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Bio 111 > Lab Exam 2 > Flashcards

Lab Exam 2 Flashcards

1
Q

Coding DNA

A

the type of DNA in the genome, encoding for protein-coding genes.
Significantly, it accounts for 1% of the human genome.
Coding DNA consists of the coding region of protein-coding genes; in other words, exons.

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2
Q

Noncoding DNA

A

The other type of DNA in the genome, accounting for 99% of the human genome. Significantly, it does not encode for protein-coding genes.
Thereby, it does not provide instructions for the synthesis of proteins.

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3
Q

Coding region of genome

A

encodes proteins that determine physical traits.

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4
Q

Non-coding region of genome

A

98-99% of human DNA; has short-tandem repeats (STRs)

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5
Q

Short-tandem repeats (STRs)

A

Unique repeating patterns in non-coding region of DNA; can be used to differentiate one person from another; present at specific locations, may be repeated , on everyone’s chromosomes (loci); 5-20% of people share the same DNA profile at any one STR site.

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6
Q

(CA)(CA)(CA)(CA)****

A

2-nucleotide repeat unit

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7
Q

(GCC)(GCC)(GCC)(GCC)****

A

3-nucleotide repeats unit

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8
Q

Steps to creating a DNA profile

A

Multiple STR regions from each DNA sample are amplified by Polymerase Chain Reaction.
These STR regions are then separated by gel electrophoresis based upon STR size.
DNA-binding fluorescent dyes allow visualization of a banding pattern.
Forensic scientists can use this information to identify criminals!

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9
Q

Polymerase Chain Reaction (PCR)

A

a method used for making billions of copies of a specific DNA sequence; using this technique, researchers can easily build up large quantities of genetic material for experimental use; a specialized DNA polymerase, Taq polymerase, is used in this reaction because of its ability to survive in high-temperature environments

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10
Q

PCR reaction components

A

1) DNA template
2) Primers
3) DNA polymerase
4) Deoxyribose nucleotide triphosphates (dNTPs)
5) Reaction buffer
6) Solvent PCR grade water

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11
Q

Primer in PCR reaction

A

short pieces of DNA specific to the sense or antisense strands; binds via hydrogen bonds

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12
Q

DNA polymerase in PCR reaction

A

Uses Taq polymerase; can withstand temperatures greater than 90^C

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13
Q

dNTPs in PCR reaction

A

will comprise the base pairs in growing strands; takes DNA base pairs and turns into dATP, dGTP, dCTP, dTTP

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14
Q

Reaction buffer in PCR reaction

A

maintains pH and contains important ions like manganese, magnesium, and potassium; stabilizes the reaction and provides important cofactors to the polymerase enzyme

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15
Q

Solvent PCR grade water in PCR reaction

A

is free of ions that can inhibit the reaction

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16
Q

DNA isolation steps

A

1) Saline + mouth rinse
2) Centrifuge
3) Discard supernatant (liquid), dont lose pellet
4) add Chelex resin and resuspend pellet
5) Place PCR tube in thermocycler for 10mins at 99^C to lyse the cells
6) Add some DNA sample into new tube and mix with master mix
7) thermocycle for 1hr

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17
Q

Thermocycler

A

has fine temperature control: ability to hold a precisely set temperature with little fluctuation; amplifies STRs in DNA

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18
Q

Chelex resin

A

absorbs ions that inhibit function of Taq polymerase (PCR)

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19
Q

Master mix contains

A

buffer, loading dye, deoxynucleotides, three pairs of primers, taq polymerase, water

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20
Q

Central Dogma

A

explains flow of genetic information to make a protein; the cellular process of transcription generates mRNA

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21
Q

Protein variation

A

Protein sequences consist of 20 commonly occurring amino acids
Different amino acids have different chemistries and structural constraints.
Each amino acid is composed of an amino group ( NH+3 ), a carboxyl group (COO-), and a side chain.
Variation in amino acid sequence (side chain) is responsible for the enormous variation in protein structure and function

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22
Q

Triplet codon

A

a three-nucleotide sequence that each amino acid is defined by

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23
Q

nonsense or stop codons

A

terminate protein synthesis; 3/64 codons

24
Q

Point mutations

A

cause single base pair to be exchanged for another; can cause silent, missense, nonsense

25
Q

Silent mutation

A

substitution doesnt change amino acid that codon codes for

26
Q

Missense mutation

A

substitution changes codon so corresponds to a different amino acid than it should

27
Q

Nonsense mutation

A

substitution changes codon so it signals an early stop of translation

28
Q

Insertion mutation

A

extra base is inserted into a sequence; can cause frameshift mutation

29
Q

Deletion mutation

A

a base is removed from sequence; can cause frameshift mutation

30
Q

Frameshift mutation

A

when base is added or removed, the entire codon sequence following the mutation changes

31
Q

gel electrophoresis

A

technique used to separate DNA fragments according to size; DNA samples are loaded into wells (usually top) at one end of gel; electric current is applied to gel; DNA fragments are negatively charged so they moved towards the positive electrode

32
Q

Influencing factors of gel electrophoresis

A

charge of molecule: DNA is neg charge so goes to pos electrode
size: smaller molecules travel faster and farther; longer molecules stay near wells and shorter molecules go farther from wells
density of gel: dense gel means slow particles; need gel that is dense enough to separate particles but wont take too long

33
Q

DNA with loading dye in gel electrophoresis

A

dye weighs down DNA so it can sink to bottom of wells and not gloat in buffer; moves quicker than DNA so indicates when to turn off power

34
Q

Buffer in gel electrophoresis

A

stabilizes pH and Mg^2+, which DNA polymerase require to function

35
Q

SYBR Green in gel electrophoresis

A

dye used in molecular biology techniques to stain nucleic acids; binds to DNA resulting in complex that absorbs blue light and transmits green light

36
Q

Reading gels steps

A

1) Measure from wells to the band of interest
2) find rate between markers
3) Subtract distance the upper ladder band migrated from distance to band
4) multiply this by rate calculated above
5) subtract this distance from molecular size from upper band

37
Q

Example of reading gels
Given:
500bp marker = 2.3cm
300bp marker = 3.5cm
Band 1 = 2.6cm

A

1) 500bp-300bp = 200bp
3.5cm-2.3cm = 1.2cm
200bp/1.2cm = 166.7bp/cm
2) 2.6cm-2.3cm = 0.3cm (did band - 500bp)
3) 0.3cm*166.7bp/cm = 50.1bp
4) 500bp-50.1bp = 449.99bp

38
Q

total magnification

A

total magnification = magnification in ocular lens x magnification of objective lens;
magnification in ocular lens is always 10x

39
Q

Operons

A

blocks of proteins that are involved in the same biochemical pathway and are coded together

40
Q

Components of operon

A

RNA polymerase, promoter, operator, repressor, 3 lactose utilizations genes

41
Q

RNA polymerase in operon

A

needed to start transcription and produce mRNA

42
Q

Promoter in operon

A

sequence of DNA that the polymerase binds

43
Q

Operator in operon

A

part of DNA that repressor can bind to (on/off switch)

44
Q

Repressor in operon

A

binding of repressor blocks RNA polymerase and prevents production of mRNA, resulting in no production of proteins

45
Q

3 lactose utilizations genes in operon

A

lacZ, lacY, and lacA

46
Q

lacZ

A

encodes beta-galactosidase (b-gal) to break lactose down to glucose and galactose

47
Q

lac repressor

A

protein that inhibits transcription of lac operon; does this by binding to operator; when bound, lac repressor gets in way of RNA polymerases way and keeps it from transcribing operon; lacI gene encodes lac repressor and is under control of own promoter; lacI is continually transcribed so lac repressor is always present

48
Q

Catabolite activator protein (CAP)

A

CAP binds to region of DNA before lac operon promoter and helps RNA polymerase attach to promotor; is regulated by cycle AMP (cAMP)

49
Q

cycle AMP (cAMP)

A

a hunger signal made by E.coli when glucose levels are low; cAMP binds to CAP, changing its shape and making it able to bind DNA and promote transcription

50
Q

when does lac operon turn on

A

1) when glucose is unavailable; causes cAMP to bind to CAP so CAP can bind to DNA
2) lactose is available; allows RNA polymerase to move forward on DNA and transcribe operon
3) both together causes strong transcription of lac operon and production of enzymes needed for lactose utilization

51
Q

B-gal

A

an enzyme produced by E.coli that catalyzes hydrolysis of disaccharide lactose to monosaccharide galactose and glucose

52
Q

ONPG

A

cleaved by g-gal into galactose and ortho-nitrophenol

53
Q

Calculating enzyme activity

A

(absorbance/elapsed time)*1000

54
Q

How to find enzyme activity

A

growth of e.coli
add lysis reagent
add z buffer and ONPG into lysed e.coli
use spectrophotometer to find absorbance
(absorbance/elapsed time)*1000

55
Q

chances
given:
chance of seeing green wrinkled peas = 1/16
chance of not seeing green wrinkled peas = 15/16
60 plants are being observed

A

(15/16)^60 = 0.02
2% chance of not seeing green wrinkled peas

56
Q

dihybrid cross

A

P gen is homo dom x homo rec
F1 gen is all hetero
F2 gen has ratio of 9:3:3:1

Bio 111 (4 decks)

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