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MCAT > Molecular Biology > Flashcards

Molecular Biology Flashcards

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MCAT flashcards
1
Q

Purines

A

A/G double ring structure with 4 nitrogen atoms

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2
Q

Pyrimidines

A

C/U/T single ring structure with 2 nitrogen atoms

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3
Q

Watson-Crick Model

A

DNA has right-handed double helix with H bonds between Bases (2 A-T, 3 C-G) in antiparallel orientation

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4
Q

Chargaff’s Rule

A

A = T, C = G

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5
Q

Annealing

A

AKA hybridization, binding of two complementary strands of DNA

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6
Q

34 angstroms

A

When the helix completes itself/completes a full turn (10 base pairs)

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7
Q

ds-DNA

A

chromosomes that store genome/genetic information (humans have 23 pairs, 46 total)

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8
Q

DNA gyrase

A

used by prokaryotes to make DNA more compact/sturdy (supercoil)

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9
Q

Histones

A

globular proteins used by prokaryotes to wrap DNA and form nucleosomes (DNA wrapped around octamer of histones)

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10
Q

Acetylation

A

loosens DNA from nucleosomes (Transcription)

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11
Q

Methylation

A

Inactivates chromosomes in eukaryotes

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12
Q

Euchromatin

A

Less dense, lighter regions of chromosomes when stained with chemicals (higher transcription rates and higher gene activity)

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13
Q

Centromere

A

Spindle fibers attach via kinetochores during cell division

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14
Q

Telomeres

A

Ends of chromosomes that prevent deterioration and fusion with neighboring chromosomes

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15
Q

Human genome

A

22 autosomes, 2 sex chromosomes

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16
Q

Intergenic regions

A

Regions of noncoding DNA (contribute to assembly of chromatin structure)

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17
Q

Nucleotide Variation

A

Single Nucleotide Polymorphisms, mutations that occur every ~1000 base pairs that cause specific traits/phenotypes

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18
Q

Copy-Number Variation

A

Structural Variations in genome lead to different copies of DNA sections

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19
Q

Repeated Sequences/Tandem Repeats

A

Short sequences of nucleotides repeated one after another, unstable if too short or if repeat is long`

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20
Q

Transcription

A

Process of reading DNA and writing information as mRNA (complementary to the DNA strand it read)

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21
Q

Translation

A

Reading of mRNA to create proteins

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22
Q

Codon

A

Nucleic acid word 3 nucleotide letters long (61 codons that specify 20 amino acids,)

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23
Q

AUG

A

start codon (methionine)

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24
Q

Retroviruses

A

Can make DNA from RNA using reverse transcriptase enzyme

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25
Q

DNA Replication

A

Synthesizing of new strand DNA using parental DNA as template

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26
Q

Helicase

A

Enzyme that separates tightly coiled DNA at nonrandom place (origin of replication ORI)

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27
Q

Topoisomerases

A

Cut one/both of the strands to unwrap the helix and prevent breakage

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28
Q

ssBP

A

single strand binding proteins protect unpackaged DNA (open complex)

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29
Q

DNA polymerase

A

synthesizes chain (from existing chain) – requires a primer (synthesized by primase) AND template (has to copy an old chain)

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30
Q

Elongation/Orientation of Replication

A

Daughter DNA is made 5’ to 3’ while template is read 3’ to 5’ –> completes this on both sides of the ORI

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31
Q

Hydrolysis of Pyrophosphate

A

Driving force thermodynamically of DNA replication

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32
Q

Replication Fork

A

Sites where unwinding continues after DNA polymerase proceeds in both directions away from ORI (Half of each template strand is replicated)

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33
Q

Leading/Lagging Strands

A

One continuous leading strand with a lagging strand that has Okazaki fragments (dependent on replication fork widening)

Leading strand = towards fork, lagging strand = away from fork

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34
Q

DNA ligase

A

Joins DNA fragments together after RNA primers replaced by DNA

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35
Q

Pro DNA Pol I

A

Adding nucleotides at RNA primer in 5’ to 3’ direction; slow processivity so about 400 base pairs from ORI, DNA pol III takes over; important for excision repair

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36
Q

Pro DNA Pol II

A

Backup for DNA Pol III (5’ to 3’ activity)

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37
Q

Pro DNA Pol III

A

Fast, accurate elongation of leading strand 5’ to 3’ activity (exonuclease/end works 3’ to 5’)

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38
Q

Proofreading Function

A

Ability of an enzyme to move backward to chop off an incorrect nucleotide

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39
Q

Pro DNA Pol IV/V

A

Not good at polymerase activity but stop other enzymes when repair pathways are activated

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40
Q

Pro vs Eu Replication

A

Prokaryotes only have one circular chromosome, duplicated genome looks like theta (theta mechanism)

Eukaryotic chromosome has several origins because of how long genome is - DNA looks like bubbles until joined/ligated together

41
Q

Telomere Replication

A

No place on lagging strand to place primer, primer cannot be replaced - DNA cannot replicate end sequences

Telomeres are disposable repeats, eventually this telomere gets too short and cell becomes senescent (nondividing) or apoptosis

42
Q

Hayflick limit

A

Number of times DNA can divide

43
Q

Telomerase

A

Adds repetitive nucleotide sequences to chromosome ends (contains RNA primer and reverse transcriptase)

44
Q

Germline Mutations

A

Can be passed onto offspring

45
Q

Somatic Mutations

A

Occur in somatic cells and cannot be passed onto offspring

46
Q

Physical Mutagens

A

Ionizing radiation ex. X ray (causes DNA breaks)- one side reparable, both sides irreparable

UV light cause pyrimidine dimers that distort DNA backbone - reparable

47
Q

Chemical Mutagens

A

Chemical compounds that can cause mutation, Chemicals covalently alter bases or if they look like base pairs can insert themselves into DNA

48
Q

Biological Agent Mutagens

A

Viruses, transposons, DNA polymerase making mistakes can all cause mutations

49
Q

Point mutations: Transitions, Transversions, Missense, Nonsense, Silent Mutation

A

Transitions - purine substituted for purine or pyrimidine for pyrimidine

Transversions - purine for pyrimidine or vice versa

Missense - one amino acid replaced by another amino acid

Nonsense - one amino acid replaced by a stop codon

Silent Mutation - codon changed for new codon (but both code for same amino acid)

50
Q

Frameshift Mutations

A

Insertions/Deletions that change reading frame of protein

51
Q

Inversion Mutation

A

Segment of a chromosome is reversed end to end

52
Q

Amplification Mutation

A

Segment of chromosome duplicated

53
Q

Translocation and Rearrangement Mutations

A

Recombination between non-homologous (not belonging to the same chromosome/containing the same genetic information)

54
Q

Loss of heterozygosity

A

Diploid organisms have two copies of each gene (so a mutation in one can be tolerated if other is normal) but deletion removing the normal copy creates a loss of heterozygosity

55
Q

Hemizygous

A

A locus where there is only one gene copy within a diploid organism

56
Q

Transposons

A

Mobile genetic elements that can jump around the genome (eukaryotic - degenerative retroviruses)

Cause inversions, deletions and rearrangements

57
Q

Types of Transposons

IS Element
Complex
Composite

A

IS Element - transposase gene with inverted repeat sequence on both sides

Complex - has additional genes

Composite - two similar or identical IS elements with central region in between

58
Q

Transposase

A

Can cut and paste into any new genetic location

59
Q

Haploinsufficiency

A

Diploid organism has only a single functional copy of a gene and this is not enough to support the normal state

60
Q

Good/Bad Mutation

A

Anemia - mutation within hemoglobin, but heterozygotes are malaria-resistant

61
Q

DNA Repair

A

Developed mechanisms to help deal with DNA damage

62
Q

Direct Reversible

A

Main mechanism of DNA repair in humans, directly reversible damage (ex. UV-induced pyrimidine photodimers)

63
Q

Homology-Dependent Repair

Excision
Post-Replication

A

Mutations can be repaired using the undamaged strand

Before DNA replication = excision repair (removes defective bases/nucleotides and replaces them)

After DNA replication = post-replication repair (mismatch repair pathway MMR targets based pairs not repaired by polymerase)

64
Q

Myelation

A

Bacterial Post-Replication Repair for only old strands

65
Q

Double Strand Break (DSB) Repair

A

Double strand breaks caused by reactive oxygen species, cells use homologous recombination and nonhomologous end-joining (can lead to deletions or translocations)

66
Q

Homologous Recombination

A

One sister chromatid helps repair DSB in another

67
Q

Nonhomologous End Joining

A

Cells that are not dividing do not have the ability to use sister chromatids (no backup chromosome)

Instead broken ends stabilized and DNA ligase connects fragments

68
Q

RNA

A

ribonucleic acid - single stranded, containing uracil, extra hydroxyl group makes RNA polymer less stable (nucleophilic attack of the backbone phosphate group)

69
Q

mRNA

A

contains information carried to the ribosome (can be translated into protein)

monocistronic (one gene one protein) in eukaryotes

polycistronic (one gene many proteins) in prokaryotes

70
Q

5’ UTR

A

5’ Region in mRNA not coded for protein that is important for initiation and regulation of transcription

71
Q

Open Reading Frame (ORF)

A

Start and stop codon located after 5’UTR

72
Q

hnRNA

A

first RNA transcribed from DNA (immature precursor to mRNA in eukaryotes). Cap, tail, splicing makes hnRNA into mature mRNA

73
Q

Non-coding RNa

tRNA
rRNA
snRNA
miRNA/siRNA
piRNA
ncRNA
A

RNA not translated into proteins

tRNA - transfer RNA, translates genetic code & carries amino acids from cytoplasm to ribosome to be added to growing protein

rRNA - ribosomal RNA component of the ribosome (catalytic function) AKA ribozymes

snRNA - small nuclear RNA form complexes in spliceosome

microRNA/small interfering RNA -function in RNA interference to help increase or decrease translation

PIWI interacting RNA - prevent transposons from moving

Long ncRNAs help control transcription

74
Q

Transcription

A

Synthesis of RNA using DNA as a template

Begins at specific spot on chromosome (start site) that begins polymerization using RNA polymerase called promoter

75
Q

Template-driven polymerization

A

Involved in both replication and transcription (driving force is removal of pyrophosphate/ negative delta G)

76
Q

Template Strand

A

Single strand of the DNA template that encodes a particular mRNA molecule (AKA non-coding, transcribed, or antisense strand)

77
Q

Coding Strand

A

AKA sense strand that has the same sequence as transcript with T instead of U

78
Q

Three Stages of Transcription

A

Initiation
Elongation
Termination

79
Q

Initation

A

RNA polymerase holoenzyme binds to dsDNA promoter and then unwinds and binds to ssDNA promoter (close to open complex)

80
Q

Elongation

A

Elongates RNA chain processively with one polymerase complex synthesizing entire RNA molecule

RNA polymerase moves along in transcription bubble (where DNA double helix is unwound)

81
Q

Termination

A

Signal that tells polymerase to fall off DNA and release the RNA (sometimes with the help of a protein called rho)

82
Q

Differences Between Prokaryotic/Eukaryotic Transcription (There are 4)

A

Location:
Pro - transcription and translation in cytoplasm
Eu - transcription in nucleus while translation in cytoplasm (nonsimultaneous)

Primary Transcript
Pro - mRNA, ready for translation
Eu - hnRNA (modified before translation)

RNA Polymerase
Pro - only one RNA polymerase
Eu - 3 types (I - transcribes rRNA, II- transcribes hnRNA/mRNA, II - transcribes tRNA)

Transcription itself

83
Q

Translation

A

Synthesis of polypeptides according to mRNA where tRNA brings specific amino acids

84
Q

tRNA

A

Transfer RNA - step and loop structure with anticodon that recognizes mRNA codon to be translated. also has amino acid receptor site

85
Q

Wobble Hypothesis

A

61 codons expect 61 distinct tRNA molecules, but there are usually fewer than 45 (suggests some tRNA molecules bind to more than one codon (first and second codon-anticodon normal, third is flexible)

86
Q

Amino Acid Activation

A

Peptide bonds not thermodynamically favorable, reaction coupling (ATP hydrolysis) done to allow amino acids to attach

Amino acid reacts with ATP to form aminoacyl AMP, then Ppi group hydrolyzed

Aminoacyl AMP is destroyed to load to tRNA where aminoacyl-tRNA synthetase enzymes specific to each amino acid

87
Q

Ribosome

A

Composed of polypeptides/ rRNA chains and has small and large subunit

80S, 40S subunit and 60S large subunit (large one has 28S rRNA molecule that has ribozyme function)

Binding sites:
A - tRNA delivers amino acid
P - growing polypeptide chain is located
E - empty tRNA sits before release

88
Q

Epigenetics

A

Changes in gene expression due to differences outside of DNA sequencing

89
Q

DNA Methylation and Chromatin Remodeling

A

Eu - turns off gene expression

Pro - alters gene expression (promoting/inhibiting transcription)

90
Q

Gene Dose

A

Increasing number of copies of a gene can increase expression

91
Q

Genomic Imprinting

A

When one allele of a gene is expressed (either maternal or paternal)

92
Q

X Chromosome Inactivation

A

Females have 2 X chromosomes, (one inactive). Humans its by random choice which X is inactivated (have highest levels of DNA methylation)

93
Q

Bacterial Regulation Mechanisms

A

Anabolic Enxymes - inhibited in excess product (repressible enzymes)

Catabolic enzymes - activated in excess substrate (inducible enzymes)

Ex. TRP vs Lac operon respectively

94
Q

Lac Operon

A

Inducible, involving lactose catabolism (contains Z, Y, A genes)

When lactose is present, lac repressor falls off which allows lactose catabolism

95
Q

TRP operon

A

Presence of tryptophan, repressor protein binds to the operon, operator turned off

96
Q

Post-Translational Modification

A

Proteins Folded, modified, transported by molecular chaperones

97
Q

Fidelity

A

Accuracy (Transcription has less fidelity than Replication)

98
Q

mRNA half-life

A

Means mRNA remains in cell longer and more protein is consequently translated

MCAT (7 decks)

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