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Molecular Bioclass 3 Flashcards

1
Q

Antiparallel orientation

A

5’ end of one chain is paired with the 3’ end of the other

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2
Q

Annealing (hybridization)

A

The bonding of two complimentary strands of DNA into a double-stranded structure

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3
Q

Melting (denaturation)

A

The separation of strands

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4
Q

Genome

A

The sum total of the organisms genetic information

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5
Q

Chromosomes

A

Eukaryotes genomes are composed of several large pieces of linear dis-DNA called chromosomes. Humans have 46. Half from mom and half from dad. 23 pairs

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6
Q

DNA gyrase

A

Uses the energy from ATP to twist the gigantic circular molecule. Breaks the dna and twists the two strands around each other making super coils

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7
Q

Histones

A

8 of them in a clump. Globular proteins that are wrapped inside dna. Have a lot of amino acids that are positively charged ( lysine and arginine) packs with the negative charged backbone of dna

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8
Q

Nucleosomes

A

Composed of dna wrapped around an octane of histones (a group of eight). The octane is composed of two units of each of the histone proteins H2a, H2b, h3 and H4. The string between the beads is a length of double helical DNA called linker DNA and is bound by a single linker histone

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9
Q

Chromatin

A

Fully packed DNA. It is composed of closely stacked nucleosomes

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10
Q

Stricture of DNA in the Nucleus

A

Deoxyribose, add base, nucleoside ,add 3 phosphates, nucleotide, polymerize with loss of two phosphates, oligonucleotide, continue polymerization, single- stranded polynucleotide, 2 complete chains H-bond in antiparallel orientation
, ds DNA chain, coiling occurs, ds helix, wrap around histones, nucleosomes, complete packing, chromatin

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11
Q

Heterochromatin

A

Chromosome portion that is darker. Rich in repeats

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12
Q

Euchomatin

A

Lighter regions of the chromosome are less dense. Unwound, active

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13
Q

Centromeres

A

Regions of the chromosome were central’s attach during cell division. The fibers attach via kinetochores. Made of heterochromatin and repetitive dna sequences

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14
Q

Kinetochores

A

Multiprotein complexes that act as anchor attachment sites for single fibers

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15
Q

Telomeres

A

At the end of the chromosome. Repeated 50 to a several hundred times. Usually 6 to 8 base unit pairs long and rich in guanine (G). Made of both single and double stranded DNA

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16
Q

Telomeres function

A

To prevent deterioration and also prevent fusion with neighboring chromosomes. No found in prokaryotes. They act as buffers blocking the ends of the chromosomes

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17
Q

RNA is different from DNA

A
  1. Single stranded (except in viruses)
  2. Contains uracil instead of thymine
  3. The pentode ring in RNA is ribose rather than 2’ deoxyribose
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18
Q

RNA less stable

A

RNA is less stable because 2’ hydroxyl can nucleophilically attack the backbone phosphate group of an RNA chain, causing hydrolysis when the remainder of the chain acts as leaving group

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19
Q

DNA is more stable

A

DNA does not have a 2’ hydroxyl

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20
Q

Heterogeneous nuclear RNA (hnRNA)

A

In eukaryotes the first RNA transcribed from DNA is an immature of precursor for RNA. Processing events are requires (splicing or adding a cap) for hnRNA to become mature mRNA. Only found in eukaryotes

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21
Q

Non-coding RNA (ncRNA)

A

Functional RNA not coded into protein. The human genome codes for thousands of rcRNAs, and there are several types. Two major types are tRNA and rRNA

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22
Q

Transfer RNA (tRNA)

A

responsible for translating the genetic code. Carries amino acids from the cytoplasm to the ribosome to be added to a growing protein

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23
Q

Ribosomal RNA (rRNA)

A

Major component of the ribosome. Humans have 4 different kind. 18S, 5.8S, 28S, and 5S. Almost all of the RNA made in a given cell is rRNA.

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24
Q

Function of rRNA

A

Serves as the catalytic function of the ribosome, which is a little odd. In most other cases enzymes are made of polypeptides.

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25
Ribozymes
Catalytic RNA, or ribonucleic acid enzymes.Since they are capable of performing specific biochemical reactions
26
Small nuclear RNA (snRNA)
Molecules (150 nucleotides) associate with proteins to form snRNP (small nuclear ribonucleic particles) complexes in the spliceosome
27
MicroRNA (miRNA) and Small interfering RNA (siRNA)
Function in RNA interference (RNAi), a form of post-transcriptional regulation of gene expression. Both can bind specific mRNA molecules to either increase or decrease translation
28
Long ncRNAs
Are longer than 200 nucleotides. They help control the basal transcription level in a cell by regulating initiation complex assembly on promoters. They also contribute to many types of post transcriptional regulation, by controlling splicing and translation, and they function in imprinting and X-chromosome inactivation
29
Embryogenesis
Cleavage > blastualtion> implantation> neurulation
30
Derivatives of the mesodermal germ layer
Skeletal muscles, kidney, and the gentian organs
31
The middle layer of the eyeball wall contains
Blood vessles
32
Purines
Bases G and A are derived from a precursor called purine 6 carbon ring w/ 5 member ring attached
33
Pyrimidines
C, T, and U and pyrimidines 6 carbon ring Sharp so they CUT
34
Backbone of DNA
Made up of sugar connected to phosphate and then another sugar
35
Phosphodiester binds
Links nucleotides covalently between 3’ hydroxy group of one deoxyribose and the 5’ phosphate group of the next deoxyribose. Starting at 5’ and going to 3’
36
Oligonucleotide
A polymer of several nucleotides linked together is termed an oligonucleotide, and a polymer of many nucleotides is a polynucleotide
37
Watson and crick model
Cellular dna is a right-handed double helix held together by hydrogen bonds between bases.
38
DNA H-bonded pair
Always a purine plus a pyrmidine A-T 2 h-bonds and G-C 3 h-bonds
39
Polymerase chain reaction (lab test)
Amplify DNA segments from just a little. Done a lot usually with more than one template. Primers Template dNTPs Taq polymerase Buffer solution
40
DNA stabilization
Phosphodiester bond in backbone H-bonds between bases Pi stacking (London dispersion forces)
41
Pi Stacking
Special London dispersion force for highly aromatic structures that allows for stacking and increased stabilization
42
Prokaryotes
Double stranded dna in a circle in the cytoplasm. They have methylated DNA. Blocks the active site for restriction enzymes. Virus dna is not methylated
43
Methylation
Protect prokaryotic dna from cutting enzymes (restriction enzymes)
44
Endonucleases
DNA digesting enzymes. Tend to cut palindromic sequence.
45
Palindromic sequence
Read 5’ to 3’ on top strand and 5’ to 3’ on the bottom strand. They are usually cleaved
46
How prokaryotes protect their DNA
Supercooling - coils the helix further DNA methylation
47
Eukaryotes liner
48
Start Codon
AUG - codes for methyanine amino acid
49
Stop Codons
UAA- you are annoying UGA - you go away UAG- you are gone No amino acid
50
Number of nucleotides in the genome
3 billion
51
Number of genes that can be transcribed
35,000 +
52
Intergenic regions
Large segments of dna in between genes. Don’t code for anything. They are what make a person unique. Has single nucleotide polymorphisms often mutated
53
Single nucleotide polymorphisms
Often mutated from person to person and is what makes us unique
54
Polymerase Errors
Point mutations Small repeats Insertions/ deletions (small, frame shift)
55
Point mutation (types)
Single base pair change that could occur. Missense Nonsense Silent
56
Missense mutation
Codon for a becomes a new codon for as. Change the amino acid. Can be simple or dire. Eg no change or sickles cell animea
57
Nonsense mutation
Codon for aa becomes STOP codon. Shortened protein. May still be functional
58
silent mutation
codon for aa becomes new codon for aa. no effect molecularly but could make less of the protein due to longer time to make the protein and can cause disease .
59
Frameshift mutations
Insertions and deletions changes the reading frame . Produces different amino acids. Unless 3 were added or removed
60
Endogenic Damage
Reactive oxygen species. Physical damage. Like oxidized dna. Can nitrogenous bases to become cross linked and form covalent bonds with each other . Can break double and single stranded dna (all of these can lead to polymerase errors.)
61
Intrastrand cross linking
Covalent bonds between adjacent bases on the same strand of dna. Endogenous damage
62
Interstrand cross linking
Covalent bonds between bases on opposite sides of a dna strand. Endogenous damage
63
Exogenous damage
Radiation and chemicals. UV radiations X rays Chemicals
64
UV radiation
Exogenous. Pyrimidine dimmers formed.
65
X rays
Double-stranded breaks and translocations. Exogenous
66
Chemicals
Can lead to physical damage or to intercalating and thus polymerase errors
67
Transposons
Changes dna on a large scale including insertions/ deletions, inversions and duplications.
68
What makes up a transposon.?
Transposase - enzyme Inverted repeats around the enzyme that act as recognition sites
69
Types of transposons 3x
IS element- (inverted sequence) Complex transposons- has the enzyme the inverted repeats and additional genes in between Composite Transposon- has two tranposons with gene region in between
70
How tranposons contribute to genetic variation
Cut and paste from the transposase. Very accurate because the inverted repeat sites are recognition sites. Pastes it in a completely random place.
71
Effect of a single transposon
Intergenic region - no effect Gene for eg. insulin would be no more insulin
72
Reducing the tranposons jumping ability
We methylated these regions
73
Bad bases (mismatch, oxidized, cross linked, diners.)
Mismatch repair pathway or the nucleotide excursion pathway
74
Mismatch repair pathway
During or shortly after replication. Because the parent strand is methylated you could assume the top strand is older and should be restored. You could also search for gaps or Okazaki fragments. Or an incomplete 3’ end.
75
Base/ nucleotide excursion repair
Can happen at any time in the cell cycle (ideally before replication). Remove the bad base and replace it with a good base
76
Broken Chromosomes (physical damage or X ray)
Homologous directed repair Non- homologous end joining
77
Homologous directed repair
Double stranded dna strand. Relies on the sister chromatid must be present so must happen after dna replication
78
Non-homologous end-joining
Can happen at anytime in the cell cycle. Legate broken ends together. Paste together whatever is left and can result in translocations. Mutagenic because usually lose base
79
DNA Rearrangements (transponsons)
Generally don’t lead to repair mechanisms
80
DNA Replication
Semiconservative 5’ to 3’ Requires a template Requires a primer
81
DNA is Semiconservative
The two parent strands can be used to create to daughter stands. So preserves one old strand couple with one new strand
82
Enzymes needed for DNA replication
Helicase Topoisomerase Single stranded binding proteins Primase DNA polymerase Ligase
83
Helicase
Unwinds dna by breaking hydrogen bonds
84
Topoisomerase
Acts like a scissors that cuts dna backbone, relaxes coils then. Then relighted the backbone back together
85
Primase
Synthesizes the primer. Needs to go in the oppositions direction of the parent strand. Can moon walk backwards to add more primers for the rest of the exposed region
86
DNA polymerase
Tacks off of the primer and begins to replicate
87
Leading strand versus lagging strand of DNA
Leading can task on and replicate. Lagging has to stop and replicate then stop and replicate to form Okazaki fragments
88
Ligase
Links Okazaki fragments to help form a single daughter strand
89
Prokaryotes DNA replication (theta replication)
5 polymerases Mains: 3 and 1
90
DNA polymerase 3
High processivity (moves fast) 5’ to 3’ and 3’ to 5’ exonuclease activity (can go back to fix errors) Adds nucleotides at ~400 Bo downstream of ORI This is the main replicating enzyme No known function in dna repair
91
DNA polymerase 1
Low processivity 5’ to 3’ and 3’ to 5’ exonuclease Also a 5’ to 3’ to remove primer Adds nucleotides at RNA primer DNA excision repair
92
DNA polymerase 2
Back up for polymerase 3. 5’ to 3’ polymerase and 3’to 5’ exonuclease DNA repair
93
DNA polymerase 4 and 5
Error prone 5’ to 3’ polymerase activity DNA repair
94
Replicating End of chromosomes in eukaryotes
Lagging strand adds our primers to the 3’ end of the parent strand. Once primers are removed the Ligase can fuse the remaining parts
95
Hayflick Limit
Average number a cell divides before it apoptosis
96
Telomere alongation
Telomerase Carrie’s it’s own template It have revers transcriptase activity
97
RNA versus DNA replication
Similarities: “start” site, 5’to3’ direction, DNA template Differences: “STOP” site, no primer, no editing
98
Primary point of translation regulation
Transcription is the main point of translation regulation
99
Prokaryotes
Transcription and translation happen at the dna time, in the same place. No mRNA processing
100
Polycistronic
Many different proteins from a single mRNA. Prokaryotes
101
Monocistronic
“One mRNA, one protein” eukaryotes
102
Eukaryotes RNA polymerase
Pol 1 - rRNA Pol 2 - mRNA Pol 3 - tRNA
103
tRNA how many are there to code for codons?
At least 20 tRNA and at most 61
104
Aminoacyl tRNA synthetase
Binds tRNA to the ribosome using 2 ATP
105
Wobble base pairing
When there is something GUI at the 5’ end of the anticodon. There’s more flexibility at the 3 point in the codon. Options include (I, G, U)
106
Prokaryotes Ribosome
Large subunit 50s Small subunit 30S Total = 70S
107
Eukaryotes Ribosome
Large subunit 60S Small subunit 40S Total = 80S
108
Prokaryotes Shine Dalgarno
Checks out the ribosome to make sure everything is running right before translation
109
Eukaryotes KOZAK Sequence
Checks out the ribosome to make sure everything is running right before translation
110
Ribosome EPA sites
E site - nothing happens P site- growing protein held here A site - new amino acid added here No amino acid for the start codon or the stop codons. Release factor is added at the stop codon, freeing the protein
111
Calculating the number of ATP to make a specific numbered polypeptide.
Number of Amino acids * 4= number of ATP Divide ATP by 30 to get number of glucose in eukaryotes

MCAT Prep (11 decks)

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