george dna v2

What is the overall biological role of DNA emphasized in the lecture?

DNA stores biological information and transmits that information to the next generation.

What is a gene as defined in the lecture?

A segment of DNA containing the information required to synthesize a functional biological product, either a protein or RNA.

What are the four common bases in DNA?

Adenine, guanine, cytosine, and thymine.

What are the four common nucleotides of RNA?

The ribonucleotides containing adenine, guanine, cytosine, and uracil.

What is the difference between a nucleoside and a nucleotide?

A nucleoside contains a sugar and base; a nucleotide contains a sugar, base, and phosphate group.

In what direction are nucleic acid sequences conventionally written?

5′ to 3′ unless a different direction is explicitly indicated.

What does 5′→3′ polarity describe in a nucleic acid strand?

The orientation of the sugar-phosphate backbone from the 5′ end toward the 3′ end.

What does Chargaff's rule state about adenine and thymine in double-stranded DNA?

The amount of adenine is approximately equal to the amount of thymine.

What does Chargaff's rule state about guanine and cytosine in double-stranded DNA?

The amount of guanine is approximately equal to the amount of cytosine.

How do the two DNA strands relate structurally?

They are complementary and antiparallel.

What does antiparallel mean for the two DNA strands?

The two strands run in opposite directions: one 5′→3′ and the other 3′→5′.

What base pairs are formed in standard double-stranded DNA?

A pairs with T, and G pairs with C.

What is the major structural feature of DNA that allows information storage and transmission?

Complementary nucleotide sequences allow one strand to serve as a template for the other.

What is the Watson-Crick form of DNA?

B-form DNA.

How does A-DNA differ from B-DNA according to the lecture?

A-DNA is a wider right-handed helix with about 11 base pairs per turn and is favored in low-water conditions; B-DNA is the usual physiological Watson-Crick form.

What is distinctive about Z-DNA?

It is a left-handed helix with a zig-zag backbone and about 12 base pairs per turn.

What DNA sequence context is associated with Z-DNA in the lecture?

Dinucleotide repeat sequences containing alternating purines and pyrimidines, such as CG or AT repeats.

What are the major and minor grooves of DNA?

They are grooves of different widths formed by the geometry of the double helix and its base-pair arrangement.

What major forces stabilize the DNA double helix?

Base-stacking interactions, electrostatic interactions involving the phosphate backbone and counterions/basic proteins, and hydrogen bonding between bases.

How does a higher G≡C content generally affect DNA duplex stability in the lecture?

Higher G≡C content increases duplex stability.

What do metal cations such as Mg2+ contribute to DNA structure?

They shield negative charges on the phosphate backbone and help stabilize the double helix.

What happens to double-helical DNA during denaturation?

The two strands separate as hydrogen bonding and base-stacking interactions are disrupted.

What conditions can cause DNA denaturation?

High temperature or extreme pH.

What is annealing or renaturation of DNA?

The spontaneous rewinding of complementary strands when temperature or pH returns toward normal conditions.

What is the hyperchromic effect?

The increase in UV absorbance that occurs when double-stranded DNA is denatured.

What is the hypochromic effect?

The decrease in UV absorbance when complementary nucleic acid strands are paired.

At what wavelength is nucleic-acid absorbance commonly monitored to follow denaturation in this lecture?

260 nm.

What is the melting temperature (Tm) of DNA?

The temperature at which half of the DNA is present as separated single strands.

How does G≡C content affect DNA melting temperature?

DNA with more G≡C base pairs has a higher melting temperature.

What is a palindrome in DNA?

A region with an inverted-repeat arrangement that reads the same forward and backward when the appropriate complementary sequence is considered.

What is a mirror repeat?

A sequence in which the inverted repeat occurs within each individual strand.

What were the three proposed models of DNA replication?

Conservative, dispersive, and semiconservative replication.

What is semiconservative DNA replication?

Each parental DNA strand serves as a template for a new complementary strand, producing daughter DNA molecules that each contain one old and one new strand.

What conclusion did Meselson and Stahl establish?

DNA replication is semiconservative.

What is the core synthetic function of a DNA polymerase?

It extends a DNA strand by adding nucleotides to a free 3′-OH, producing DNA in the 5′→3′ direction.

Why does DNA polymerase require a primer?

DNA polymerase needs a pre-existing free 3′-OH group from which nucleotide addition can begin.

What major activities are shown for bacterial DNA polymerase I?

5′→3′ polymerase activity, 3′→5′ exonuclease proofreading activity, and 5′→3′ exonuclease activity used in primer removal/repair-related functions.

Which bacterial DNA polymerase is identified as the primary enzyme for DNA synthesis in the lecture?

DNA polymerase III.

Which eukaryotic polymerase is identified with primary leading-strand synthesis?

DNA polymerase epsilon.

Which eukaryotic polymerase is identified with lagging-strand synthesis?

DNA polymerase delta.

What eukaryotic polymerase is associated with primer initiation?

DNA polymerase alpha.

What enzyme makes the RNA primer in bacteria?

Primase.

What role is associated with telomerase in DNA replication?

It is associated with replication of chromosome ends/telomeres.

What is the leading strand?

The strand synthesized continuously in the direction of replication-fork movement.

What is the lagging strand?

The strand synthesized discontinuously as short DNA segments that are later joined.

What are Okazaki fragments in the context of DNA replication?

Short DNA segments synthesized discontinuously on the lagging strand.

What is bidirectional DNA replication?

Replication that proceeds from an origin in two directions, creating two replication forks.

How does replication differ between a typical circular chromosome and a long linear chromosome in the lecture?

A circular chromosome can use one origin with two forks, whereas long linear chromosomes use multiple origins, creating multiple replicons with two forks per origin.

What is a replication origin?

A DNA site at which replication begins.

What is a replication fork?

The moving region where parental DNA is separated and new DNA strands are synthesized.

What is the functional sequence of events on the lagging strand?

Primer formation, discontinuous DNA synthesis, removal/replacement of primer-containing segments, and joining of the DNA pieces.

Why can the leading strand be synthesized continuously while the lagging strand cannot?

The leading-strand template is oriented so polymerization proceeds continuously toward the moving fork, whereas the antiparallel lagging template requires repeated initiation.

What is a DNA template?

A nucleic acid strand that provides the sequence pattern used to direct synthesis of a complementary strand.

What is a primer in DNA synthesis?

A short nucleic acid segment complementary to the template that provides a free 3′-OH for nucleotide addition.

What type of nucleic acid commonly makes the primer for DNA replication?

RNA.

What is a nucleosome?

A fundamental unit of chromatin in which DNA is wrapped around a histone protein core.

What is the histone core of the nucleosome shown in the lecture?

A histone octamer composed of H2A, H2B, H3, and H4 proteins, with two copies of each in the core.

What is the role of histone H1 in the chromatin structures shown?

H1 associates with nucleosomal DNA and contributes to higher-order chromatin organization, forming the chromosome/chromatosome structure shown.

What is chromatosome in the lecture's structural diagram?

A nucleosomal structure containing the histone core plus H1-associated DNA.

Why does wrapping DNA around histones aid chromosome organization?

It compacts the long DNA molecule into an organized chromatin structure.

What is chromatin?

The organized DNA-protein material that makes up eukaryotic chromosomes.

Why must eukaryotic DNA be highly organized into chromatin?

The genome is extremely long and must be packaged into chromosomes while remaining accessible for biological processes.

What broad relationship exists between chromatin structure and genetic information?

Chromatin packaging organizes DNA and influences how the genetic information is accessed and maintained.

What sugar is present in DNA?

Deoxyribose.

What sugar is present in RNA?

Ribose.

Which base distinguishes RNA from DNA?

RNA uses uracil, whereas DNA uses thymine.

Why is RNA generally more susceptible to base-catalyzed hydrolysis than DNA?

The ribose sugar of RNA contains a 2′-OH group that can participate in base-catalyzed cleavage of the phosphodiester backbone.

What structural feature allows RNA to form diverse structures and perform diverse functions?

Its single-stranded nature and ribose chemistry allow extensive internal base pairing and folding.

Can RNA carry genetic information?

Yes. The lecture notes that RNA can carry genetic information, including in RNA viruses and as a template for reverse transcription.

Can RNA act as a catalyst?

Yes. Catalytic RNAs are called ribozymes.

What is the primary role of ribosomal RNA (rRNA)?

It is a structural and functional component of ribosomes.

What is the primary role of messenger RNA (mRNA)?

It serves as an intermediate carrying information used for protein synthesis.

What is the primary role of transfer RNA (tRNA)?

It acts as an adaptor that translates information in mRNA into a specific amino acid sequence.

What are noncoding RNAs (ncRNAs)?

RNAs that do not function primarily as templates for protein synthesis and can perform a wide variety of regulatory or other cellular functions.

What is a major role of microRNAs (miRNAs) and small interfering RNAs (siRNAs) noted in the lecture?

They participate in gene regulation and can promote mRNA cleavage.

What is the role of small nucleolar RNAs (snoRNAs)?

They participate in processing events associated with rRNA transcripts.

What is the 45S precursor rRNA transcript in eukaryotes?

A large precursor transcript that is processed to produce mature 18S, 5.8S, and 28S rRNAs.

What is the general role of spacer sequences in precursor rRNA?

They separate the mature rRNA sequences within the precursor transcript and are removed during processing.

What major processing events convert 45S precursor rRNA into mature rRNAs?

Modification such as methylation followed by cleavage/processing to release the mature 18S, 5.8S, and 28S rRNAs.

Why must precursor rRNA be processed before mature rRNAs function?

The precursor contains additional sequences and requires specific cleavage and chemical modification to form mature rRNA molecules.

What are the three major eukaryotic nuclear RNA polymerases?

RNA polymerase I, RNA polymerase II, and RNA polymerase III.

Which eukaryotic RNA polymerase synthesizes most ribosomal RNA precursors?

RNA polymerase I synthesizes the major rRNA precursor that gives rise to 18S, 5.8S, and 28S rRNAs.

Which eukaryotic RNA polymerase synthesizes mRNA?

RNA polymerase II.

Which eukaryotic RNA polymerase synthesizes tRNA and other small RNAs emphasized in the lecture?

RNA polymerase III.

What common substrate do RNA polymerases use to synthesize RNA?

Ribonucleoside 5′-triphosphates.

In what direction is RNA synthesized during transcription?

5′→3′.

Relative to the template DNA strand, how is the RNA sequence related?

It is complementary to the DNA template strand.

Where does transcription initiate on a gene?

At a promoter where the transcription machinery is recruited.

What is an exon?

A segment of a precursor RNA that is retained in the mature RNA after processing.

What is an intron?

A segment of precursor RNA that is removed during RNA splicing.

What is RNA splicing?

The processing reaction that removes introns and joins the retained RNA segments.

What is RNA tailing?

Addition or extension of nucleotides at an RNA end during processing; for eukaryotic mRNA this includes polyadenylation at the 3′ end.

What major processing steps do most human mRNAs undergo before export from the nucleus?

5′ capping, splicing, and polyadenylation.

Why are precursor RNAs processed?

Many RNAs require end modification, segment removal, and/or chemical modification to become functional mature molecules.

What is heterogeneous nuclear RNA (hnRNA)?

A term used for immature nuclear RNA transcripts that undergo processing to form mature eukaryotic mRNA.

What is the classic secondary structure of tRNA?

A cloverleaf structure formed by intramolecular base pairing.

What is the tertiary structure of tRNA?

A compact three-dimensional folded structure formed from the cloverleaf secondary structure.

What is the main function of the tRNA anticodon region?

It pairs with the complementary codon in mRNA during translation.

What is the main functional role of the amino acid attachment end of tRNA?

It carries the specific amino acid used during protein synthesis.

What is the role of the stem regions in tRNA structure?

They are formed by complementary base pairing and help establish the folded tRNA framework.