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Molecular Biology Exam 1 Flashcards
Lectures 1-7
262
Biology
Undergraduate 3
01/26/2015

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Term
What is Gregor Mendel known for?
Definition
Basic laws of inheritance
Term
What is Frederick Miescher known for?
Definition
Isolated Nuclein composition: acidic and basic
Term
What is Frederick Griffith known for?
Definition
Transformation experiment: Transformed non-pathogenic pneumonia into pathogenic pneumo
Term
What did the Transformation experiment focus on?
Definition
S strain - encapsulated; highly pathogenic
R strain - unencapsulated; nonpathogenic
Dead mice vs. Living mice
Term
What are Avery, MacLeod, and McCarty known for?
Definition
Determined transforming substance: Deoxyribonucleic acid (DNA)
Term
What did Avery, MacLeod, and McCarty's results confirm?
Definition
DNA is destroyed by DNAse
DNA is unaffected by proteolytic enzymes
Term
What is DNA composed of?
Definition
Adenine
Guanine
Thymine
Cytosine
Deoxyribose
Phosphate
Term
What are the Purines
Definition
Adenine
Guanine
Term
What are the Pyrimidines
Definition
Thymine
Cytosine
Term
Erwin Chargaff's Rules
Definition
Base composition of DNA varies w/species
DNA from diff. tissues from same spec is the same
DNA bases do not change with age, nutrition, or environment
In all DNAs, A=T, G=C
Term
What are Rosalind Franklin and Maurice Wilkins known for?
Definition
X-ray diffraction studies
Term
What are James Watson and Francis Crick known for?
Definition
3-D Model of DNA
Term
What are the key aspects of the 3-D model proposed and accepted by science of DNA?
Definition
Double Stranded
Double Helix
Hydrophilic backbone of deoxyribose & phosphate
DNA strands not identical but complementary
Term
What does DNA stand for?
Definition
Deoxyribo Nucleic Acid
Term
What does DNA do?
Definition
Stores genetic information
Term
Where is DNA found?
Definition
Found in nucleus (most) & mitochondria (some)
Term
What does RNA stand for?
Definition
Ribo Nucleic Acid
Term
How many types of RNA are there?
Definition
Approximately 20
Term
True or False:
The 3 types of RNA that we looked at in lecture are each involved in translating DNA sequence into protein
Definition
True
Term
Where is RNA found?
Definition
Usually in cytoplasm
Term
Is RNA Single Stranded or Double Stranded (Usually)?
Definition
Single
Term
Is DNA Single Stranded or Double Stranded (Usually)?
Definition
Double
Term
How many Nucleotide polymers does DNA have?
Definition
Millions
Term
How many Nucleotide polymers does RNA have?
Definition
10's to 1000's
Term
Is Uracil a Purine or Pyrimidine?
Definition
Pyrimidine
Term
What type of sugar defines nucleic acid type?
Definition
Pentose
Term
What is at Position 2' of Ribose?
Definition
OH
Term
What is at Position 2' of Deoxyribose?
Definition
H
Term
Nucleoside
Definition
Sugar + Purine or Pyrimidine
Term
What is the nucleoside of Adenosine?
Definition
Deoxyadenosine
Term
What is the nucleoside of Cytidine?
Definition
Deoxycytidine
Term
What is the nucleoside of Guanosine?
Definition
Deoxyguanosine
Term
What is the nucleoside of Uridine?
Definition
Thymidine
Term
Nucleotide
Definition
Nucleoside + Phosphate
Term
RNA: Adenylate's nucleotide becomes what?
Definition
adenosine-5'-monophosphate
Term
What does the Phosphate group from 1 nucleotide connect to from another nucleotide?
Definition
Sugar
Term
What does the sugar group from 1 nucleotide connect to from another nucleotide?
Definition
Phosphate
Term
Where does the 5' phosphate group bind to sugar on next nucleotide?
Definition
3' position
Term
End of strand with free phosphate end called ____ end
Definition
5'
Term
End of strand with hydroxyl group is ____ end
Definition
3'
Term
Nucleotide sequence is ALWAYS written or read in a _____ manner using base abbreviations
Definition
5' to 3'
Term
G-C has how many hydrogen bonds?
Definition
3
Term
A-T has how many hydrogen bonds?
Definition
2
Term
The phosphate-deoxyribose backbones are the _____ of the ladder
Definition
sides
Term
The Nitrogen bases hydrogen bonded to each other are the ______ of the ladder
Definition
rungs
Term
Are the 2 strands of DNA parallel or antiparallel?
Definition
antiparallel
Term
What is the sequence for the other strand of the following:
5'-ACTCCGA-3'
Definition
5'-TCGGAGT-3'
Term
What would the sequence for the other strand of the following appear "in nature":
5'-ACTCCGA-3'?
Definition
3'-TGAGGCT-5'
Term
The two complementary strands ____ or ____ to each other through hydrogen bonds between the bases
Definition
Anneal
HYBRIDIZE
Term
True or False:
Each DNA strand has the potential to deliver and code for information
Definition
True
Term
What is the length of DNA given in terms of?
Definition
Base Pairs
Term
What are the 3 types of RNA that we covered in lecture?
Definition
mRNA
rRNA
tRNA
Term
What does mRNA do?
Definition
Copy of DNA code for making protein
Term
What does rRNA do?
Definition
Part of ribosomal machinery (used to make protein)
Term
What does tRNA do?
Definition
Carries Amino Acids to Ribosome where Protein is Formed
Term
True or False:
RNA is easily degraded and is referred to as transient
Definition
True
Term
In vivo, ____ degrades and forms uracil; leading to a DNA mutation
Definition
Cytosine
Term
True or False:
Any uracil found in DNA is corrected by "proofreading" system
Definition
True
Term
Does DNA have an Uracil?
Definition
No
Term
Genome
Definition
Entire set of DNA that makes up a particular organism
Term
Organism's genome contains ______ sequence information necessary for making the proteins that produce a complete organism
Definition
All
Term
Almost all genome located in nucleus EXCEPT tiny piece located in ______
Definition
Mitochondria
Term
energy-producing organelles
Definition
Mitochondria
Term
Each ______ cell contains a complete copy of genome
Definition
somatic
Term
Germ cells have ______ genome
Definition
1/2
Term
Human genome
________ bp of DNA
Definition
3,000,000,000
Term
In the Human Genome _____%: Genes encode for protein
Definition
5
Term
In the Human Genome _____%: Noncoding sequences between and within genes
Definition
95
Term
In the Human Genome, ______ bp make up the Mitochondrial DNA
Definition
16,000
Term
How many Mitochondrial genes in the Human Genome code for energy production proteins?
Definition
37
Term
Chromatin
Definition
Dispersed form in nondividing cells
Term
What does Chromatin consist of?
Definition
Proteins (histone & non-histone) + DNA
Term
Chromosomes
Definition
Nucleic acid molecule coding for genetic info
Term
Human genome stretched out _______ long
Definition
6 feet
Term
Nucleus ~ ____ microns
Definition
2-5
Term
Nucleosome
Definition
DNA wrapped around histones (protein)
Term
Supercoils
Definition
Coiling of a coil
Term
Human Chromosome has _____ total alleles
Definition
46
Term
How many human chromosomes are Somatic?
Definition
44 (22 pairs)
Term
How many human chromosomes are sex chromosomes?
Definition
2
Term
Allele
Definition
Any one of a number of different forms of the same gene at a given locus (position) on a chromosome
Term
Homozygous
Definition
Same
Term
Heterozygous
Definition
Different
Term
Genotype
Definition
Set of alleles inherited by an individual
Term
Phenotype
Definition
Observable effect of the genotype
Term
5 Reasons for extracting nucleic acids
Definition
Genetic Testing
Cancer characterization
Human identity testing - paternity
Human identity testing - forensics
Infectious organisms
Term
Name a few specimens consistent with Nucleic acid extraction and quantification
Definition
Blood
Urine
Semen
Buccal swab
Tissues
Cultured MOs
Term
What is the stability of DNA?
Definition
Relatively stable
Term
DNA is in what kind of strands?
Definition
Long, thin strands, which may break (shearing)
Term
True or False:
You should avoid excessive & rough pipeting and vortexing to avoid sheering DNA
Definition
True
Term
What is the most common RNA target in nucleic acid extraction?
Definition
mRNA
Term
Characterize RNA
Definition
Small, unstable, easily degraded
Term
Are the following DNA or RNA viruses?
HIV
HCV
Definition
HIV & HCV are RNA Viruses
Term
What kind of genes produce mRNA?
Definition
Active
Term
True or False:
You should use Universal Precautions when doing nucleic acid extraction
Definition
True
Term
Use ____ _____ ____ when performing nucleic acid extraction to prevent contamination of pipettes (which can contaminate samples)
Definition
Aerosol Resistant Tips
(ART)
Term
True or False:
Small mistakes can lead to big consequences since working with small samples
Definition
True
Term
Pulse spin
Definition
Short bursts of centrifuge reaching full speed
Term
What can over vortexing lead to?
Definition
Shearing of Nucleic acid
Term
3 Basic steps in nucleic acid extraction
Definition
Cell lysis
Digest proteins
Purify DNA
Term
DNA Extraction Protocol
Liquid Phase
Definition
*Cell lysate added to solvents w/ different solubility constants
*DNA present in one layer
*DNA layer separated, precipitated out, then rehydrated
Term
DNA Extraction Protocol
Solid Phase
Definition
*Cells lysed & treated w/ proteinases
*DNA precipitated by + OH
*DNA resuspended & + to column with silica
*Centrifuge
*DNA attaches to column
*Column rinsed with buffer
*DNA eluted from column w/ diff buffer
*Purified DNA in bottom of tube
Term
True or False:
DNA bind irreversibly to silica depending on pH
Definition
False
Term
True or False:
DNA Extraction Solid-Phase protocol is fast, safe, and yields very clean DNA
Definition
True
Term
True or False:
Some RNA may also be extracted with the DNA extraction solid-phase protocol
Definition
True
Term
What can you add to the solid phase DNA extraction protocol to remove RNA?
Definition
RNase
Term
What is the Average yield of solid phase DNA extraction protocol?
Definition
6 micrograms from 200 microliters whole human blood
Term
What is the size of the yield in DNA extraction solid-phase protocol
Definition
~ 20-30 kb
Up to 50 kb
Term
Should you avoid multiple free-thaw cycles?
Definition
Yes
Term
RNA Extraction
Process _____ specimens promptly
Definition
Fresh
Term
RNA Extraction
Place RNA in special _____
Definition
preservative
Term
RNA Extraction
________ in liquid nitrogen
Definition
Snap-freeze
Term
RNases _______ (hands, water, equipment, everywhere)
Definition
ubiquitous
Term
What kind of components do you need for RNA Extraction?
Definition
RNase free
Term
What should you use to remove DNA which can interfere with test results?
Definition
DNase
Term
Should you wear gloves while performing RNA Extraction?
Definition
Yes
Term
Nucleic acids absorb UV light at _________ nM
Definition
260
(A260)
Term
Proteins absorb UV at _____ nM
Definition
280
(A280)
Term
Ratio of ___ to _____: Very clean nucleic acid preparation
Definition
1.8
2.0
Term
Ratio of ____ to ______: Acceptable for some tests (PCR) but not others (sequencing)
Definition
1.6
1.8
Term
Ratio of _____: Not acceptable
Definition
<1.6
Term
Acceptable ratio is for what kind of tests?
Definition
PCR
Term
What kind of tests does Ratio of 1.6 to 1.8 not work with?
Definition
Sequencing
Term
1.0 OD unit at A260 = _____ micrograms/mL double stranded DNA
Definition
50
Term
1.0 OD260 unit = ______ micrograms/mL RNA
Definition
40
Term
A DNA sample gives the following results:
Total volume = 100 microliters
Specimen diluted 1:5
Diluted specimen OD260 = 0.5 units
Diluted specimen OD280 = 0.300 units
What is the purity calculation?
Definition
1.7
Term
How do you determine purity calculation?
Definition
OD260 / OD280
Term
A DNA sample gives the following results:
Total volume = 100 microliters
Specimen diluted 1:5
Diluted specimen OD260 = 0.5 units
Diluted specimen OD280 = 0.300 units
What is the Yield calculation?
Definition
12.5 micrograms DNA
Term
A DNA sample gives the following results:
Total volume = 100 microliters
Specimen diluted 1:5
Diluted specimen OD260 = 0.5 units
Diluted specimen OD280 = 0.300 units
How do you determine the Yield?
Definition
0.5 x 50 = 25 micrograms/milliliter
25 x 5 = 125 micrograms/milliliter
125 / 1000 = 0.125 micrograms/microliter
Multiply by the total volume
Term
Replication
Definition
DNA Synthesis
Term
Transcription
Definition
RNA Synthesis
Term
Translation
Definition
Protein Synthesis
Term
Who proposed Replication, Transcription, and Translation?
Definition
Francis Crick
Term
What is the Revised Central Dogma of Molecular Biology?
Definition
Retroviruses transcribe RNA into DNA with Reverse Transcriptase
Term
True or False:
Reverse Transcriptase is an enzyme
Definition
True
Term
DNA Replication
Definition
Process to make replica or identical copy of genomic DNA
Term
Is DNA replication semi-conservative?
Definition
Yes
Term
Semi-conservative
Definition
After replication each double strand of DNA composed of 1 "new" and 1 "parent" DNA strand
Term
What assures that DNA is copied exactly in DNA Replication?
Definition
Base-Pairing
Term
DNA Replication
ENZYMES in sequential order
Definition
Helicase
Topoisomerase
Primase
DNA polymerase III
Term
Helicase
Definition
Unwinds and Separates DNA double strand
Term
True or False:
Special proteins prevent rejoining of double strands during DNA Replication
Definition
True
Term
Topoisomerase
Definition
Reduces supercoiling which occurs during unwinding
Term
Primase
Definition
Produces RNA primer
Term
DNA polymerase III
Definition
Adds appropriate nucleotide to 3' end of new DNA strand
Term
What does DNA polymerase require to do its job?
Definition
Template
RNA Primer
Term
Template
Definition
Parent DNA strand
Term
RNA Primer
Definition
Complementary to DNA template
Term
Newly synthesized DNA strands are _____ to parent strand
Definition
anti-parallel
Term
Leading strand
Definition
Replicated continuously from 3' end of the parent strand (template) with the newest end of the forming strand facing into the replication fork
Term
What is the direction of strand formation?
Definition
5' to 3'
Term
Lagging strand
Definition
Formed in pieces
Term
DNA polymerase replicates DNA only in ____ to _____ direction
Definition
5'
3'
Term
What are the pieces of the Lagging strand called?
Definition
Okazaki fragments
Term
With the Okazaki fragments the 5' to 3' synthesis occurs in direction ______ to fork movement
Definition
opposite
Term
Each Okazaki fragment has its own ____ ____ formed by primer
Definition
RNA primer
Term
After Okazaki fragment complete, __________ removes RNA primer and replaces it with DNA
Definition
DNA polymerase I
Term
Ligase
Definition
Links the Okazaki fragments
Term
True or False:
Replication occurs at multiple sites on chromosome at the same time
Definition
True
Term
RNA Synthesis - Transcription
Definition
DNA information transferred to a newly assembled piece of RNA
Term
What is the first step in RNA synthesis
Definition
DNA double helix unwinds
Term
Does RNA polymerase reads only 1 strand?
Definition
Yes, the template
Term
In which direction is RNA synthesized?
Definition
5' to 3'
Term
What is the sugar in RNA?
Definition
Ribose
Term
Template for RNA
Definition
The 3' to 5' DNA strand
Term
Where does mRNA, copy of the "non template" DNA strand, travel to in order to be read to form protein?
Definition
Cytoplasm
Term
Where is the location of the following:
RNA polymerase I
Definition
Nucleolus
Term
Where is the location of the following:
RNA polymerase II
Definition
Nucleoplasm
Term
Where is the location of the following:
RNA polymerase III
Definition
Nucleoplasm
Term
Where is the location of the following:
mt RNA polymerase
Definition
Mitochondria
Term
What is the product of the following:
RNA polymerase I
Definition
rRNA
Term
What is the product of the following:
RNA polymerase II
Definition
mRNA
Term
What is the product of the following:
RNA polymerase III
Definition
tRNA
Term
What is the product of the following:
mt RNA polymerase
Definition
mtRNA
Term
What does the following stand for:
mtRNA
Definition
Mitochondria RNA
Term
What does the following stand for:
mRNA
Definition
Messenger RNA
Term
What does the following stand for:
rRNA
Definition
Ribosomal RNA
Term
What does the following stand for:
tRNA
Definition
Transfer RNA
Term
What 2 type of cells are RNA polymerases?
Definition
Eukaryotic
Prokaryotic
Term
What type of cells are the enzymes RNA polymerase I-III and mt RNA polymerase?
Definition
Eukaryotic
Term
Promoters
Definition
DNA regions that signal RNA polymerase starting point
Term
True or False:
Factors (proteins) help RNA polymerase recognize promoter
Definition
True
Term
In the Initiation step of Transcription what size section of the DNA helix unwinds?
Definition
Short
Term
What happens during the Elongation step of Transcription?
Definition
RNA polymerase moves along DNA
Synthesizes RNA 5' to 3'
Term
What happens during Termination step of Transcription
Definition
Terminator sequence: Stop RNA polymerase
Termination factors (proteins)
Term
What are the 3 steps of Transcription?
Definition
Initiation
Elongation
Termination
Term
Where does Post-transcriptional processing take place?
Definition
Nucleus
Term
pre-mRNA
Definition
RNA first transcribed from DNA
Term
What does the pre-mRNA contain?
Definition
Introns
Exons
Term
Introns
Definition
Noncoding
Term
Where do Introns stay?
Definition
Within the nucleus
Term
Exons
Definition
Coding
Term
Where do Exons exit
Definition
The Nucleus
Term
What happens during RNA splicing?
Definition
Noncoding introns are removed from pre-mRNA
Term
What is RNA splicing done by?
Definition
Spliceosomes (special enzymes)
Term
True or False:
Introns vary in size and sequence among individuals
Definition
True
Term
True or False:
Exons vary in size and sequence among individuals
Definition
False
Term
True or False:
Intron variations are used in DNA fingerprinting
Definition
True
Term
True or False:
Intron variations are not used in gene function
Definition
True
Term
mRNA additional processing:
5' Cap
Definition
Special modified nucleotide added to 5' end
Term
What does the 5' Cap do?
Definition
Helps protect mRNA
Term
mRNA additional processing:
Poly(A) tail
Definition
Added to 3' end; can be used to help isolate mRNA
Term
What occurs with the Poly(A)tail in mRNA additional processing?
Definition
*poly(T)s attached to column in solid phase extraction protocol
*Poly(A)tail hybridizes to Poly T and mRNA attaches to column
Term
True or False:
The number of As in Poly(A)tail varies
Definition
True
Term
Translation
Definition
Synthesis of protein using mRNA as template
Term
mRNA transported to _____ for protein synthesis
Definition
Cytoplasm
Term
Linear sequence of amino acids joined by ______ bonds
Definition
Peptide
Term
How many Amino Acids are used to make proteins?
Definition
20
Term
Which end has the Amino terminus?
Definition
5'
Term
Which end has the Carboxy terminus?
Definition
3'
Term
What is another name for Codon?
Definition
Triplet Code
Term
Codon:
____ nucleotides encode for 1 amino acid
Definition
3
Term
If there are 62 codons, how many nucleotides are in the triplet code?
Definition
4
Term
True or False:
The Genetic code is redundant
Definition
True
Term
What is another word for redundant?
Definition
Degenerate
Term
True or False:
An amino acid may be encoded by more than 1 codone
Definition
True
Term
What is the START Codon
Definition
AUG
Term
What does AUG code for?
Definition
Methionine
Term
True or False:
ALL proteins start with Methionine
Definition
True
Term
What are the STOP Codons?
Definition
UAA
UAG
UGA
Term
Do Codons overlap?
Definition
NO
Term
True or False:
Mutations or errors in genomic DNA carry through to mRNA and may change protein composition (depending on the error)
Definition
True
Term
Do mutations or errors in genomic DNA Always change protein composition?
Definition
NO
Term
What is the following an example of?
5'UUUAUGGUACUUAAAGGCCCCUAUUAGGGG-3'
Definition
mRNA
Term
What is the following an example of?
5' UUU AUG GUA CUU AAA GGC CCC UAU UAG GGG 3'
Definition
Codons
Term
What is the following an example of?
5' Met Val Leu Lys Gly Pro Tyr Stop
Definition
Amino Acids
Term
True or False:
The Genome is the entire set of genes
Definition
True
Term
What is the role of tRNA in translation?
Definition
Carries amino acids to ribosome to be added to polypeptide
Term
True or False:
Each tRNA molecule is specific for only 1 amino acid
Definition
True
Term
True or False:
Each tRNA molecule is specific for 1 specific mRNA codon
Definition
True
Term
tRNA ______ is complementary to mRNA codon
Definition
anticodon
Term
Codon for Phe in mRNA: UUC
Anticodon of tRNA for Phe is _____
Definition
AAG
Term
Polyribosome
Definition
Multiple ribosomes on a strand of mRNA
Term
Ribosomal enzyme catalyzes formation of _____ bond
Definition
peptide
Term
True or False:
The appropriate tRNA base pairs with codon
Definition
True
Term
Codons on mRNA are "read" by _______
Definition
tRNA
Term
Ribosome binds to _____ at initiation site to form initiation complex
Definition
mRNA
Term
Where can you find the Protein-ribosomal RNA complex?
Definition
Ribosome
Term
How fast is the helicase unwinding the double helix?
Definition
Speed of a Jet Engine
Term
What are the 2 reagents in the lysis solution
Definition
Detergent
Proteinase K
Term
What does the Detergent do in the lysis solution?
Definition
Dirupts cell membrane & Nuclear envelope causing cell to burst open and release DNA
Term
What does the Proteinase K do in the lysis solution?
Definition
Cuts apart the histones to free DNA
Term
What is the purpose of the concentrated salt solution?
Definition
Cause proteins and other cellular debris to clump together
Term
What is the purpose of adding isopropyl alcohol to the DNA suspension
Definition
Causes DNA to clump out of solution and can be seen with the naked eye
Term
How can DNA be stored for many years?
Definition
Freezer
Term
The number of histones in a nucleosome is:
Definition
8
Term
The number of nucleosomes in chromatin is:
Definition
6
Term
The number of nuclei that can fit onto the tip of a needle is
Definition
10,000
Term
Name the reasons for isolating DNA
Definition
Genetic Testing
Body identification
Analysis of forensic evidence
Term
True or False:
The four DNA purification steps are collect cheek cells, burst cells to release DNA, separate DNA from protein and debris, and isolate concentrated DNA.
Definition
True
Term
True or False:
The purpose of the salt solution is to cause proteins and the DNA to clump together
Definition
False
Term
Name the purpose of adding isopropyl alcohol to the DNA suspension
Definition
DNA will come out of solution
Term
What project did Maurice Wilkins work on before his DNA studies?
Definition
Bomb
Term
Name the scientist who played a key role in developing the X-ray diffraction technique
Definition
Maurice Wilkins
Term
In what country did Watson, Crick , Wilkins, and Franklin do their work on DNA?
Definition
England
Term
Who made the X-ray diffraction images which provided key DNA information?
Definition
Rosalind Franklin
Term
What is the most likely reason Rosalind Franklin was not awarded the Noble Prize?
Definition
She died and the Noble Prize is only given to living people
Term
What was James Watson's approximate age when he and Frances Crick determined the structure of DNA?
Definition
22
Term
Did Waston and Crick spend long hours in the lab gathering data for determining DNA structure?
Definition
NO
Term
Select all of the scientists who recieved the Noble Prize for determinig DNA structure
Definition
Watson
Crick
Wilkins
Term
Which enzyme joins DNA fragments together by reforming the sugar-phosphate bonds of DNA?
Definition
Ligase
Term
What is the name of the process used to transfer DNA into bacteria.
Definition
transformation
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