Cell Test 3 - Do You Know It, Dingus?

Front 1

Where is DNA found in the chloroplast and mitochondria? What shape is it?

Back 1

Stroma of chloroplast, matrix of mitochondria, closed and circular

Front 2

What are Chargaff's rules?

Back 2

All members of species have same percentage of 4 bases

A%=T% and G%=C%

Front 3

Who performed studies using mice and bacteria, showing that transformation of non-pathogenic bacteria occured?

Back 3

Griffith

Front 4

Who injected mice with DNAse to prove that DNA was responsible for the transformation killing the mice?

Back 4

Avery

Front 5

Who determined that bacteriaphage inject DNA into their victim, not protein, using labeled S and P?

Back 5

Hershey-Chase

Front 6

Who got the first X-ray structure of DNA

Back 6

Rosalind Franklin

Front 7

Who determined the binding patterns of DNA

Back 7

Watson-Crick

Front 8

How many bonds to A/T and G/C have?

Back 8

2/3

Front 9

What are the basic characteristics of DNA structure?

Back 9

Antiparallel, right-handed double helix, sugar-phosphage backbone on the outside

Front 10

Which type of DNA is left-handed?

Back 10

Z

Front 11

What direction is positive supercoiling, and where is it seen to occur?

Back 11

In the same direction as the helix (right handed)

Compaction of DNA / Barr Bodies

Front 12

What direction is negative supercoiling, and where is it seen?

Back 12

Direction opposite to helical winding

DNA denaturation, transcriptino and replication

Front 13

What is responsible for supercoiling?

Back 13

Gyrase

Front 14

What is Tm?

Back 14

Point where 50% of DNA is separated. Higher if there is more G/C

Front 15

What are topoisomerases? Which type cuts 1 / 2 strands? Which type is gyrase?

Back 15

relieve overwinding due to supercoiling. Type 1 cuts 1 strand, type 2 cuts 2. Gyrase is type 2.

Front 16

Size of genomes?

Back 16

virals: 300 - 2.5mbp

Proks: 3E5 to 8mbp

plants: as big as 1E11

humans: 3E9

Front 17

What is the C-Value Paradox?

Back 17

The variance in genome size between organisms of similar complexity.

Front 18

What were restriction enzymes originally used for? How do they work?

Back 18

Bacterial antivirals.

Recognize recognitions sequences, cut them into restriction fragments.

Front 19

What charge is DNA and how does that work for Gel Electrophoresis? How can restriction enzymes be used with this?

Back 19

Negatively charged, pulled to positive end of battery. Restriction enzymes used to cut and make restriction map.

Front 20

5 Steps of southern blotting?

Back 20

Restriction cutting.

Electrophoresis.

Blotting.

Probing (Radioactive)

Autoradiography.

Front 21

What technique is mainly used for sequencing? How does it work?

Back 21

Sanger Dideoxy

fluroescently labels ddNTPs and watches the order in which they are sequenced. ddNTP prematurely cancels elongation of strand.

Front 22

What percentage of the genome is composed of tandem repeats? Where are they found and what function do they serve? What is the most important tandem repeat?

Back 22

10-15%

cluster around centromere, serve as attachment of spindle fibers during cell division.

telomeres are the most important tandem repeat. (TTAGGG)

Front 23

Which enzyme replaces telomeres? In which type of cells does this occur?

Back 23

Telomerase. Germ line cells.

Front 24

What are the various size categories of tandem repeats, and how are they used in forensics?

Back 24

Satellite: 1E5 - 1E7

minisatellite: 1E2 - 1E5

Microsatellite: 1-4bp repeats, up to 200 bp site

Individual variation allows for genome identification

Front 25

What are three disorders caused by tandem repeats?

Back 25

Huntington's

Fragile X

Myotonic Dystrophy

Front 26

What percentage of the genome is composed of interspersed repeated DNA?

Back 26

25-40%

Front 27

How is DNA packaged in Prokaryotes?

Back 27

negative supercoiling, wrapped around basic protein cores, in a NUCLEOID.

often attached to membrane or wall.

Front 28

What are typical genes found on plasmids, and how long do they take to replicate?

Back 28

fertility, antibiotic resistance, toxins

20 minutes

Front 29

How is DNA packaged in euks? Terms for loosely /tightly packed DNA?

Back 29

nucleosome beads formed by DNA and basic histone proteins held by ionic bonds. (H2a, 2b, 3, 4)

Histone 1 compacts beads into chromatin fibers, which are further looped by nonhistone proteins.

Euchromatin / Heterochromatin.

Front 30

How many membranes does the nuclear envelope have?

Back 30

2

Front 31

What is the name for the space between the nuclear membranes?

Back 31

perinuclear space

Front 32

What is a nuclear localization sequence?

Back 32

amino acid sequence which targets proteins to the nucleus

Front 33

What is the nuclear lamina?

Back 33

protein sheath lining the inside of the inner nuclear membrane.

Front 34

What is the role of the nucleolus?

Back 34

ribosome factory.

Front 35

What is the nucleolus organizer region (NOR)?

Back 35

rRNA gene repeat region

Front 36

How much time does cell replication take for mammals? How much of that time is mitosis?

Back 36

18-24 hours

1 hour

Front 37

What are the 3 stages of interphase, and their characteristics?

Back 37

G1: checkpoint with possible entry into G0

8-10 hours

S: DNA replication

6-8 hours

G2: another checkpoint

4-6 hours

Front 38

What cells are normally in G0?

Back 38

Neurons

hepatic cells

immune system cells

Front 39

What is the term for how DNA replicates? Who performed experiments to demonstrate it, and what heavy ion was used?

Back 39

Semiconservative

Meselson-Stahl

N15

Front 40

How many replication origins do bacteria have? Euks?

Back 40

1

many

Front 41

Detail Bacterial DNA replication initiation:

What's different for euks?

Back 41

initiator protein binds at origin

DNA unwinds

DNA polymerase accesses interior of helix

5-3 synthesis

Euks have multiple proteins, origin recognition complex, and multiple orgins of replication.

Front 42

What is the term for DNA polymerase with it's subunit molecules?

Back 42

holoenzyme

Front 43

What enzyme unwinds the DNA for replication?

is this energy dependent?

Back 43

helicase, yes

Front 44

Which DNA polymerase is used for replication in proks? euks?

Where are new NTPs added?

Back 44

DNA Pol III / alpha

3' OH

Front 45

What type of proofreading is done by most DNA pols?

Back 45

3-5 exonuclease

Front 46

How long are okazaki fragments?

Back 46

1-2 thousand ps for proks

1-10 of that for euks

Front 47

How long are RNA primers for DNA replication? Are they needed for each lagging strand fragment? What enzyme makesthem? What replaces them?

Back 47

1-10nt's

yes.

primase

DNA Pol I

Front 48

Explain the roles of these players in replication:

SSPs

topoisomerases

ligase

Back 48

hold strands apart

relieve tension from overwinding

Attach sections of DNA

Front 49

Is gyrase ahead or behind of the fork?

Back 49

ahead

Front 50

What causes the end gap problem?

Back 50

No 3' OH to replace primers

Front 51

What are the three stages of PCR?

What species provides the polymerase?

Back 51

denaturation

Annealing

Elongation

Thermus Aquaticus

Front 52

How does mismatch repair work? what type of problem does it fix?

How does it know which is the parent strand?

Back 52

Wrong nucleotide inserted

endonuclease nicks the backbone

exonuclease removes the bad boy

parent has methylated adenines

Front 53

How does Nucleotide Excision Repair work? What does it fix?

Which skin condition is associated with this mechanism?

Back 53

thymine dimers and bulky damage

single cuts on both sides of distortion by NER endonuclease

helicase unwinds DNA

DNA Pol fills in gap

ligase seals it

xeroderma pgmentosum

Front 54

How does Base Pair Excision work? What does it fix?

Back 54

Base cleaved off the sugar

endonuclease cuts on one side of sugar, removes it

Polymerase replaces it

Front 55

What are the 2 techniques for repairing double stranded breaks?

Back 55

Nonhomologous end joining: messy

Homologous recombination: uses other copy of chromosome for a map

Front 56

Main differences between uracil and thymine?

Back 56

Uracil is cheaper. Cytosine deaminates into it, so it would cause problems in DNA code. Thymine has addition CH3 group.

Front 57

What happens in prophase?

Back 57

chromosomes condense

sister chromatids held at centromeres

nucleolus vanishes

centrosomes move towards poles

Front 58

What happens in prometaphase:

Back 58

nuclear envelope disappears

kinetochore forms at centromeres, spindle fibers attach, begin to move

Front 59

How does tubulin subunit subtraction work?

Addition?

Back 59

subtracted from kinetochore microtubules, shortening them and pulling the chromosomes towards the poles.

Addition to polar microtubules pushes the poles apart.

Front 60

Where does ATP-dependent motor action happen in mitosis?

Back 60

Kinetochore and centrosome, pulls chromosomes towards centrosomes

pushes antiparallel microtubules apart

where astral microtubules attach centrosomes to cell cortex, pulls centrosomes to poles

Front 61

How does cytokinesis happen in animals? Plants?

Back 61

Cleavage: cleavage furrows form, contractile ring of actin and myosin causes pinching.

No cleavage: cell plate forms by mictrotubule array of phragmoplast which forms wall

Front 62

What does the checkpoing in mitosis check for?

Back 62

Makes sure all chromosomes are attached to spindle prior to anaphase

Front 63

What molecule rises and falls during the cell cycle, and helps trigger replication and mitosis and that?

Back 63

cyclins / Cdk proteins

Front 64

What are homologous chroosomes?

Back 64

Pairs of chromosomes (1 from each parent)

Front 65

Term for when both traits are expressed? Where is this seen?

Back 65

Codimance

AB blood type / Sickle cell

Front 66

Term for when trait is only present in one copy:

Back 66

hemizygous

Front 67

Which organisms are always haploid?

briefly diploid?

alternate generations?

Back 67

bacteria

fungi

mosses

Front 68

When does cross over occur?

Back 68

Pachytene stage of prophase 1

Front 69

At what stage in prophase 1 do duplicated homologous chromosomes begin to par as a tetrad? What is this process called? What is the complex called?

Back 69

zygotene

synapsis

synaptonemal complex

Front 70

What is chiasma? At what stage is it seen? At what point is it the only connection between the chromosomes?

Back 70

The visible part of crossover action.

diplotene.

diakinesis.

Front 71

What are the stages of prophase 1?

Back 71

leptotene

zygotene

pachytene

diplotene

diakinesis

Front 72

After meiosis 1, are cells haploid or diploid?

Back 72

haploid, but with duplicated chromosomes

Front 73

How many total polar bodies are formed?

Back 73

3

Front 74

When can nondisjunction occur?

Back 74

anapase 1: homologous chromosomes

anaphase 2: sister chromatids

Front 75

What is aneuploidy? Associated diseases?

Back 75

having a bad number of chromosomes

klinefelter, turner, downs

Front 76

What is a genetic chimera?

Back 76

when nondisjunction occurs in mitosis

Front 77

What was the result of Mendel's F1? F2?

Back 77

All the same phenotype (heterozygous)

1/4 vs 3/4 phenotypes

Front 78

Mendel's Laws:

Back 78

Inheritance is Discrete

2 alleles of gene are distinct

independent assortment

Front 79

5 parts of chromosomal theory of inheritance?

Back 79

Nuclei have pairs of homologous chrmosomes (one from each parent)

chromosomes retain individuality

parental chromosomes synapse

each member of homologous pair is functionally equivalent

parental members segregate independently

Front 80

What is a linkage group?

Back 80

genes with loci on same chromosome

Front 81

How is genetic mapping done?

Back 81

every 1% of recombination is used as a centimorgan distance unit.

Front 82

How does viral recombination occur?

Back 82

coinfection (often in pigs)

Front 83

What type of phage puts its genome into host genome? What are the implications of this?

Back 83

Transducing phage.

Transfer of host genome to next host is possible. Shigella toxin given to E. coli in this manner

Front 84

How does bacterial conjugation occur? What factor is necessary for this to occur? what are hfr cells?

Back 84

F+ donor cell forms F-pilus with F- acceptor, mating bridge is formed.

F-factor encoded on F-plasmid.

F-plasmid integrated into chromosome, cell is now capable of transferring genomic DNA during conjugation.

Front 85

Difference between transformation and transfection? What is electroporation?

Back 85

Transformation i with plasmids, cosmids, artificial chromosomes.

transfection is with phage or viral vectors.

electric current used to drive DNA into cells.

Front 86

Difference between genomic and cDNA libraries?

Back 86

genomic: full genome

cDNA: reverse transcriptase used to look at only the genes being expressed.

Front 87

what does agrobacterium tumiaciens do?

Back 87

puts Ti plasmid into plants that forms gall and lets it live. Useful for plant genetic modification.

Front 88

What are auxotrophs?

Back 88

mutants unable to grow without nutritional supplement

Front 89

What end of tRNA is charged with the amino acid?

Back 89

3'

Front 90

Role of:

snRNA

snoRNA

SRP rna

siRNA

Back 90

forms spliceosome

processing of rRNA transcripts in nucleus

signal peptide recognition of peptides targeted to RER

regulation of gene expression

Front 91

Which DNA strand is read when making the RNA? Which actually has the gene sequence present on the formed RNA?

Back 91

Template (antisense) and coding (sense)

Front 92

How many RNA polymerases are there for proks? euks?

Back 92

1

3

Front 93

What subunits comprise the core enzyme of RNA polymerase?

Back 93

2 alpha, beta, and beta prime

Front 94

What does the holoenzyme consist of for RNA polymerase in proks?

Back 94

core enzyme plus sigma factor

Front 95

what is a transcription unit?

Back 95

single stretch of DNA transcribed into single RNA molecule.

Front 96

What is an operon?

Back 96

polycistronic string with multiple genes

Front 97

Detail Transcription for proks:

Back 97

holoenzyme binds upstream of promoter element (-10 and -35 elements)

helicase unwinds

synthesis begins (PPi released) (springs forward 7-8bp's at a time)

sigma factor comes off (after~9nt's)

core enzyme continues synthesizing 5-3

termination signal or rho sequence

Front 98

Detail termination signal based termination and rho terminatino in proks:

Back 98

Termination signal encountered, GC-hairpin loop formed followed by string of U's. loop pulls the weak U's off the DNA, and deattachment happens.

rho sequence encountered, rho factor (protein) binds to this sequence and ATP unwinds the RNA from the DNA, deattachment occurs

Front 99

What do Euk RNA Pols I-III synthesize? where are they foud

Back 99

I: 28, 18, and 5.8S rRNA (nucleolus)

II: mRNA and snRNA (nucleoplasm)

III: tRNA, 5S rRNA (nucleolus)

Front 100

What are the main 4 promoter elements for Euk transcription? what combinations are seen?

Back 100

Initiator region: 1nt upstream, generally A

TATA box: 25bp upstream

TFIIB (BRE): upstream of TATA

DPE: 30bp downstream from startpoint

TATA/Inr/BRE

DPE/Inr/

Front 101

What do the TFII's do?

Back 101

D: binds to TATA

A: binds to DNA

B: binds to D

F: Binds to PolII and B, bring the Pol in

E/H: whatever

Front 102

How does termination occur for RNA Pols I and III in euks?

Back 102

I/III: termination signals, no hairpins

II: endonuclease cleaves mRNA 10-35nt's downstream from AAUAAA sequence. poly A tail added to tail.

Front 103

What percentage of all RNAs do m, r, and t compose?

Back 103

r: 7-80

t: 10-20

m: less than 10

Front 104

can eukaryotic mRNA sequences code for multiple proteins? proks?

Back 104

no

yes

Front 105

What S units to prokaryotic rRNAs have? euks?

Back 105

50S (23, 5)

30S (16)

60S (28, 5.8, 5)

40S (18)

Front 106

Which rRNA S unit is a ribozyme?

Back 106

28S

Front 107

What are tandem arrays for rRNA? How are they processed? Which Pol is responsible for this?

Back 107

multipe copies of pre-rRNA genes (except for 5S), separated by spacers.

Spacers must be cut out. (snoRNAs)

Methyl groups added to 2' OH of ribose

RNA Pol I

Front 108

how are tRNA units processed?

Back 108

5' leader sequence removed

CCA must be at 3' end

15% of bases are chemically modified

may need intron removal

folded into 4-5 clover shape

70-90nt's

Front 109

How is mRNA processed?

Back 109

5'-5' cap added (7-methyl guanosine)

some caps may methylate the next 2 bases

Poly-A-tail added after transcript is cleaved, for protection and recognition for transport (not H1)

Introns removed by spliceosome (snRNP/A

5' site cleaved, makes 2'-5' bond with A inside of intron, 3' site cleaved, and exons are joined.

Front 110

What are the 2 self-splicing mechanisms? where are they found?

Back 110

1: no production of lariat (fungi, plants, phage

2: forms lariat (fungus, plant, protist)

Front 111

What is the purpose of Guide RNA? What are some specific changes seen?

Back 111

Helps modify transcripts accordingly. C's turned into U's, U's turned into C's, A's to I's.