNA and 14N-DNA bands
would normally appear
- RESULT: new DNA was a hybrid molecule containing
15N strand and 14N strand
- After 2 cell division:
- 2 discrete bands: 1 made of 14N- 14N DNA an

A

Meselson and Stahl Experiment

101
Q

a model of DNA replication where the parental double helix remains INTACT and a second, all new-copy is made

A

Conservative model (k: INTACT)

102
Q

a model of DNA replication where the two strands of the parental molecule separate and each functions as a TEMPLATE

A

Semiconservative model (k:TEMPLATE)

103
Q

a model of DNA replication where each strand of both daughter molecules contain a MIXTURE of old and new synthesized parts

A

dispersive model (k: MIXTURE)

104
Q

initiation starts with_______ (origin of replication)
typically has a lot of ___ pairings
-The are easier to break due to only having ____ h bonds (no.)
-There are multiple origins in the cell happening at the same time
-Formation of ___ stranded DNA templates

A

orisite
A-T
2
single

105
Q

Proteins or Enzymes in Initation

A

Helicase
SSBPS (single stranded binding proteins)
DNA gyrase/Topoisomerase

106
Q

an enzyme in initiation which separate 2 strands of DNA

A

Helicase

107
Q

a protein in iniation which maintains the 2 single stranded templates
-protects it from enzymes like nucleases that breaks phosphodiester bonds

A

SSBPS(SINGLE STRANDED BINDING PROTEINS)

108
Q

an enyzme in initiation which is needed to relax tension brought by the unbinding of DNA at the fork
nuclease domain: cuts DNA
ligase domain: restitches cut area

A

DNA gyrase

109
Q

key enzyme for replication

A

DNA polymerase

110
Q

main enzyme that catalyzes the synthesis of new strands, adds DNA nucleotides to primer

A

DNA polymerase

111
Q

enzyme that dominantly adds DNA nucleotides to primer

A

DNA polymerase

112
Q

where are nucleotides added? 5’ or 3’

A

3’ end

113
Q

in Elongation and Replication you need a RNA ___ to proceed

A

primer

114
Q

synthesis of DNA strand is always in the ___ to ____ direction

A

5’ to 3’ direction

115
Q

an enzyme that adds RNA primer in elongation

A

primase

116
Q

direction of the leading strand

A

3’ tp 5’ parental strand (antiparallel)
K: 3 LEAD

117
Q

How many primer is needed in the leading strand? since it can synthesize continuously

A

1 RNA primer only

118
Q

Leading strand
Eukaryotes: 11 +/-1 nucleotides long
Prokaryotes - 10 - 60 nucleotides long

A

number of nucleotides in leading strand

119
Q

In leading and lagging strand the direction for the following are always:
Proofreading -
Synthesis -

A

Proofreading: 3’ to 5’
Synthesis - 5’ to 3’

120
Q

direction of the lagging strand

A

DNA Pol III: 5’ to 3’ parental strand direction

121
Q

direction of the lagging strand

A

DNA Pol III: 5’ to 3’ parental strand direction

122
Q

lagging strand requires ____ primers (adverb of quantity) since they cannot synthesize continuously

A

several/many/ a lot

123
Q

Okazaki fragments:
Prokaryotes - approx. 1000 - 2000 nucleotides long
Eukaryotes - approx 100 to 200 nucleotides long

A

no. of okazaki fragments in lagging strand
K: thousands first 1-2
hundreds 1-2

124
Q

enzymes and proteins in Elongation

A

DNA polymerase
Primase
DNA Pol I
Ligase

125
Q

enzyme that removes RNA primers and fills gap left by primers since RNA primase cannot stay in DNA molecules

A

DNA Pol I: K: LEFT BY PRIMERS

126
Q

DNA POL I removes RNA primer in ____ direction exonuclease activty

A

5’3 direction K: remove and synthesize direction 5’ to 3’ same lang

127
Q

what is the indicator that replication will now terminate?
-can be initiated by protein for termination or because of structure of replication site

A

when 2 identical molecules are produced

128
Q

this is released when nucleoside triphosphate binds with OH end, releasing 2 phosphates

A

Pyrophosphate

129
Q

The simultaneous syntehsis of leading and lagging strands (new model or looping) is catalyzed by the enzyme

A

replisome

130
Q

replisome is composed of DNA pol III (enzyme) which acts as pairs with 2 catalytic cores: primosome (____ + ____)

A

helicase + primase (K: HP Laptop)

131
Q

when do telomeres get shorter?

A

as DNA replicates repeatedly through our lives

132
Q

what END of the DNA is molecule is the longer side 3’ or 5’?

A

3’

133
Q

Telomeres (do/do not) code for RNA genes to prevent gene loss

A

do not code

134
Q

Upon splitting, DNA polymerase cannot add at the complementary strand with extended and because there is no free ___ end

A

3’ OH end

135
Q

this refer to the maximum amount of times the DNA can replicate before genes can become affected (shortening of telomeres)

A

Hayflick Limit

136
Q

enyzme that lengthens telomere of linear ends
-complex of proteins and RNA templates

A

Telomerase

137
Q

telomerase elongate the ____ end used to extend other strand

A

3’ end

138
Q

what is the common telomore end in nucleotides?

A

TTAGGG PAIRS WITH AAUCCC

139
Q

Significant of Replication
-faithful copying of DNA to produce 2 ___________ molecules
-identical to each other and ___ molecule
-transmit biological information from parent cell to daughter cells (generation to generation)
cell division cannot occur without replication of DNA

A

2 DNA molecules
parent molecule

140
Q

can cell divison occur without the replication of DNA?

A

NO

141
Q

Mechanism of High Precision Replication
1. Specificity of base pairing
2. Proof-reading ability of DNA polymerases
3. Excision/Removal repair mechanisms

A

Mechanism of High Precision Replication

142
Q

enzyme responsible for the repair of thymine dimer (thymine pairs with each other)
-excision and filing

A

Endonuclease

143
Q

enzyme responsible for the hydrolysis of bond between damaged base and sugar

A

N glucosidase activity

144
Q

Chromosome Organization
Prokaryotic Chromosome
Double Stranded
approx _____ um long or __ mm
-4x10^6 bp (1kb =1000bp)
-amount of DNA is approx. 1000x the length of E. Coli

A

11,000 um long or 1.1 mm

145
Q

which is longer in chromosome organization? Prokaryotic or Eukaryotic

A

Eukaryotic Chromosomes

146
Q

contains the genetic material of prokaryotes

A

nucleoid

147
Q

how many independent domains are there in the packing of prokaryotes

A

10 independent domains

148
Q

packing of prokaryotes contains about 10 independent domains
each loop is about ________ bp (40kb) of supercoiled DNA

A

40,000

149
Q

Packing of Prokaryotes
Histone like protein (protein _)
Protein for DNA packing (Protein _)

A

Histone like protein - protein Hu
Protein for DNA packing - Protein H

150
Q

how many chromosomes are there in a eukaryotic cell?

A

46

151
Q

what is the actual DNA LENGTH

A

6ft (from end to end)

152
Q

how many bp are there in a eukaryotic chromosome?

A

5500000000 (5.5x10^9)

153
Q

how many cm is 1 chromosome?

A

7.2 cm (0.01 mm length)

154
Q

Recite or discuss the chromosome packing

A

Nucleosome formation - DNA + histone proteins
Chromatosome formation - nucleosome + histone octamer
Solenoid Formation - 6 nucleosomes per coil which forms the chromatin thread 30 nm chromatin fiber
Loop formation which is 300 nmn in length

BIO 30 (9 decks)

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