Genetics Lab Final

Front 1

Restriction enzymes are _____ which mean they can cleave the phosphodiester bond within a polypeptide chain

Back 1

endonucleases

Front 2

Enzymes that work by cleaving nucleotides one at a time from the end of a polynucleotide chain

Back 2

exoenzymes

Front 3

nucleotide sequence recognized for cleavage by a restriction enzyme

Back 3

restriction site

Front 4

Bacteria protect their own DNA from the endonuclease by using the modification enzyme ___________ which adds methyl groups to its own DNA and therefore prevents the endonuclease from recognizing its own sequence and cleaving its own DNA

Back 4

methyltransferase

Front 5

Single stranded overhangs that have an affinity for their complimentary sequences and can reconnect through hybridization

Back 5

sticky ends

Front 6

enzymes that cut both ribose backbones at the same place leaving ______ ______ that have no affinity for other pieces of DNA

Back 6

blunt ends

Front 7

Restriction endonucleases that are large multi subunit complexes that include both the endonucleases and methyltransferase activities

Back 7

Type I and Type III

Front 8

Restriction endonucleases that can cleave at distant random sites which can be 1000 base pairs or more from the recognition sequence

Back 8

Type I

Front 9

Restriction endonuclease that requires ATP as source of energy

Back 9

Type I and III

Front 10

Restriction endonucleases that are homodimeric or tetremeric enzymes that cleave DNA at defined sites of 4-8 bp in length

Back 10

Type II

Front 11

Restriction endonucleases that require Mg2+ ions for catalysis

Back 11

Type II

Front 12

Restriction endonucleases that require no ATP to catalyze the reaction

Back 12

Type II

Front 13

Restriction endonucleases that cleave the DNA at about 25 base pairs from the recognition sequence

Back 13

Type III

Front 14

An engineered DNA sequence that maximizes the number of restriction sites in a very small sequence of a plasmid

Back 14

Multiple Cloning site (MCS)

Front 15

We isolated ______ from our transformed E. coli cells.

Back 15

puc19

Front 16

_____ has a multiple cloning site, ampicillin resistance gene for selecting your transformants, and the lac operon and promoter that would allow you to clone your gene into that location and induce expression of your gene with the carbohydrate lactose

Back 16

puc19

Front 17

The enzyme ______ added to DNA fragments will reattach the ribose backbone.

Back 17

ligase

Front 18

When the gene of interest creates a genetic polymer where multiple copies link end to end

Back 18

concatemer

Front 19

column chromatography done at higher pressure to speed up the process

Back 19

HPLC (High Pressure Liquid Chromatography)

Front 20

Volatilizes liquids and separates the molecules as a gas

Back 20

gas chromatography

Front 21

Separates smaller molecules

Back 21

thin layer chromatography

Front 22

Separates DNA ro RNA fragments based on the size of the fragment

Back 22

agarose gel electrophoresis

Front 23

The ______ the percent of agarose in your gel, the ______ the pore between strands.

Back 23

higher, smaller

Front 24

DNA migrates to the __________ pole of the apparatus due to its __________ charged phosphate backbone.

Back 24

positive, negatively

Front 25

Low percentage gels are best for resolving _____ molecular weight fragments and vice versa.

Back 25

high

Front 26

Loading buffer contains _______ to make your sample heavier than water so it will stay in the well if properly pipetted.

Back 26

glycerol

Front 27

______ is added to the loading buffer to sharpen the bands and give better resolution.

Back 27

SDS

Front 28

_______ _______ is added to give a colored band that migrates on the gel at the same rate as an ~500 bp DNA fragment.

Back 28

Bromophenol Blue

Front 29

The gels are resolved using a voltage between ___ and ____ volts.

Back 29

30 , 120

Front 30

Standard which is 100 bp ladder (100, 200, 300 bp fragments)

Back 30

HindIII digest of Lambda Phage DNA

Front 31

To generate a standard curve, plot _______ vs. ______.

Back 31

log of molecular weight (base pairs) vs. distance the fragments migrated

Front 32

Sequences often found flanking the centromere location on a chromosome

Back 32

Highly repetitive centromeric DNA

Front 33

DNA repeats that form satellite bands when centrifuging genomic DNA in a cesium chloride gradient

Back 33

Satellite DNA

Front 34

Sequences that have propagated themselves by replicating and then moving to new locations in the genome

Back 34

Transposed Sequences

Front 35

Elements that move to new locations in the genome

Back 35

Transposons or jumping genes

Front 36

Short sequences that repeat two or more times. EX: ATTCG ATTCG. also called mini satellite or micro satellite DNA depending on the repeat size

Back 36

Variable Number Tandem Repeats (VNTR)

Front 37

Repeated sequences that range between 15-100 base pairs

Back 37

minisatellites

Front 38

Repeated sequences that range between 2-6 base pairs in length

Back 38

microsatellites

Front 39

Intervening sequences that are find in a mRNA and are excised out during mRNA processing indicating they are non-functional DNA

Back 39

introns

Front 40

In DNA fingerprinting, we extracted DNA from buccal cells using _______ + _________.

Back 40

extraction buffer + proteinase K

Front 41

Extraction buffer contains the detergent _____ which will lyse the cells by perturbing the lipid bilayer.

Back 41

SDS

Front 42

_______ is an enzyme that will degrade contaminating proteins.

Back 42

Proteinase K

Front 43

This was used to further purify the buccal DNA by denaturing any remaining proteins

Back 43

chloroform/phenol

Front 44

Hydrophilic DNA is in the ______ phase and hydrophobic molecules will be in the ______ layer.

Back 44

aqueous, organic

Front 45

Proteins that have been denatured by the chloroform will pack into the _____ during centrifugation.

Back 45

interface

Front 46

These two primers are required to amplify DNA

Back 46

forward and reverse primers

Front 47

A primer of ___-___ bases is considered to be the optimal length.

Back 47

18-22

Front 48

The temperature where half the DNA will melt into single strands

Back 48

primer melting point (52-58 degrees Celcius)

Front 49

The ____ content of a primer gives fair estimation of a primer's melting point

Back 49

G-C

Front 50

______ annealing temperature will produce insufficient primer-template hybridization resulting in low PCR product yield.

Back 50

too high

Front 51

_____ annealing temperature may possible lead to non-specific products caused by a high umber of base pair mismatched.

Back 51

too low

Front 52

A max number of di-nucleotide repeats acceptable in an oligo is _____ di-nucleotides.

Back 52

4

Front 53

PCR reagents needed for amplification

Back 53

DNA polymerase, Nucleotides, template DNA, reaction buffer, primers

Front 54

Three steps to PCR

Back 54

denaturation, annealing, extension/elongation

Front 55

an automated heat block which is programmed to raise and lower the temperature for each of the steps of the PCR

Back 55

Thermocycler

Front 56

a DNA polymerase that was isolated from a thermophilic bacteria and is heat stable (doesn't need to be re-added every cycle of PCR)

Back 56

Taq polymerase

Front 57

rapid, small scale isolation of plasmid DNA from transformed bacteria

Back 57

miniprep of plasmid DNA

Front 58

_____ and ____ will cause all DNA to fall out of solution and be pelleted in a centrifuge during mini prep.

Back 58

alcohol and salt

Front 59

Plasmid DNA is much _______ than genomic DNA.

Back 59

smaller

Front 60

Solution I of miniprep contains

Back 60

glucose, EDTA, Tris, Lysozyme

Front 61

in solution I of miniprep , maintains correct osmotic conditions

Back 61

glucose

Front 62

in solution I of mini prep, chelates divalent cations (Ca++, Mg++)

Back 62

EDTA

Front 63

in solution I of mini prep, pH buffer maintains biological pH (~7)

Back 63

Tris

Front 64

In solution I of mini prep, digests polysaccharides to weaken cell wall

Back 64

lysozyme

Front 65

Solution II of mini prep contains

Back 65

NaOH and Triton

Front 66

In solution II of mini prep, raises pH to 12.5 to denature DNA into single strands

Back 66

NaOH

Front 67

In solution II of mini prep, a detergent that lyses cells by perturbing lipid bilayer

Back 67

triton

Front 68

Solution III of mini prep contains

Back 68

Sodium acetate

Front 69

In solution III of mini prep, lowers pH to 7 to allow DS DNA

Back 69

sodium acetate

Front 70

Occurs at the level of protein-protein interactions and the wildtype phenotype can be achieved without any change in the genetic sequences of the organism.

Back 70

complementation

Front 71

type of complementation where the proteins are different and assemble into a heterodimer and involves two different gene products

Back 71

intergenic complementation

Front 72

type of complementation where the proteins are the same and assemble into a homodimer and involves isoforms of the same gene product produced by two different alleles of the same gene

Back 72

intragenic complementation

Front 73

a protein that differs slightly in its amino acid sequence when compared to the wild type protein

Back 73

isoform

Front 74

system used to study intergenic complementation

Back 74

lambda (T4) bacteriophage

Front 75

two common T4 mutants that cannot lyse the host cells

Back 75

rIIa and rIIb