3. Biology: Nucleic Acids, DNA, RNA, and Early Life Evolution

What are the three components of a nucleotide?

A phosphate group, a five-carbon sugar, and a nitrogenous base.

What are purines and pyrimidines?

Purines are nucleotide bases like adenine and guanine, while pyrimidines include cytosine, uracil, and thymine.

What is a nucleoside?

A nucleoside consists of a sugar and a base, e.g., adenosine is a nucleoside made of adenine and ribose.

What is a phosphodiester bond?

A chemical linkage between adjacent nucleotide residues formed during the polymerization of nucleotides.

What direction do DNA and RNA strands grow?

DNA and RNA are synthesized in the 5' to 3' direction.

What happens during the condensation reaction of nucleotide polymerization?

A covalent bond is formed between nucleotides, releasing a water molecule.

What is the significance of activated nucleotides?

Activated nucleotides, like ATP, provide the energy needed for the polymerization of nucleic acids.

What is the primary structure of nucleic acids?

The primary structure is the sequence of nucleotides, often abbreviated by the first letter of each base.

What is the significance of the unlinked 3' hydroxyl and 5' phosphate ends of nucleic acid strands?

They indicate the directionality of the strands and are not bonded to any nucleotides.

What is the primary structure of DNA?

The primary structure of DNA consists of a sugar-phosphate backbone bonded with phosphodiester bonds and nitrogenous bases extending from it.

What is the secondary structure of DNA?

The secondary structure of DNA is characterized by two antiparallel strands twisted into a double helix.

What does 'antiparallel' mean in the context of DNA strands?

Antiparallel means one strand runs in the 5' to 3' direction while the other runs in the 3' to 5' direction.

What is base stacking in DNA? (Stacking Interactions)

Base stacking refers to the stabilizing interaction between adjacent nitrogenous bases in DNA, where the flat bases lie on top of each other, held together by hydrophobic forces and van der Waals interactions.

Why does DNA twist into a double helix?

DNA twists into a double helix to minimize contact between hydrophobic bases and surrounding water, stabilize through base stacking, and reduce charge repulsion between negatively charged backbones.

How are the strands of DNA separated?

The strands of DNA are separated by breaking the hydrogen bonds holding them together using heat or enzyme-catalyzed reactions.

What is the major groove in the DNA double helix?

The major groove is the wider groove in the double helix structure where proteins can bind to specific DNA sequences.

What is the minor groove in the DNA double helix?

The minor groove is the narrower groove in the double helix structure.

What are supercoils in DNA?

Supercoils occur when the double helix is overwound or underwound, relieving tension by twisting into extra coils, which compacts DNA.

What is the role of histones in DNA structure?

Histones are DNA-binding proteins that help package DNA into a compact structure for cell division, forming movable units like chromosomes.

What is the secondary structure of RNA?

The secondary structure of RNA arises from complementary base pairing between purines and pyrimidines within the same strand.

What is an RNA hairpin?

An RNA hairpin is a secondary structure formed when a single strand folds back on itself, creating a stem of paired bases and a loop of unpaired bases.

What stabilizes the secondary structure of RNA?

The secondary structure of RNA is stabilized by hydrogen bonds between paired bases, stacking interactions, and ionic shielding.

What is the tertiary structure of RNA?

The tertiary structure of RNA is formed when secondary structures fold into more complex shapes.

What are bulges in RNA structure?

Bulges are extra unpaired bases sticking out of one side of a stem in RNA secondary structure.

What are internal loops in RNA structure?

Internal loops are unpaired bases on both strands inside a stem in RNA secondary structure.

What are multibranch junctions in RNA structure?

Multibranch junctions occur where several stems meet at one loop in RNA secondary structure.

What is the significance of the sugar-phosphate backbone in DNA?

The sugar-phosphate backbone is polar and negatively charged, allowing DNA to interact well with water and remain soluble.

What is the hydrophobic effect in DNA structure?

The hydrophobic effect refers to the tendency of the nonpolar interior of DNA to minimize contact with water, contributing to the stability of the double helix.

What distinguishes RNA molecules from DNA in terms of structure?

RNA molecules are more diverse in shape, size, and reactivity compared to DNA.

What is the secondary structure of RNA primarily composed of?

Mostly local base-pairing, forming stems, loops, and bulges.

What does the tertiary structure of RNA involve?

Distant parts of the RNA coming together through long-range interactions.

What are ribozymes?

RNA enzymes that catalyze reactions, similar to protein enzymes.

What is the central dogma of molecular biology?

It summarizes the flow of genetic information: DNA → RNA → Proteins.

What is the role of RNA polymerase?

An enzyme that polymerizes ribonucleotides into RNA strands using DNA as a template.

What is a genotype?

The genetic makeup determined by the sequences of bases in an organism's DNA.

What is a phenotype?

The observable traits of an organism, resulting from the proteins it produces.

What is an allele?

A variant of a gene that differs in DNA sequence at the same locus on a chromosome.

What is the genetic code?

The set of rules by which sequences of three RNA bases (codons) are translated into specific amino acids.

What is meant by the degeneracy of the genetic code?

Most amino acids are coded by more than one codon.

What does it mean that the genetic code is not ambiguous?

Each codon corresponds to only one specific amino acid.

What is the reading frame in mRNA?

The way the cell divides an mRNA sequence into groups of three bases (codons) for translation.

What is the role of DNA polymerase?

An enzyme that polymerizes deoxyribonucleotides into DNA strands.

What does the term 'template theory' refer to?

The hypothesis that DNA serves as a template for RNA synthesis, as demonstrated by experiments with artificial DNA.

What does the term 'conservative' refer to in the context of protein function?

It conserves protein function, making mutations less harmful.

How does the conservative nature of protein function affect humans?

It makes humans less vulnerable to single base changes in their sequences and minimizes the phenotypic effects of these mutations.

What is the nontemplate strand of DNA?

The strand of DNA that is not transcribed during RNA synthesis.

What is the first step of transcription?

Using genetic information to synthesize an RNA version of the instructions in DNA.

What catalyzes the formation of a phosphodiester linkage during transcription?

RNA polymerase.

What are NTPs?

Nucleoside Triphosphates used for RNA synthesis, containing ribose sugar.

What are dNTPs?

Deoxyribonucleoside Triphosphates used for DNA synthesis, containing deoxyribose sugar.

What is the function of promoters in transcription?

Regions of DNA that promote the start of transcription and guide RNA polymerase.

What is a holoenzyme in the context of transcription?

The complex formed by the bacterial RNA core enzyme and sigma factor.

What are the -10 and -35 boxes?

Specific sequences within promoters that are recognized by RNA polymerase for transcription initiation.

What is the +1 site in transcription?

The site where transcription starts.

What is the transcription bubble?

The area of DNA where strands are separated by RNA polymerase during transcription.

What happens during the elongation phase of transcription?

RNA polymerase adds nucleotides to the 3' end of the growing RNA strand.

What triggers the termination of transcription in bacteria?

The transcription of a DNA sequence called a transcription-termination signal.

What is the significance of the sigma factor in transcription initiation?

It helps RNA polymerase recognize the start of genes by binding to promoter regions.

What is the direction of RNA synthesis during transcription?

RNA is synthesized in the 5' to 3' direction.

How does RNA polymerase recognize the template strand?

The sigma factor binds to specific promoter sequences, determining which strand will be the template.

What is the role of the transcription-termination signal?

It indicates where RNA polymerase should stop transcribing.

What is the process of matching NTPs to DNA bases during transcription?

Each NTP pairs with a complementary DNA base at the active site of RNA polymerase.

What happens to sigma after RNA polymerase moves past the +1 site?

Sigma is released from the promoter.

What is the significance of the transcription bubble's structure?

It allows RNA polymerase to efficiently read DNA and build RNA strands.

What is the primary element in regulating gene transcription?

The control of genes that are transcribed, including when and to what level they are transcribed.

What role does the hairpin structure play in transcription?

It can end transcription by causing a jam, requiring additional proteins to assist in separating RNA from RNA polymerase.

How do eukaryotic and bacterial transcription processes differ?

Eukaryotic cells have designated locations and times for transcription and translation, while bacteria can translate mRNA before transcription is complete.

What are the three major RNA polymerases in eukaryotic cells?

RNA polymerase I, II, and III, each responsible for synthesizing different types of RNA.

What is the TATA box?

A sequence found in eukaryotic promoters that helps initiate transcription.

What are General Transcription Factors?

Proteins that assemble at the promoter to facilitate the binding of RNA polymerase during transcription.

What is the poly(A) signal?

A sequence of DNA near the end of each gene that signals the termination of transcription.

What modifications occur to eukaryotic pre-mRNA after transcription?

Capping at the 5' end, splicing to remove introns, and polyadenylation at the 3' end.

What is splicing?

The process of removing introns from pre-mRNA and joining exons together to form mature mRNA.

What are exons?

Coding regions of a gene that are retained in the final mRNA after splicing.

What are introns?

Non-coding regions of a gene that are transcribed into pre-mRNA but removed during splicing.

What is a spliceosome?

A large complex made of proteins and small nuclear RNAs (snRNAs) that performs splicing.

What is the role of snRNPs?

Small nuclear ribonucleoproteins that are the building blocks of spliceosomes.

What is the function of the 5' cap added to pre-mRNA?

It protects the mRNA from degradation and assists in ribosome binding during translation.

What is the poly(A) tail?

A long sequence of adenine nucleotides added to the 3' end of mRNA that protects it from degradation and aids in translation.

What is the significance of alternative splicing?

It allows for the production of multiple protein variants from a single gene, increasing diversity.

What is RNA processing?

The series of modifications that convert the primary RNA transcript into a mature RNA molecule.

Why are RNA bases sometimes modified after transcription?

Post-transcriptional modifications improve RNA stability, folding, and function, particularly for tRNA, rRNA, and snRNA.

What is the primary transcript?

The initial RNA molecule produced when a gene is transcribed.

What is the UTR (Untranslated Region)?

Regions of mRNA that are not translated into protein, located at the 5' and 3' ends of the mRNA.

What is the role of poly(A) polymerase?

An enzyme that adds adenine nucleotides to the 3' end of the mRNA during polyadenylation.

What is the function of the ribozyme in splicing?

snRNA molecules in the spliceosome catalyze the cutting and joining reactions during splicing.

How do introns contribute to gene regulation?

They can contain signals that control the expression of the gene.

What is the role of UTRs in mRNA?

UTRs regulate how, when, where, and how much mRNA is translated or degraded, with the 5' UTR controlling ribosome binding and translation start, and the 3' UTR affecting stability, degradation, and localization.

How do UTRs stabilize mRNA?

UTRs protect mRNA from degradation by enzymes, acting as shields that keep the RNA intact longer for protein production.

What is the function of exons in mRNA processing?

Exons are spliced together in the same order they appeared in DNA and pre-mRNA, while introns are removed.

What is a polyribosome?

A polyribosome is formed when two or more ribosomes simultaneously translate one mRNA, increasing protein production.

What is the structure of tRNA?

tRNA has a cloverleaf secondary structure and an L-shaped tertiary structure, with an anticodon at one end and an amino acid attachment site at the other.

What is the purpose of the anticodon in tRNA?

The anticodon base-pairs with the mRNA codon, ensuring the correct amino acid is added to the growing polypeptide chain.

How are amino acids attached to tRNAs?

Aminoacyl-tRNA synthetase uses ATP to attach the correct amino acid to the tRNA's 3' CCA end, creating a 'charged' tRNA.

What is the wobble hypothesis?

The wobble hypothesis explains how fewer tRNAs can recognize all 61 codons by allowing flexible base-pairing at the third codon position.

What is wobble pairing?

Wobble pairing is the flexible, non-standard base pairing that occurs between the 3' base of an mRNA codon and the 5' base of a tRNA anticodon.

How does the ribosome ensure accurate translation?

The ribosome's decoding center checks the first two base pairs strictly but allows flexibility at the third base, ensuring correct amino acid addition.

What is the significance of the N-terminus and C-terminus in polypeptides?

Polypeptides have an N-terminus (free NH3⁺/amino group) at the start and a C-terminus (free COO⁻/carboxyl group) at the end, which can be chemically modified.

What is the role of aminoacyl-tRNA synthetases?

Aminoacyl-tRNA synthetases are enzymes that attach specific amino acids to their corresponding tRNAs, ensuring accurate translation of the genetic code.

What happens during the charging of a tRNA?

Aminoacyl-tRNA synthetase attaches the correct amino acid to the tRNA's 3' CCA end, resulting in a 'charged' tRNA ready for protein synthesis.