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MCAT BIochem > DNA & Biotechnology > Flashcards

DNA & Biotechnology Flashcards

1
Q

Nucleoside

A

Five carbon sugars (pentoses) bonded to a nitrogenous base & formed by a covalently linked base to the C1 of the sugar

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2
Q

Nucleotides

A

One or more phosphate groups attached to C5’ of a nucleoside

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3
Q

How are sugar backbones linked

A

3’ to 5’

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4
Q

What is at the 3’ end of the DNA strand?

A

Free OH

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5
Q

What is at the 5’ end of the DNA strand?

A

Phosphate group

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6
Q

How is DNA read?

A

5’ to 3’

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7
Q

Huckel’s rule

A

Nitrogenous base has 4n +2 pi electrons

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8
Q

What kind of handed-ness is biological ?

A

Right-handed- makes a turn every 3.4 nm with 10 bases

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9
Q

Recombiant DNA

A

Allows DNA fragments from any source to be multiplied by either gene cloning or polymerase chain reaction (PCR)
Uses recombinant plasmids

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10
Q

DNA cloning

A

Produces large amounts of desired sequence
Must litigate DNA of interest into a vector piece of DNA forming a recombinant vector
If also includes antibiotic resistance gene- kill off all others so that there will only be resistant ones

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11
Q

Restriction enzymes/endonucleases

A

Enzymes that recognize specific double-stranded DNA sequences that are palindromic -antiparallel
Allow for insertion into vectors with “Sticky ends”

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12
Q

Aromatic characteristics

A

Cyclic
Planar
Conjugated with alternating single & multiple bonds or lone pairs making at least one unhybridized p-oribital for each atom in the ring
Hucke’s rule=4n +2 pi electrons

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13
Q

Calculating amount from opposite using Chargaff?

A

Remember to take out all of pyrimadine or purine from the total before halving

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14
Q

Z DNA

A

Left-handed helix with turns ever 4.6 nm and 12 bases a turn

High GC content- unstable

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15
Q

What on DNA may provide sites for binding ?

A

Major and minor groves

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16
Q

Reannealing

A

Bring DNA strands back together

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17
Q

probe DNA

A

Used in PCR & detection of certain DNA to reanneal with target DNA sequences to show presence of gene of interest- hybridization

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18
Q

What is the charge of a histone?

A

Basic

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19
Q

H1 histone protein

A

Seals off the DNA as it enters & leaves the nucleosome to add stability

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20
Q

Heterochromatin

A

Remains compact during interphase and is transcriptionally silent
HIghly repitive sequences

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21
Q

What kind of DNA do centromeres contain?

A

Heterochromatin with highly repetve GC sequences

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22
Q

Where are telomeres most likely located?

A

At the 5’ end ( no complete synthesis here bc needed a start place)

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23
Q

DNA topoisomerases

A

Work ahead of DNA helicase to relax strands that have become super-coiled during replication
Uses negative supercoils

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24
Q

How does DNA Polymerase read the DNA strands

A

3’ to 5’

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25
What is the difference in orgin of replication in prokaryotic & eukaryotic cells?
Prokaryotic- have one | Eukaryotic- have multiple
26
What synthesizes DNA in Prokaryotic cells?
DNA Polymerase III
27
What synthesizes DNA in Eukaryotic cells?
DNA Polymerase a, sigma, e
28
What removes RNA primers in Prokaryotic cells?
DNA Polymerase I
29
What removes RNA primers in Eukaryotic cells?
RNase H
30
What replaces RNA with DNA in prokaryotic cells?
DNA Polymerase I
31
What replaces RNA with DNA in eukaryotic cells?
DNA Polymerase sigma
32
Are there telomeres in prokaryotic DNA?
No
33
Oncogenes
Mutated genes that cause cancer
34
Antioncogenes
Normally function to suppress tumor progression | Like p53 or Rb
35
Where is DNA mutations more highly likely?
In the lagging strand
36
Mismatch repair
Machinery in G2 phase of cell that have enzymes that detect and remove errors in replication that were missed during S phase MSH2 and MLH1
37
Nucleotide excision repair
Elimates thymine dimers from UV light dimerization | Uses excision endonuclease to cut phosphodiester backbone and cut out thymine dimer
38
Base excision repair
Detect base errors like conversions to uracil or other small, non-helix distorting bases Base is recognized by a glycosylase and leaves a AP site (apurinic/apyrimidinc)/abasic site
39
AP Endonucleases
In base excision repair | AP site is recognized and AP endonucleaser removes the damaged sequence from DNA
40
How are DNA fragments multiplied?
Gene cloning or polymerase chain reaction (PCR)
41
How does gene cloning take small amounts of heterogenous DNA make large amounts of homogenous DNA?
Place into recombinant plasmids and select a colony to lyse the bacteria and take out the plasmids to be used
42
What do DNA sequences recognized by restriction endonucleases look like?
Palindromic (Can cut between the same two on each side of the DNA) Isolated from bacteria
43
What is the advantage of "stick ends"?
Allow restriction fragment to recombine with vector DNA | Vector cut with the same restriction enzyme to allow for fragments to be inserted directly into the vector
44
DNA libraries
Large collections of known DNA sequences | DNA fragments are digested randomly and cloned into vectors to be studied
45
Genomic libraries
Contain large fragments of DNA and include coding and noncoding regsions (exons and interons)
46
cDNA (Complementary DNA)
Made by reverse transcribing mRNA LACKS INTERONS Also called expression libraries
47
What do cDNA libraries produce?
Sequence specific genes, identify disease mutations, produce recombinant proteins (insulin), or prodcues transgenic animals
48
Why can only cDNA libraries be reliably used to make things?
Genes may chance be split into multiple vectors in genomic libraries
49
What enzyme is used to make genomic libraries?
Restriction endonucleases
50
What enzyme is used to make cDNA libraries?
Reverse transcriptase
51
Which genes libraries can be expressed in a cloning host in recombinant proteins?
cDNA libraries only
52
Hybridization
Joining of complementary base pair sequences (DNA-DNA or DNA-RNA) Uses tow single-stranded sequences
53
Polymerase Chain Reaction (PCR)
Produce millions of copies of DNA without amplifying DNA in bacteria Primers complementary to DNA flanking region of interest, nucelotides, and heat resistant DNA polymerase are needed Heat needed to pull DNA apart DNA is denatured, replicated, and reanealed to double DNA amount each time
54
What is the charge on DNA strands and what will they migrate towards?
Negative charge | Migrate toward anode
55
What gel is used in DNA electrophoresis?
Agrose gel
56
Southern blot
Used to detect the presence and quantity of various DNA strands in a sample
57
Steps in Southern blot
DNA cut by restriction enzymes and separated using gel electrophoresis Fragments transferred to a membrane Membrane probed with many copies of a single-stranded DNA to bind complementary strands to make double strand (probes labeled to indicate desired sequence)
58
Dideoxyribonucleotides
Contains hydrogens at C3' so that polymerase can no longer add to the chain
59
How can DNA be sequenced
Using dideoxyribonucleotides, modified bases causes the sample to contain many fragments of individual nucleotides and the fragments can be read using gel electrophoresis that will separate them by size
60
Gene therapy
Transfer a normal copy of a gene into the affected tissues of diseases where a gene is mutated or inactive
61
What must be done to a retrovirus during retrovirus gene therapy?
Retrovirus DNA must be replaced by therapeutic human DNA so that the retrovirus won't be able to self-replicate
62
Transgenic mice
Altered at the their germ line by producing a cloned gene into fertilized ovum into embryonic stem cells -->newly developed offspring will contain transgene in all cells
63
Transgene
Cloned gene introduced into mice cell germ line
64
Knockout mice
Gene has been intentionally deleted to study human disease
65
What kind of diseases are transgenic mice useful for studying?
Dominant gene disorders
66
What is the advantage of using stem cells?
Cloned genes can be introduced in cultures and one can select for cells with transgene successfully inserted
67
Chimera
Resulting offspring from stem cell insertion has patches of cells with transgene and ones that don't
68
How many hydrogen bonds are between cytosine and guanine?
3
69
How many hydrogen bonds are between adenine and thymine
2
70
What does prokaryotic DNA not have?
No histones means no nucleosomes
71
What does cytosine transform to in the presence of heat?
Uracil

MCAT BIochem (8 decks)

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