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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
Transcription Initiation
The DNA molecule unwinds and separates to form a small open complex RNA Polymerase binds to the promoter of the template strand
26
Transcription Elongation
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
27
Transcription Termination
A terminator sequence in the DNA indicates where the gene ends Trigger processes which release the transcript RNA from the transcriptional complex
28
Processing
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
29
Splicing and Alternate Splicing
Introns Exons Exons allow for one gene to code for multiple proteins
30
Steps in Translation
Initiation Elongation Termination Post Translational Processing
31
Translation Initiation
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
32
Translation Elongation
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
Translation Termination
Translation will stop when the ribosomal complex reaches the stop codon on the mRNA Once this sequence is reached, the protein is released
34
Post Translational Processing
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
How Much of Our Genome is Composed of Coding Genes
1%
36
We Have How Many Genes
20,000
37
What Does It Mean to Turn Up or Over Express a Gene
To make too many copies of a protein
38
How Many Amino Acids Exist Naturally
About 500
39
How Does a Gene Get Turned On
Factors outside the cell send signals that alter the chromatin structure in a way that exposes the promoter region of a gene
40
What Enzyme Builds mRNA
RNA polymerase
41
Where In the Cell Does Splicing Occur
The nucleus
42
DNA to mRNA to tRNA
A to U then U to A
43
Understand
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
BioBits Lab
Clear, green, green, green Same Clear, red, clear, clear
45
Reagents in BioBits Pellet
RNA polymerase Ribosomes tRNAs Amino acids Translation factors Energy source Buffer Cell-free extract Fluorescent/reporter proteins
46
Function of Promoter
Tells transcription machinery to start
47
Function of Aptamer
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
Function of Coding Sequence
Instructions for making protein
49
Function of Terminator Sequence
Tells RNA polymerase to stop copying DNA into RNA
50
Difference Between mRNA and Proteins
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
Genomics
Interaction of genes with each other or the environment
52
Number of Base Pairs in the Human Genome
Three billion bp
53
Identified Species Compared to Yearly Extinction Rate
Species going extinct before we can name them Helps conservation efforts Preserve record of biodiversity before its lost
54
DNA Barcoding Controversies
Incomplete database Genetic overlap Oversimplification Ethical concerns of data Cost and resources Lack of standardization
55
DNA Barcoding Answers
Can species, biodiversity monitoring, alike species, authenticity, invasive species Can't ecological interactions, behaviour, environmental factors, complex history, detailed functions, and population
56
Barrier Filter Tip Use
Cross contamination Aerosol contamination
57
Spin Column Use
Purify After cell lysis, contaminents pass through Washing Released
58
Cell Lysis
Breaking open cell to relase contents
59
Small Piece for DNA Extraction
Minimize contamination Prevent degradation
60
Electropherogram
DNA Sequencing with peaks
61
QS Score
Reflects accuracy of each base score Higher better, max usually 30
62
CRL Score
Base calling confidence Higher better
63
Phred Score
Error probability Higher more confident, max usually 30
64
BLAST
Compare sequence to database
65
MUSCLE
Sequence alignment and comparison
66
E-Value
Number of matches Lower means more significant match
67
Copies Made During PCR
One billion
68
What's Needed For PCR
Primer DNA Polymerase Nucleotides Buffer
69
Added to PCR Tube For PCR
Master mix which includes DNA Polymerase Buffers
70
PLEASE ASK ABOUT
Buffers in PCR Grey lines in DNA barcoding
71
Binding Proteins
Bind to specific regions of DNA Start DNA replication Turn genes on and off Fix damaged DNA Package DNA
72
Steps of DNA Replication
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
Reading Primes
Five prime where phosphate group is attatched to the fifth carbon Three prime where hydroxyl group is attatched to third carbon
74
When Does DNA Replication Happen Naturally
Synthesis
75
Charge of DNA
Negative charge
76
Running Buffer Purpose
Provide ions for electrical conductivity Stablization
77
Why Does One Pyrimidine Bond With a Purine
Complementary shapes A and T form two hydrogen bonds C and G form three hydrogen bonds
78
Discovered DNA
Miescher
79
Conversions
1 ml = 1,000 uL 1 L = 1,000 mL 1 L = 1,000,000 uL

Biotechnology (5 decks)

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