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GENOME > MIDTERM 1 > Flashcards

MIDTERM 1 Flashcards

1
Q

Liter

A

L= 1 known conversion factors

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2
Q

Milliliter

A

mL: .001L, 1 x 10^-3 L.

One thousandth of a liter

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3
Q

Microliters:

P2
P20
P200
P1000

A

P2: .2-2 ul
P20: 2-20 ul
P200: 20-200 ul
P1000: 200-1000ul

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4
Q

Stock solution

A

A concentrated for of a reagent that is often diluted. nX n>1. Given names that correspond to how concentrated they are.

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5
Q

Conversion Units

A

M,m,X,%, and some unit over another unit (g/l, mg/ml,etc.)

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6
Q

DNA

A

A complex molecule containing the genetic information that make up the chromosomes

carrier of genetic information

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7
Q

mRNA

A

messenger RNA; type of RNA that carries instructions from DNA in the nucleus to the ribosome

mRNA happens in nucleus

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8
Q

pre-mRNA

A

-occurs in transcription

-Immature mRNA; the first strand of mRNA produced in transcription
that contains both introns and exons

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9
Q

tRNA

A

-Transfer RNA provides linkage between mRNA and amino acids and transfers amino acids to ribosomes

  • present in the cytoplasm

-Transfer amino acids to match the correct mRNA codon

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10
Q

INtrons

A

“stayes IN the nucleus”

-non-coding region of DNA
-does not code for protein

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11
Q

EXons

A

“EXIT/Expresses”

  • expressed sequence of DNA
  • codes for a protien
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12
Q

rRNA

A

-Type of RNA that combines with proteins to form ribosomes

  • occurs in cytoplasm
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13
Q

Spliceosome

A

Complex of enzymes that serves to splice out the introns of a pre-mRNA transcript this releases the introns and join the two exons

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14
Q

Splicing

A

proccess of removing introns and reconnecting exons in a pre-mRNA

  • removal of introns
  • occurs in nucleus
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15
Q

Ribosome

A
  • Cytoplasmic organelles at which proteins are synthesized.

-the “body” that makes proteins

  • Uses the amino acids made by tRNA to create proteins that will have a certain task
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16
Q

cDNA

A

-“copy DNA”

-ONLY EXONS

-“complementary DNA”

-Synthesized in a lab

-it is produced by synthetically doing reverse transcription of mRNA. Because of eukaryotic mRNA splicing, cDNA contains no introns

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17
Q

gDNA

A

-“genomic DNA”

-the original, hard copy of genetic material for a cell

  • contains both exons and introns
  • found in body
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18
Q

Reverse Transcription

A
  • Synthesis of DNA from an RNA template
    (RNA—–>DNA)
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19
Q

Reverse Transcriptase

A

-Enzyme responsible for the formation of cDNA

-copy of RNA made through reverse transcriptase

-the DNA copy synthezised by reverse transcriptase is cDNA

  • cDNA serves as a template for PCR
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20
Q

Protein

A
  • an organic compound that is made of one or more chains of amino acids (codon) and that is a main component of all cells
  • A set of specific nucleotides encodes for a specific protein
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21
Q

DNA Polymerase

A

-Enzyme invovled in “DNA replication” that joins individual nucleotides to produce a DNA molecule

-enzyme that synthesizes new copies of DNA

-Needs a primer

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22
Q

RNA Polymerase

A

Enzyme that links together the growing chain of RNA nucelotides during ‘transcription’ using a DNA strand as a template

-enzyme that makes RNA from DNA template

-Doesn’t need a primer

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23
Q

Polymerase chain reaction (PCR)

A

A technique that amplifies DNA of specific genes

  • PCR includes to incubate with specific primers, DNA polymerase molecules, and nucleotides
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24
Q

PCR step 1

A

Denaturing 98°C

  • Heat up to break apart double-stranded DNA molecules
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25
Q

PCR step 2

A

Annealing 50-70°C

  • cooled down to allow primers to bind to each DNA strand on opposite ends of the segment in order to be copied
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26
Q

PCR step 3

A

Extension 72°C

-TAQ polymearse synthesizes the first set of cDNA to form new strands

  • makes polymerase extend to 3’ to 5’
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27
Q

Polymorphism

A

If two individuals have sequence differences at the same place in the genome

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28
Q

Insertion Deletion (indel)

A

When 1 or more nucleotides of DNA is present in one individual and absent in another

*it is represented as dashes in programs

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29
Q

Single Nucleotide Polymorphism (SNPs)

A

Difference at one nucleotide in a DNA sequence among the genome sequence

  • sickle cell anemia were a SNP caused a change of glutamic acid to valine

EX: A is changed to G

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30
Q

Transposable Element

A

A segment of DNA that can move spontaneously within or between chromosomes. A mobile genetic sequence

  • can cause mutations
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31
Q

BLAST

A

Helps analyze DNA sequence

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32
Q

Blast Hit

A

Bioinformatics page that allows us to see the sequence of nucleotides within a DNA sample. We can see introns and exons and specific base pair length

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33
Q

Multiple sequence Alignment

A

the alignment of three or more biological sequences (proteins or nucleic acid) of similar length

we used the program MUSCLE

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34
Q

Primers

A

Short segments of DNA that guide DNA polymerase to the section of DNA to copy

-main job is to bind to bases

-In our experiment, the priers bind around the Actin gene

  • 1 Forward and 1 Reverse
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35
Q

Taq

A

-Short for taq polymerase; a heat stable DNA polymerase that is used during PCR to synthesize new DNA strands

  • it can withstand high temperatures of PCR
36
Q

Negative control

A

Control group where conditions produce a negative outcome. Negative control groups help identify outside influences which may be present that were not accounted for when the procedure was created

-ddH2O

-typically water

37
Q

Master Mix

A

Special reaction buffer with all the components needed for PCR to occur.

  • free nucleotides, TAQ polymerase, primers, and reaction buffer

-Needed for new strand of DNA to be synthesized

-added before temperature change

38
Q

Gene expression

A

The process by which information encoded in DNA directs the synthesis of proteins or, in some cases, RNAs that are not translated into proteins and instead function as RNAs

39
Q

Antibiotic Selection

A

Used to recover transformants. Scientists use antibiotic resistance genes as genetic markers to identify which bacteria were transformed

40
Q

Plasmid

A

A small ring of DNA that carries accessory genes separate from those of the bacterial chromosomes

the genes carried in plasmind provide bacteria with genetic advantages such as antibiotic resistance

41
Q

Bacterial Transformation

A

Ability of bacteria to alter their genetic makeup by “up taking foreign DNA” from another bacterial cell and incorporating it into their own

42
Q

Constitutive Promoter

A

“Active all the time”

Housekeeping cell

The RNA polymerase binds to the promoter, which then allows transcription to occur

43
Q

Conditional Promoter

A

“Requires a Condition to turn on”

In order for RNA polymerase to bind to the promoter and initiate transcription, a transcription factor must attach to it; hence, a sugar or hormone must be present. The transcription factor will bind to the sugar or hormone, enabling the RNA polymerase to bind to the promoter and initiate transcription.

44
Q

Synonymous

A

-Silent mutation

-does not change the amino acid, therefore does not change the protein

-Protein function is retained

45
Q

Non-Synonymous

A

-A mutation in a gene that changes the amino acid sequence of the protein that gene encodes

-Detrimental to a protein function

46
Q

Missense

A

A DNA change that results in a different amino acid

47
Q

Nonsense

A

A DNA change that results in a premature “STOP” codon

-the most detrimental SNP effect

48
Q

Identifying the number of reactions

A

(# of given samples) + 1 Negative control (water) + 1 positive control (master mix)

49
Q

Competent

A

Plasmid mixed with bacterial cells that have been treated with calcium chloride to make them capable of taking up DNA

50
Q

Tranformants

A

Cells that take up plasmid

51
Q

Why is GFP userful?

A

Visualizing the presence of the gene doesn’t require sacrificing the tissue to be studied.

52
Q

What is the correct description of the steps of PCR in correct order from first to last:

A
  1. Double helix is melted to singe strands
  2. Primers bind to template DNA
  3. Primers are extended by DNA polymerase to make new strand
53
Q

What is used as the negative control in the PCR experiment?

A

Water

54
Q

How much agarose is requires to make a 2% gel with a volume of 200mL 1X TAE?

A

4g

55
Q

The key term ‘Polymorphism’ most closely means what when broken down?

A

Many forms

56
Q

What does PCR stand for?

A

Polymerase Chain Reaction

57
Q

T/F: the purpose of the DNA polymorphism experiment is to look for genetic differences among individuals of different species

A

False

*looking for differences among SAME species

58
Q

A PCR reaction experiment that includes 1 unknown DNA sample and 2 controls (positive and negative) you will need how many total reactions in the Master Mix?

A

4

*always add one more in case of pipet errors

59
Q

Match the following reagents with the correct component of the lab they were use in (the master mix or gel of electrophoresis):

  1. DNA Polymearse
  2. DNTPs (nucleotides)
  3. Ethidium Bromide (EtBr)
  4. Agrose
  5. Tris-Acetate EDTA buffer (TAE)
  6. Primers
A
  1. DNA Polymearse: Master Mix
  2. DNTPs (nucleotides) : Master Mix
  3. Ethidium Bromide (EtBr): GEL
  4. Agrose: Gel
  5. Tris-Acetate EDTA buffer (TAE): GEL
  6. Primers: Master Mix
60
Q

What does the “Denature” step of PCT refer to?

A

Double helix DNA strands is heated and separated into single strands

61
Q

gDNA is a copy of____, while cDNA is a copy of ____

A

Genomic DNA, mRNA

62
Q

Of the choices below, what is the worst combination of SNP type and gene location?

  1. Nonsynonymous SNP in an exon.
  2. Synonymous SNP in an intron.
  3. Synonymous SNP in an exon.
  4. Nonsynonymous SNP in an intron.
A
  1. Nonsynonymous SNP in an exon
63
Q

What organelle transfers amino acids to the growing protein in the cytoplasm via translation?

A

Ribosome

64
Q

DNA molecules have a ____________ charge, so larger DNA molecules will travel _____________ through the agarose gel compared to smaller DNA molecules. [HINT: The gels run from the black wire (negative anode) to the red wire (positive anode)

A

negative, a shorter distance

65
Q

How does translation stop adding amino acids to the growing protein?

A

There is a stop codon in the mRNA

66
Q

You run PCR and gel electrophoresis examining a gene where the expected band length is 1500 nucleotide base pairs (bp). Which of the following scenarios would show two bands in one lane on the agarose gel. Select ALL that apply. (Allele = one version of a gene)

  1. Two different alleles, one with a synonymous SNP compared to the other allele.
  2. Two different alleles, one with a 500 bp insertion in an intron in the gDNA compared to the other allele.
  3. Two different alleles, one with a nonsynonymous (missense) SNP compared to the other allele.
  4. Two different alleles, one with a 500 bp insertion in an exon compared to the other.
  5. Two different alleles, one with a nonsynonymous (nonsense) SNP in an exon early in the gene compared to the other allele.
A
  1. Two different alleles, one with a 500 bp insertion in an exon compared to the other
67
Q

This transcribes the DNA into pre-mRNA

A

RNA polymerase

68
Q

Has a complementary sequence of mRNA and carries an amino acid to the new growing protein

A

tRNA

69
Q

Non-coding region removed during splicing

A

Intron

70
Q

Contains introns and exons before splicing

A

pre-mRNA

71
Q

What is the correct order of steps in PCR?

A

Denaturing–>Annealing–>Extension

72
Q

What animals was GFP originally clored from

A

Jelly fish

73
Q

Which of the following molecules and processes of genetic information transfer occur in Nucleus?

1.Translation
2.Transcription
3.Splicing.
4.tRNA

A
  1. Transcription
  2. Splicing
74
Q

T/F: During thr 3 steps of PCR, the temperature gets colder before it warms up again.

A

True

75
Q

What is incorrect about gel electrophoresis?

A
  • DNA fragments that are very small appear at the top of the gel
  • Gel electrophoresis along can be used to detect SNPs
76
Q

To be able to clone GFP for expression in a new organism than the original, introns need to first be removed, what type of molecule did the scientists clone?

A

cDNA

77
Q

Competent cells are fragile, which means that you should not do what:

A
  1. Centrifuge
  2. Pipette them up and down
    3.Vortex
78
Q

Describe how conditional gene expression functions.

A

Controls when the gene of interest is expressed as protein

79
Q

Why are competent cells used in bacterial transformation?

A

Competent cells are capable of taking up plasmids

80
Q

Which of the following statements about setting up a PCR reaction is incorrect? Select all that apply.

  1. The number of reactions of master mix prepared should equal the number of samples
  2. The C1V1=C2V2 equation should be used to determine what volume of MyTaq is needed for the reaction.
  3. Template for all samples should be added to the master mix before aliquoting into strip tubes
  4. After all components are added to create the mastermix it should not be mix
A

1,3,4

81
Q

What is the name of the molecule that turns off a gene by preventing mRNA polymerase from binding to the promoter?

A

Transcription Factor

82
Q

What volume of a 75% stock solution is needed to make 10 µl of a 12% working solution, and how much water will need to be added to the stock?

A

1.6 µl of stock, and 8.4 µl of water

83
Q

What volume of stock and water is required to make 500 µl of a 2X solution starting with 10X stock?

A

100 µl of stock and 400 µl of water

84
Q

Solve:

ddH2O ?

Forward Primer 0.5

Reverse Primer 0.5

2xMytaq ?

Subtotal ?

DNA 5.0

Grand total 20.0

A

Solve:

ddH2O 4.0 24.0

Forward Primer 0.5 3.0

Reverse Primer 0.5 3.0

2xMytaq 10 60

Subtotal 15 90

DNA 5.0 ——

Grand total 20.0 ——–

85
Q

Nymphia needs to make 50 mL of diluted TAE solution for
her experiment. The prep room has 100 mL of 1X (M) TAE
stock solution. What concentration of TAE will Nymphia
need to prepare?

A

2X

GENOME (2 decks)

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