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molecular cell biology > exam 3 > Flashcards

exam 3 Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

what do genes do

A

Genes pass down hereditary information and provide ‘instructions’ for how cells function, regulate, and form structures.

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2
Q

what are genes made of

A

DNA, which can code for amino acid sequences (proteins) or RNA (non-protein functions).

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3
Q

how is genetic information replicated?

A

DNA molecules replicate to produce two copies, distributed into each daughter cell.

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4
Q

what are transcription and translation

A

Transcription: RNA is synthesized by copying information from DNA using enzymes.
Translation: RNA’s base sequence directs the creation of a polypeptide.

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5
Q

when was DNA discovered and by who

A

1869, Friedrich Miescher

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6
Q

what evidence showed DNA is genetic material?

A

Griffith’s Experiment: Showed a “transforming principle” could convert R-strain bacteria into pathogenic S-strain.

Avery’s Experiment: Found DNA was the transforming substance by isolating nucleic acid from S-strain bacteria.

Hershey & Chase Experiment: Confirmed DNA, not protein, was injected into bacteria by phages.

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7
Q

what roles do bacteriophages play in genetic studies

A

infect bacteria, showing how DNA or RNA is the genetic material for replication and cell function.

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8
Q

what is the structure of DNA

A

double helix, with a sugar phosphate backbone on the outside, right handed helix (B-DNA)

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9
Q

What did Chargaff discover about DNA?

A

A=T and G=C in all DNA samples, with variation among species.

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10
Q

how does DNA replicate

A

The double helix separates, and each strand serves as a template for a new complementary strand.

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11
Q

how is DNA packaged in eukaryotes

A

DNA wraps around histones to form nucleosomes.
Nucleosomes coil into 30-nm chromatin fibers.
Chromatin fibers further fold into loops to form chromosomes.

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12
Q

Positively charged proteins that stabilize negatively charged DNA and organize it into chromatin.

A

histones

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13
Q

Loosely packed, transcriptionally active DNA.

A

euchromatin

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14
Q

Highly condensed, transcriptionally inactive DNA.

A

heterochromatin

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15
Q

what are the two types of repeated DNA sequences?

A

Tandemly repeated DNA and Interspersed repeated DNA

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16
Q

how are Interspersed repeated DNA arranged

A

Scattered sequences like LINEs and SINEs.

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17
Q

how is Tandemly repeated DNA arranged

A

Sequences arranged in rows, such as microsatellites and minisatellites.

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18
Q

what are transposons

A

Mobile genetic elements that can move and leave copies of themselves in the genome.

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19
Q

What is unique about mitochondrial and chloroplast DNA

A

Circular DNA with no histones.
Mitochondria: 16,569 bp encoding 37 genes.

Chloroplasts: ~120,000 bp encoding ~120 genes.

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20
Q

how do organelles depend on the nuclear genome

A

They rely on nuclear genes for most protein synthesis while encoding some of their polypeptides.

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21
Q

how can DNA melting temperature indicate stability

A

Higher Tm reflects tighter DNA binding due to more GC content and base stacking interactions

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22
Q

describe nucleic acid hybridization

A

A method where complementary sequences bind to identify specific nucleic acids, used in FISH.

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23
Q

what are histone modifications

A

Tags like methyl or acetyl groups alter chromatin structure, affecting gene expression.

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24
Q

explain histone codes

A

The combination of histone tags that regulate DNA activity and chromatin state.

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25
Q

two main products of genes

A

RNA transcription and protein

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26
Q

role of mRNA in protein synthesis

A

encodes instructions for translation and assembles amino acids into a polypeptide

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27
Q

how are genetic codes read

A

In triplets called codons, each coding for an amino acid or a stop signal.

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28
Q

key properties of the genetic code

A

Unambiguous, nonoverlapping, degenerate, and nearly universal.

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29
Q

What did Beadle and Tatum conclude in their experiments on bread mold?

A

The one gene–one enzyme hypothesis: each mutation disables one enzymatic step in a metabolic pathway.

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30
Q

What modification to the one gene–one enzyme hypothesis did Ingram propose?

A

One gene–one polypeptide, based on his study of sickle-cell anemia.

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31
Q

How many possible codon combinations exist in a triplet genetic code?

A

64

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32
Q

wobble hypothesis

A

Flexibility in tRNA anticodon pairing with more than one codon, especially at the third codon base.

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33
Q

What does AUG codon signify in translation?

A

The start codon, coding for methionine.

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34
Q

differences in eukaryotic and bacterial translation initiation

A

Bacteria use Shine-Dalgarno sequences and N-formylmethionine; eukaryotes use methionine and require more initiation factors.

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35
Q

polyribosome

A

cluster of ribosomes translating a single mRNA simultaneously.

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36
Q

what triggers termination in translation

A

Stop codons recognized by release factors.

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37
Q

what role do molecular chaperones play

A

They assist in proper folding of newly synthesized proteins and repair misfolded ones.

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38
Q

Hsp70 and Hsp60

A

Types of molecular chaperones that prevent aggregation and assist in folding of proteins.

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39
Q

How does a nonsense mutation affect translation?

A

Converts an amino acid codon to a stop codon, prematurely ending translation.

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40
Q

what is nonsense mediated decay

A

A process to destroy defective mRNAs containing premature stop codons.

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41
Q

what’s the energy cost of polypeptide elongation

A

Hydrolysis of at least 3 high-energy phosphoanhydride bonds per amino acid addition.

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42
Q

whats the central dogma of molecular biology

A

The central dogma describes the flow of genetic information: DNA → RNA → Protein

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43
Q

role of mRNA in protein synthesis

A

Carries genetic information from DNA to ribosomes.

44
Q

role of rRNA in protein synthesis

A

Forms the core of ribosome structure and catalyzes protein synthesis.

45
Q

role of tRNA in protein synthesis

A

Transfers amino acids to ribosomes during protein synthesis.

46
Q

how does transcription differ in prokaryotes and eukaryotes?

A

Prokaryotes: Transcription and translation occur simultaneously without compartmentalization.

Eukaryotes: Transcription occurs in the nucleus; translation occurs in the cytoplasm.

47
Q

the four stages of transcription are …

A

Binding, initiation, elongation, and termination.

48
Q

enzyme that’s central to transcription and its purpose

A

RNA polymerase synthesizes RNA by adding complementary ribonucleotides to a DNA template.

49
Q

how does bacterial transcription start

A

RNA polymerase binds to the promoter region, often containing conserved sequences like the -10 (TATAAT) and -35 (TTGACA) regions.

50
Q

what happens during elongation in transcription

A

RNA polymerase moves along the DNA template, synthesizing RNA in the 5’ → 3’ direction while the DNA helix unwinds and rewinds.

51
Q

what mechanisms terminate bacterial transcription

A

Rho-independent: A GC-rich hairpin loop followed by a U-rich sequence.

Rho-dependent: The rho protein unwinds the RNA-DNA hybrid to release RNA.

52
Q

How many RNA polymerases are present in eukaryotes, and what do they synthesize?

A

3, RNA Pol I: rRNA.

RNA Pol II: mRNA, snRNA, microRNA.

RNA Pol III: tRNA, 5S rRNA.

53
Q

What are the core promoter elements in eukaryotic transcription?

A

Initiator (Inr) sequence.

TATA box.

TFIIB recognition element (BRE).

Downstream promoter element (DPE).

54
Q

How is transcription initiation different in eukaryotes?

A

Requires transcription factors (TFs) to assemble a preinitiation complex with RNA polymerase.

55
Q

What modifications occur during RNA processing?

A

Addition of a 5’ cap.

Addition of a 3’ poly(A) tail.

Splicing to remove introns and join exons.

56
Q

What is the function of the 5’ cap and poly(A) tail?

A

5’ Cap: Protects RNA from degradation and aids in ribosome binding.

Poly(A) Tail: Enhances mRNA stability and facilitates export to the cytoplasm.

57
Q

What is RNA splicing

A

The removal of introns and joining of exons in pre-mRNA to form mature mRNA.

58
Q

what structures catalyze splicing

A

Spliceosomes, composed of snRNPs and snRNA.

59
Q

What are the two types of self-splicing introns?

A

Group I: Excised as linear fragments.

Group II: Excised as lariat structures.

60
Q

What are examples of exceptions to the central dogma?

A

RNA viruses performing reverse transcription to synthesize DNA from RNA.

RNA-dependent RNA synthesis in some viruses.

61
Q

what enzyme catalyzes reverse transcription

A

Reverse transcriptase.

62
Q

What is the nucleolus?

A

nuclear structure where ribosome assembly occurs, containing DNA for rRNA production.

63
Q

What are snoRNAs, and what do they do?

A

Small nucleolar RNAs guide chemical modifications like methylation during rRNA processing.

64
Q

How are tRNAs processed?

A

Removal of 5’ leader sequence.

Replacement of the 3’ terminal sequence with CCA.

Addition of modified nucleotides.

65
Q

What encloses eukaryotic chromosomes?

A

A nucleus bounded by a double-membrane nuclear envelope.

66
Q

What mediates transport through the nuclear envelope?

A

Nuclear pores allow two-way transport between nucleoplasm and cytosol.

67
Q

What is the nuclear lamina?

A

A thin, dense meshwork of fibers lining the inner surface of the inner nuclear membrane, providing mechanical strength.

68
Q

what are nuclear pores

A

Specialized channels in the nuclear envelope where inner and outer membranes fuse, lined by a nuclear pore complex (NPC).

69
Q

What is the function of the nuclear pore complex?

A

It facilitates the movement of small molecules, ions, and larger molecules like proteins and RNA.

70
Q

How are large molecules transported through nuclear pores?

A

using nuclear localization signals (NLS) recognized by importins.

71
Q

What is the Ran/Importin pathway?

A

A mechanism for nuclear import involving importins and the Ran-GTP cycle to transport proteins with NLS.

72
Q

How does nuclear export work?

A

It involves exportins and Ran-GTP, with RNA often exported using adaptor proteins with nuclear export signals (NES).

73
Q

Where are chromatin fibers located in the nucleus?

A

Each chromosome occupies its own distinct region called a chromosome territory

74
Q

What is the main structural difference in nuclear support between plants and animals?

A

Plants and fungi lack nuclear lamins and use different proteins for nuclear structure.

75
Q

What are the main phases of the cell cycle involving DNA replication?

A

DNA doubles during S phase, separated by G1 and G2 phases before mitosis.

76
Q

how is DNA replicated

A

each strand of the double helix serves as a template for a complementary strand.

77
Q

difference between leading and lagging strand synthesis

A

The leading strand is synthesized continuously; the lagging strand is synthesized in Okazaki fragments.

78
Q

What is the role of primase in replication?

A

Synthesizing RNA primers to initiate DNA synthesis.

79
Q

What enzymes unwind the DNA helix?

A

DNA helicases, stabilized by single-stranded DNA-binding proteins (SSBs).

80
Q

How is supercoiling prevented during replication?

A

Topoisomerases create swivel points in DNA strands.

81
Q

What is a replication origin in E. coli?

A

An AT-rich region called oriC, where replication begins.

82
Q

How do eukaryotic origins of replication differ from prokaryotes?

A

Eukaryotic replication involves multiple replicons with AT-rich sequences.

83
Q

What is the role of telomeres?

A

Protect chromosome ends by preventing loss of coding DNA during replication.

84
Q

How does telomerase function?

A

It adds repeated DNA sequences to chromosome ends using an RNA template

85
Q

What happens to telomeres in somatic cells?

A

They shorten over time, signaling cell aging and apoptosis.

86
Q

What is the significance of selective gene expression in bacteria?

A

allows cells to be efficient by producing only what is needed, with related functions often clustered in operons that can be turned on or off.

87
Q

two types of operons in bacteria?

A

Inducible operons (catabolic enzymes, turned on by substrate) and repressible operons (anabolic enzymes, turned off by end product).

88
Q

How do allosteric repressor proteins regulate operons?

A

They bind to the operator to prevent transcription unless a substrate (inducible operons) or end product (repressible operons) changes their conformation.

89
Q

What is substrate induction?

A

A process where enzymes like β-galactosidase are produced only in the presence of a substrate like lactose.

90
Q

How does end-product repression work?

A

When the concentration of an end product (e.g., tryptophan) is high, the production of enzymes needed to synthesize it is repressed.

91
Q

What is the lac operon, and what does it include?

A

A group of three genes (lacZ, lacY, lacA) with a promoter, operator, and regulatory gene (lacI) that controls lactose metabolism.

92
Q

What does the lacI gene encode?

A

The lac repressor protein, which binds to the operator to block transcription of the lac operon.

93
Q

How is the lac operon induced?

A

The inducer (allolactose) binds to the repressor, changing its shape so it cannot bind to the operator, allowing transcription to occur.

94
Q

What role does cyclic AMP (cAMP) and CAP play in the lac operon?

A

When glucose is low, cAMP binds to CAP, which activates transcription by enhancing RNA polymerase binding to the promoter.

95
Q

What is catabolite repression?

A

mechanism where the presence of glucose suppresses the lac operon by reducing cAMP levels.

96
Q

How is the trp operon regulated?

A

It is repressed by tryptophan (corepressor), which activates the repressor protein to block transcription.

97
Q

What is attenuation in the trp operon?

A

A regulatory mechanism where leader mRNA forms hairpin loops based on tryptophan levels, controlling transcription continuation.

98
Q

What happens at high tryptophan levels in the trp operon?

A

Regions 3 and 4 form a terminator hairpin, stopping transcription.

99
Q

What happens at low tryptophan levels in the trp operon?

A

Regions 2 and 3 form an antiterminator hairpin, allowing transcription to proceed

100
Q

What are riboswitches?

A

mRNA regions that bind small molecules to alter their shape, regulating transcription or translation.

101
Q

What role do CRISPR sequences play in bacterial immunity?

A

They incorporate viral DNA into spacers, directing Cas proteins to cleave invader DNA during future attacks.

102
Q

What distinguishes eukaryotic gene regulation from bacterial regulation?

A

Eukaryotic regulation is more complex due to multicellularity and differentiation, involving chromatin remodeling, histone modifications, and DNA methylation.

103
Q

the five levels of eukaryotic gene control?

A
  1. Genome, 2. Transcription, 3. RNA processing/export, 4. Translation, 5. Post-transcriptional control.
104
Q

What is genomic equivalence?

A

a concept that all cells in an organism have the same DNA, though only specific genes are expressed based on cell type.

105
Q

What is the significance of nuclear transplantation experiments?

A

showed that differentiated nuclei can direct the development of an entire organism, demonstrating totipotency.

106
Q

difference between pluripotent and multipotent stem cells?

A

Pluripotent stem cells can become any cell type except placental cells, while multipotent stem cells can differentiate into several but limited types.

molecular cell biology (2 decks)

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