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FINAL Flashcards

1
Q

Discovered Existence of DNA

A

Meischner 1871

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2
Q

Proved DNA Was Molecule of Heredity

A

Hershey and Chase 1953

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3
Q

Chargaff’s Rule

A

Determined that the number of Adenine bases equals the number of Thymine bases
Cytosine bases equals the number of Guanine bases

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4
Q

Wilkins and Franklin

A

Using X-Ray
Famous Photo 51 (Franklin)
Determined the structure was a double helix

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5
Q

Watson and Crick

A

Discovery of structure
Wilkins gave Crick the famous photo 51 generated by Rosalind Franklin
Rushed to make a model and got it inside out
Franklin showed them that the hydrophobic bases should be on the inside and the hydrophilic sugar/phosphates on the outside

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6
Q

Held Together

A

A and T double hydrogen bonds
C and G with triple hydrogen bonds
Pyrimidines one ring structures, Thymine and Cytosine
Purines two ring structures, Adenine and Guanine

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7
Q

Genes That Are Sequenced

A

Plants rbcL gene, Chloroplast gene
Animal CO1 gene, Mitochondrial gene
Fungi ITS Gene, Nuclear intron near ribosomal RNA gene

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8
Q

Reads VS Builds

A

Three to five
Five to three

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9
Q

DNA Polymerases

A

I is the enzyme that removes the RNA Primers and adds nucleotides to the section
II performs elongation in eukaryotes and creates a covalent bond between the nucleotides

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10
Q

PCR Developed By

A

Mullis

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11
Q

Steps to PCR

A

Denaturing
Annealing
Extending

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12
Q

Denaturing

A

Breakdown of DNA , separate the DNA into single strands by heating it to 94-98 degrees Celsius for one to two minutes, and the heat breaks the hydrogen bonds

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13
Q

Annealing

A

Lower the temperature back down to 50-65 degrees Celsius in order to get the primers to anneal, or base pair, to their complementary sequences

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14
Q

Extending

A

Raise the temperature back up to 72 degrees Celsius which allows the DNA polymerase, which works to copy the DNA, to attach at the primer site and copy the target section of DNA

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15
Q

Primer Dimer

A

Tells you that PCR worked

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16
Q

In Vitro VS In Vivo

A

Outside
Inside

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17
Q

DNA Replication VS PCR

A

Helicase, primase, and ligase
Uses heat
Both use polymerase

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18
Q

DNA Sequencing Methods

A

Sanger
Shotgun
SBS
Nanopore

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19
Q

Sanger Sequencing

A

Only sequences small sections of DNA Determines the order of the bases by replicating fragments of DNA using PCR where the last nucleotide is known

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20
Q

Shotgun Sequencing

A

Sequences the entire genome
The genome is cut into smaller fragments using multiple different restriction enzymes
The fragments are sequenced using Sanger sequencing

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21
Q

SBS

A

Most common type of sequencing used today
Nucleotides are labeled with a fluorescent tag
The DNA fragment is sequenced as PCR occurs in real time

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22
Q

Steps in Protein Synthesis

A

Transcription, DNA is copied to make mRNA, occurs in the nucleus.
Translation, The mRNA is translated into a protein, occurs at the ribosome.

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23
Q

Steps in Transcription

A

Gene turned on
Initiation
Elongation
Termination
Processing

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24
Q

Gene Control Regions

A

Start Site, start location for transcription
Promoter, not transcribed into mRNA, but plays a role in the transcription of the gene
Enhancers, some transcription factors (activators) bind to regions called enhancers and increase the rate of transcription
Silencers, other transcription factors (repressors) bind to the silencer regions and depress the rate of transcription

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25
Q

Transcription Initiation

A

The DNA molecule unwinds and separates to form a small open complex
RNA Polymerase binds to the promoter of the template strand

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26
Q

Transcription Elongation

A

RNA polymerase then adds the RNA nucleotides moving along the strand of DNA in a 3’ to 5’direction and building the mRNA in a 5’ to 3’ direction

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27
Q

Transcription Termination

A

A terminator sequence in the DNA indicates where the gene ends
Trigger processes which release the transcript RNA from the transcriptional complex

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28
Q

Processing

A

The 5’ end is capped
The 3’ end has a poly A tail added to it, important for export of the mRNA and stability of the mRNA in the cytoplasm (the tail shortens over time and when it is short the mRNA is degraded by the cell)
Splicing and alternate splicing occur

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29
Q

Splicing and Alternate Splicing

A

Introns
Exons
Exons allow for one gene to code for multiple proteins

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30
Q

Steps in Translation

A

Initiation
Elongation
Termination
Post Translational Processing

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31
Q

Translation Initiation

A

The small subunit of the ribosome binds at the 5’ end of the mRNA and moves in a 3’ direction until it meets the start codon
It forms a complex with the large subunit of the ribosome and the initiation tRNA molecule

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32
Q

Translation Elongation

A

mRNA is read by the ribosome in sections of three bases called a codon
The tRNA brings the corresponding amino acid to the ribosome
The sequence of 3 bases on the tRNA is called the anti-codon
An enzyme called peptidyl transferase links the amino acids together using peptide bonds

33
Q

Translation Termination

A

Translation will stop when the ribosomal complex reaches the stop codon on the mRNA
Once this sequence is reached, the protein is released

34
Q

Post Translational Processing

A

Last proteins are folded and modified Certain proteins must be altered before they can function
Some need sugars
Some need to be cut by enzymes (insulin)
Others need to aggregate together (hemoglobin)

35
Q

How Much of Our Genome is Composed of Coding Genes

36
Q

We Have How Many Genes

37
Q

What Does It Mean to Turn Up or Over Express a Gene

A

To make too many copies of a protein

38
Q

How Many Amino Acids Exist Naturally

39
Q

How Does a Gene Get Turned On

A

Factors outside the cell send signals that alter the chromatin structure in a way that exposes the promoter region of a gene

40
Q

What Enzyme Builds mRNA

A

RNA polymerase

41
Q

Where In the Cell Does Splicing Occur

A

The nucleus

42
Q

DNA to mRNA to tRNA

A

A to U
then U to A

43
Q

Understand

A

Genes must constantly be transcribed and translated in order to make enough protein in the quantities needed by the cell
Genes can be fully on, only
partially on, or off

44
Q

BioBits Lab

A

Clear, green, green, green
Same
Clear, red, clear, clear

45
Q

Reagents in BioBits Pellet

A

RNA polymerase
Ribosomes
tRNAs
Amino acids
Translation factors
Energy source
Buffer
Cell-free extract
Fluorescent/reporter proteins

46
Q

Function of Promoter

A

Tells transcription machinery to start

47
Q

Function of Aptamer

A

Small RNA or DNA sequence that binds to a molecule
A lock that fits to a specific key
Helps regulate the gene by activating orblocking processes depending on the prescence of the key molecule
If unpresent, unregulated gene expression, loss of sensing, or inefficiency

48
Q

Function of Coding Sequence

A

Instructions for making protein

49
Q

Function of Terminator Sequence

A

Tells RNA polymerase to stop copying DNA into RNA

50
Q

Difference Between mRNA and Proteins

A

mRNA is transient to allow cells to adapt protein production quickly to changing conditions
Proteins are stable because they carry out essential, long term functions

51
Q

Genomics

A

Interaction of genes with each other or the environment

52
Q

Number of Base Pairs in the Human Genome

A

Three billion bp

53
Q

Identified Species Compared to Yearly Extinction Rate

A

Species going extinct before we can name them
Helps conservation efforts
Preserve record of biodiversity before its lost

54
Q

DNA Barcoding Controversies

A

Incomplete database
Genetic overlap
Oversimplification
Ethical concerns of data
Cost and resources
Lack of standardization

55
Q

DNA Barcoding Answers

A

Can species, biodiversity monitoring, alike species, authenticity, invasive species
Can’t ecological interactions, behaviour, environmental factors, complex history, detailed functions, and population

56
Q

Barrier Filter Tip Use

A

Cross contamination
Aerosol contamination

57
Q

Spin Column Use

A

Purify
After cell lysis, contaminents pass through
Washing
Released

58
Q

Cell Lysis

A

Breaking open cell to relase contents

59
Q

Small Piece for DNA Extraction

A

Minimize contamination
Prevent degradation

60
Q

Electropherogram

A

DNA Sequencing with peaks

61
Q

QS Score

A

Reflects accuracy of each base score
Higher better, max usually 30

62
Q

CRL Score

A

Base calling confidence
Higher better

63
Q

Phred Score

A

Error probability
Higher more confident, max usually 30

64
Q

BLAST

A

Compare sequence to database

65
Q

MUSCLE

A

Sequence alignment and comparison

66
Q

E-Value

A

Number of matches
Lower means more significant match

67
Q

Copies Made During PCR

A

One billion

68
Q

What’s Needed For PCR

A

Primer
DNA Polymerase
Nucleotides
Buffer

69
Q

Added to PCR Tube For PCR

A

Master mix which includes
DNA Polymerase
Buffers

70
Q

PLEASE ASK ABOUT

A

Buffers in PCR
Grey lines in DNA barcoding

71
Q

Binding Proteins

A

Bind to specific regions of DNA
Start DNA replication
Turn genes on and off
Fix damaged DNA
Package DNA

72
Q

Steps of DNA Replication

A

Helicase
Binding proteins
Primase makes short stretch of RNA
Elongation
DNA nucleotides to RNA primer
DNA polymerase proofreads
Builds
Enzymes remove RNA primers
Ligase seals backbone

73
Q

Reading Primes

A

Five prime where phosphate group is attatched to the fifth carbon
Three prime where hydroxyl group is attatched to third carbon

74
Q

When Does DNA Replication Happen Naturally

75
Q

Charge of DNA

A

Negative charge

76
Q

Running Buffer Purpose

A

Provide ions for electrical conductivity
Stablization

77
Q

Why Does One Pyrimidine Bond With a Purine

A

Complementary shapes
A and T form two hydrogen bonds
C and G form three hydrogen bonds

78
Q

Discovered DNA

79
Q

Conversions

A

1 ml = 1,000 uL
1 L = 1,000 mL
1 L = 1,000,000 uL

Biotechnology (3 decks)

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