Cell And Molecular Biology

Front 1

What makes an acid?

Back 1

Hydrogen donors (+) charge

Front 2

Bond length of H-H

Back 2

0.074 nm

Front 3

Bond length of H-C

Back 3

0.109 nm

Front 4

Bond length of C-C

Back 4

0.154 nm

Front 5

Bond length of C=C

Back 5

0.134 nm

Front 6

Bond length of C---C (triple bond)

Back 6

0.120nm

Front 7

Diameter of DNA?

Back 7

2nm

Front 8

Distance between 2 bases?

Back 8

6A

Front 9

Diameter of H2O?

Back 9

2.7 A

Front 10

What degree is the major groove?

Back 10

240 degrees

Front 11

What degree is the minor groove?

Back 11

120 degrees

Front 12

Where do proteins bind to in DNA to get information in order to recognize DNA to replicate it?

Back 12

Bind at the floor of the DNA grooves, using hydrogen bonds

Front 13

What is the rule to determine what percentage of other bases there are if you already know one percentage?

Back 13

Chargaff's rule

Front 14

Each nucleosome associates with how many base pairs of DNA?

Back 14

~150 bp

Front 15

How big is a DNA helix?

Back 15

2nm

Front 16

How big is a nucleosome?

Back 16

10nm

Front 17

How big is a chromatin fiber?

Back 17

30 nm

Front 18

How big is are looped domains?

Back 18

300 nm

Front 19

How big are heterochromatins?

Back 19

700 nm

Front 20

How big is a chromosome?

Back 20

1400nm

Front 21

What is the packing ratio for chromosomes during cell division?

Back 21

15,000-20,000

Front 22

What is oxidation?

Back 22

Lose electrons to other molecules, releases energy

Front 23

is a hydrogen bond covalent or not?

Back 23

non covalent

Front 24

What is a nucleoside?

Back 24

Sugar and base

Front 25

What is a 3'5' phosphodiester bridge?

Back 25

Phosphate group linked to 2 adjacent nucleotides via 2 phosophoester bonds

Front 26

What is a condensation reaction?

Back 26

Chemical reaction that results in joining of 2 molecules by removal of H2O molecule.

Front 27

What is an example of a condensation reaction?

Back 27

Phosphodiester bond in nucleic acids

Front 28

What is a hydrolysis reaction?

Back 28

Cleavage of chemical bonds by the addition of water.

Front 29

What is an example of a hydrolysis reaction?

Back 29

Breaking bonds between phosphate groups in ATP

Front 30

Condensation reaction between an acid and an alcohol?

Back 30

Ester bond

Front 31

Condensation reaction between an acid and an acid?

Back 31

Anhydride bond

Front 32

A single molecule of H20 can form non covalent bonds with how many other water molecules?

Back 32

4

Front 33

What is the name of each type of protein?

Back 33

H2A, H2B, H3, H4

And there are 2 of each one. And one linker protein called H1

Front 34

What is a glycosidic bond?

Back 34

A sugar with a base

Front 35

What is a nucleotide?

Back 35

base+sugar+phosphate

Front 36

Where is the (-) Charge in the DNA?

Back 36

phosphate linkage between base makes (-) charge

Front 37

What kinds of bonds connect single nucleotides into a nucleic acid polymer?

Back 37

-2 ester linkages

Phosphodiester bonds

Front 38

RNA has OH, or H in the 2nd carbon?

Back 38

RNA has OH on the second carbon

Front 39

Which one, amine or amide is NR3+?

Back 39

Amine

Amide is a "peptide bond"

Front 40

Why is there a twist in the DNA helix?

Back 40

The phosphate sugar backbone is hydrophilic while the base interior is hydrophobic. This allows the bases to stack more closely which also closes up holes so that water can't touch the bases.

Also the twist is inherent in the DNA itself and the bond angle with the phosphate.

Front 41

What does chargaffs rule state?

Back 41

Any cell of all organisms should have a 1:1 ratio of pyrimidine and purine bases. (base pair rule)

Front 42

What is the difference between a cow and a bacterias DNA?

Back 42

Bacteria is small, circular, denatures fast once started, and only has a single copy

Cows are repeated quickly and then non repeated and go from fast to slow.

Front 43

Eukaryotic DNA is wrapped around a set of proteins called?

Back 43

nucleosome

Front 44

All DNA and associated protein is in what?

Back 44

A chromatin

Front 45

What is the diameter of a nucleus?

Back 45

6 micrometers

Front 46

Where are chromosomes?

Back 46

all DNA in the nucleus

Front 47

Cells that are continually dividing are said to be what?

Back 47

cycling

Front 48

What are the phases of mitosis?

Back 48

Prophase

Prometaphase

Metaphase

Anaphase

Telophase

Cytokinesis

Front 49

what are alpha and beta tubulins together called?

Back 49

A heterodimer

Which means 2 proteins

Front 50

How many protofilaments in a microtubule?

Back 50

13

Front 51

What is dynamic instability of microtubules cause by?

Back 51

rapid cycles of growth and shrinkage

Front 52

Growth and shrinkage rate depends on what?

Back 52

1. compare tubulin dimers added on 2. Rate DTP is hydrolyzed by beta tubulin

Front 53

How is Beta tubulin hydrolyzed?

Back 53

GTP=GDP+P2

Front 54

What is rescue?

Back 54

GTP hydrolyze to GDP=microtubule grows

Front 55

What is catastrophe?

Back 55

rate of new tubulin dimer slows GTP on cap because hydrolyzed to GDP before a new dimer is added, microtubule comes apart

Front 56

when has a cell reached metaphase?

Back 56

When the chromosomes are on the equator the metaphase plate

Front 57

When has the cell left metaphase and entered anaphase?

Back 57

When the sister chromatids seperate

Front 58

What forces control chromosome movements?

Back 58

Motor proteins

Front 59

Which cell organelles have their own DNA?

Back 59

mitochondria and cytoplasm

Front 60

Which cell organelle packages and processes proteins?

Back 60

Golgi apparatus

Front 61

What is mm?

Back 61

10^-3

Front 62

What is micrometers?

Back 62

10^-6

Front 63

What is nanometers?

Back 63

10^-9

Front 64

What is angstroms?

Back 64

10^-10

Front 65

What is pm?

Back 65

10^-12

Front 66

functional group: alcohol

Back 66

:)

Front 67

Functional group: carboxyl

Back 67

:)

Front 68

Functional group: carbonyl

Back 68

:)

Front 69

Functional group: ketone

Back 69

:)

Front 70

Functional group: aldehyde

Back 70

:)

Front 71

Functional group: Phosphate

Back 71

:)

Front 72

Functional group: hydroxyl

Back 72

:)

Front 73

Functional group: thiol (sulfhydrl)

Back 73

:)

Front 74

Ether bond

Back 74

:)

Front 75

Ester bond

Back 75

:)

Front 76

Phosphoester bond

Back 76

:)

Front 77

Anhydride bond

Back 77

:)

Front 78

Phosphoanhydride bond

Back 78

:)

Front 79

glycosidic bond

Back 79

:)

Front 80

Approximate length of a non-covalent hydrogen bond

Back 80

1.5-2.5 A

Front 81

What is the bond energy for a H-H bond?

Back 81

435 kJ/mol

Front 82

What is the bond energy for a H-C bond?

Back 82

414 kJ/mol

Front 83

What is the bond energy for a C-C bond?

Back 83

331 kJ/mol

Front 84

What is the bond energy for a C--C bond?

Back 84

590 kJ/mol

Front 85

What is the bond energy for a C---C bond?

Back 85

812 kJ/mol

Front 86

Draw a ribose

Back 86

:)

Front 87

Draw a 2'-deoxyribose

Back 87

:)

Front 88

Draw an alpha-D-ribose

Back 88

:)

Front 89

Draw a beta-D-ribofuranose

Back 89

:)

Front 90

Draw an adenine

Back 90

:)

Front 91

Draw a guanine

Back 91

:)

Front 92

Draw a cytosine

Back 92

:)

Front 93

Draw a uracil (RNA)

Back 93

:)

Front 94

Draw a thymine (DNA)

Back 94

:)

Front 95

Draw adenosine

Back 95

:)

Front 96

Draw guanosine

Back 96

:)

Front 97

Draw Cytidine

Back 97

:)

Front 98

Draw uridine

Back 98

:)

Front 99

Draw deoxyadenosine

Back 99

:)

Front 100

Draw cytidine monophosphate

Back 100

:)

Front 101

Draw deoxyadenosine triphosphate

Back 101

:)

Front 102

What is the name of each type of protein in a nucleosome?

Back 102

H2A, H2B, H3, H4 two of each of those and a linker protein called histone 1 that links 8 proteins together

Front 103

Draw 5' GUA 3'

Back 103

:)

Front 104

Distance along a DNA helix per turn

Back 104

10 base pairs, 3.4 nm length

Front 105

Distance along the helix from one base to the next

Back 105

0.34 nm

Front 106

Distance between sugars

Back 106

6 A

Front 107

Why is there a major and minor groove?

Back 107

from the overall geometry of the Watson-Crick base-pair. from the offset pairing of the two strands in the helix. if the glycosidic bonds stuck straight out at 90 angles on both sides, then the grooves in DNA would be symmetrical. Because the glycosidic bonds are at an angle (relative to the interface between the AT or GC pairs), one of the "faces" of the base pair is larger than the other.

Front 108

Why do DNA binding proteins to interact with the bases (the internal parts of the DNA molecule) on the major groove side?

Back 108

Because the backbones are not in the way, more space, access base, more information

Front 109

How do you know which is a major and which is a minor groove?

Back 109

The major groove occurs where the backbones are far apart, the minor groove occurs where they are close together.

Front 110

Where do Proteins bind to in the grooves?

Back 110

At the floor of the DNA grooves, using hydrogen bonds

Front 111

Why does the absorbance increase as the number of double standed DNA become single stranded DNA?

Back 111

UV absorbance of DNA solution increases because many bases are in free form and do not form hydrogen bonds with complementary bases.

Front 112

What is hyperchromic shift?

Back 112

The phenomenon of UV absorbance increasing as DNA is denatured

Front 113

If DNA is rich in C-G pairs, what happens to melting point?

Back 113

It increases because C-G pairs have 3 hydrogen bonds more stability, more heat needed to break apart.

Front 114

Do different DNA renature at different concentrations over different spans of time?

Back 114

yes

Front 115

Cool DNA to what degree to have a nucleation even and "zip up" renatured DNA?

Back 115

20˚

Front 116

What are the main differences between Prokaryotic and Eukaryotic DNA packaging

Back 116

Prokaryotes- much smaller genome, package into nucleoid area by DNA Gyrase.

Eukaryotes- much larger genome, package DNA into chromatin, Histones proteins

Front 117

How are the proteins different in prokaryotes and eukaryotes?

Back 117

Prokaryotes - nucleoid - assiciated proteins <- formed looped structures, circular

Eukaryotes - Histones <-tight coiling = linear structure

Front 118

How does DNA wrap around histones?

Back 118

The histones are positively charged and so the negative charged DNA wraps around it in a specific conformation

Front 119

What is a nucleosome

Back 119

Consists of 8 histone proteins connected by a linker protein with DNA sequence wrapped around the 8 histone proteins

Front 120

Draw, label, explain the cell cycle

Back 120

:)

Front 121

Draw, label, and explain mitosis and the events that define each phase

Back 121

:)

Front 122

What is the kinetochore and its function?

Back 122

Set of proteins on the surface of the centromere. Appears on chromatids during cell division. Purpose: It allows spindle fibers to attach to it and pull apart chromatids.

Front 123

Draw, label, explain mitotic spindle, including microtubule polarity, all microtubule types, and involved microtubule motors

Back 123

:)

Front 124

Diameter of a microtubule?

Back 124

25 nm

Front 125

Length of 2 tubulins together (alpha/beta tubulin)

Back 125

8nm

Front 126

Diameter of inside of microtubule?

Back 126

15 nm

Front 127

General function of microtubules?

Back 127

transportation- routes organelles move through the cell

Form structures such as cilia and flagella

Front 128

Function of microtubules in mitosis?

Back 128

Provides the "road" for motor proteins to "walk"

Front 129

What do astral microtubules do?

Back 129

anchor the whole spindle apparatus along the axis of cell division.

Front 130

What do polar microtubules do?

Back 130

pushing the spindle apparatus apart during mitosis.

Front 131

What do kinetochore microtubules do?

Back 131

attach to kinetochore

Front 132

How do microtubules assemble?

Back 132

From tubulin heterodimers -> oligomers -> linear protofiliment -> sheet of 13 protofiliments -> closing microtubule -> elongating microtubule.

Front 133

In microtubules, is the (+) end the top or bottom?

Back 133

Top

Front 134

Alpha or beta tubulin gets hydrolyzed?

Back 134

Beta-tubulin, on top

Front 135

What are centrosomes for relating to microtubules?

Back 135

Initiation site for assembly of microtubules

Front 136

How are microtubules oriented in animal cells?

Back 136

What are you asking?

Centrioles are right angles to each other

Front 137

Describe chromosome movement during mitosis

Back 137

:)

Front 138

interpret a thermal denaturation or renaturation profile

Back 138

:)

Front 139

Requirements for DNA replication in the cell (enzymes) (6)

and what do they do?

Back 139

DNA ligase - connect okazaki fragments together

Helicase - unwinds DNA

DNA gyrase - topisomere - relieves overwound DNA from helicase

Primase- Makes RNA Primer - Provide free 3' hydroxyl.

Single stranded biding protein - Prevents DNA strands from getting back together again

DNA polymerase III - Makes new strand of DNA - adds deoxyribonucleotides to end of RNA primer

DNA polymerase I - replaces RNA primer with DNA

dNTPs (dATP, dGTP, dCTP, dTTP)

Front 140

Requirements for DNA replication in the lab (reagents and enzymes)

And what do they do?

Back 140

DNA template

Heat - to denature strands

MgCl2 - To provide free ions for DNA polymerase?

dNTP - to provide stock of dATP, dGTP, dCTP, dTTP

Buffer - to regulate ph and salinity conditions for enzyme

enzyme - DNA polymerase - Taq polymerase - To place DNA on template

Front 141

How long are okazaki fragments for prokaryotes?

Back 141

~1000 nucleotides

Front 142

How long are okasaki fragments for eukaryotes?

Back 142

~100-200 nucleotides

Front 143

How are type 1 and type 2 topoisomerases different?

Back 143

Type 1 - single stranded break in DNA back bone

Type 2 - double stranded break in DNA backbone

Front 144

Why do you need ligase?

Back 144

Because Polymerase I can't make the connection because there is no triphosphate

Front 145

In what direction is leading and lagging strand synthesized?

Back 145

5'-3'

Front 146

What are telomeres?

Back 146

Forms caps at the end of chromoromes, contain a unique DNA sequence which is repeated several times.

Front 147

What enzyme is responsible for providing a template for the template strand?

Back 147

Telomerase

Front 148

How long is the average human chromosome?

Back 148

IDK

Front 149

Rate of eukaryotic DNA polymerase?

Back 149

IDK

Front 150

Where does replication occur?

Back 150

Origins of replication (ORI)

Front 151

ORI in eukaryotes every how many b?

Back 151

50-300 kb

Front 152

What is ORC?

Back 152

Origin recognition complex

Front 153

Bacteria synthesizes DNA how fast?

Back 153

1,000 bases/sec