Nucleic Acid Structure
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Questions and Answers

What distinguishes the semi-conservative nature of DNA replication?

  • Each new double helix contains two new strands.
  • One strand of each new double helix is from the original molecule. (correct)
  • Both strands of the original double helix are newly synthesized.
  • Only one strand is replicated during the process.

Which protein is responsible for unwinding the DNA strands during replication?

  • Helicase (correct)
  • DNA polymerase
  • Single-strand binding protein
  • Initiator proteins

What type of DNA sequences are referred to as replication origins?

  • Single-stranded DNA regions only
  • Random sequences across the DNA
  • Specialized sequences rich in AT base pairs (correct)
  • Regions with high GC content

During the initiation of DNA replication in eukaryotes, which complex includes the inactive helicase?

<p>The pre-initiation complex (D)</p> Signup and view all the answers

What is formed when a sugar is joined to a nitrogenous base?

<p>Nucleoside (A)</p> Signup and view all the answers

What is the function of single-strand binding proteins during DNA replication?

<p>To prevent re-formation of base pairs in unwound DNA. (B)</p> Signup and view all the answers

Which statement about DNA polymerase is true?

<p>It requires a template strand and a primer to synthesize DNA. (A)</p> Signup and view all the answers

At which carbon of ribose or deoxyribose is a phosphate group attached to form a nucleotide?

<p>5' carbon (A)</p> Signup and view all the answers

Which experiment demonstrated the semi-conservative nature of DNA replication?

<p>Meselson and Stahl Experiment (B)</p> Signup and view all the answers

How are mononucleotides linked together in a polynucleotide chain?

<p>3',5' phosphodiester bonds (D)</p> Signup and view all the answers

Which of the following names a common nucleoside?

<p>Adenosine (D)</p> Signup and view all the answers

What is formed at the sites where double-stranded DNA becomes single-stranded during replication?

<p>Replication forks (A)</p> Signup and view all the answers

In what sequence is a polynucleotide typically written?

<p>5' to 3' (A)</p> Signup and view all the answers

Why are phosphate groups negatively charged at cellular pH?

<p>They lose protons. (A)</p> Signup and view all the answers

What term is used for a nucleotide with two phosphate groups?

<p>ADP (A)</p> Signup and view all the answers

What structure do DNA strands usually form in cells?

<p>Double helix (A)</p> Signup and view all the answers

What is one main function of RNA in living systems?

<p>Acts as a template for protein production (B)</p> Signup and view all the answers

Which of the following correctly distinguishes DNA from RNA?

<p>DNA contains deoxyribose; RNA contains ribose (C)</p> Signup and view all the answers

Which of the following is not a purine?

<p>Thymine (C)</p> Signup and view all the answers

What is the role of nucleosomes in eukaryotic cells?

<p>Package DNA into a compact form (B)</p> Signup and view all the answers

Which statement about the nitrogenous bases in nucleic acids is true?

<p>Cytosine is present in both DNA and RNA (A)</p> Signup and view all the answers

Which structure forms the backbone of nucleic acid polymers?

<p>Phosphate groups and monosaccharides (B)</p> Signup and view all the answers

What effect do changes in sequence or conditions have on the melting temperature of a DNA double helix?

<p>Higher GC content generally raises melting temperature (A)</p> Signup and view all the answers

Which of the following correctly pairs each type of RNA with its main function?

<p>tRNA: Carries amino acids to the ribosome (B)</p> Signup and view all the answers

What is the primary purpose of cDNA in molecular biology?

<p>To express eukaryotic proteins in prokaryotic cells (C)</p> Signup and view all the answers

What is the function of reverse transcriptase in the synthesis of cDNA?

<p>To synthesize DNA from RNA (D)</p> Signup and view all the answers

What does the presence of introns in genomic DNA imply for cDNA preparation?

<p>cDNA lacks introns (D)</p> Signup and view all the answers

What is the role of DNA polymerase in PCR?

<p>To extend primers and synthesize new DNA strands (A)</p> Signup and view all the answers

Which step in PCR requires a decrease in temperature?

<p>Annealing (D)</p> Signup and view all the answers

Why was the discovery of thermostable polymerases significant for PCR?

<p>It allowed enzyme addition only at the start of the reaction (C)</p> Signup and view all the answers

What is the approximate temperature to denature DNA during PCR?

<p>95 °C (B)</p> Signup and view all the answers

How many times are the PCR steps usually repeated?

<p>About 30 times (C)</p> Signup and view all the answers

What are the consensus sequences for the -10 and -35 elements in bacterial promoters?

<p>-10: TATATT, -35: TTGACA (D)</p> Signup and view all the answers

Which factor does NOT contribute to the differential regulation of transcription in bacterial promoters?

<p>Variability of RNA polymerase enzymes (C)</p> Signup and view all the answers

What occurs when lactose binds to the Lac repressor in E. coli?

<p>The repressor undergoes a conformational change and detaches from the operator (D)</p> Signup and view all the answers

Which protein acts as a repressor for the Lac operon?

<p>Lac repressor (B)</p> Signup and view all the answers

How do activator proteins, like CAP, enhance transcription?

<p>By improving recruitment and activity of RNA polymerase (A)</p> Signup and view all the answers

In the context of the Lac operon, what is the primary carbon source preferred by E. coli?

<p>Glucose (C)</p> Signup and view all the answers

Why do some bacterial promoters have different activity levels?

<p>Different affinities of -10 and -35 sequences for RNA polymerase (B)</p> Signup and view all the answers

What represents positive control in the regulation of the Lac operon?

<p>CAP binding to the promoter (B)</p> Signup and view all the answers

What is the main reason that DNA synthesis on the lagging strand occurs discontinuously?

<p>It must occur in the direction opposite to the replication fork. (C)</p> Signup and view all the answers

How long are Okazaki fragments in E. coli compared to humans?

<p>They are longer in E. coli. (B)</p> Signup and view all the answers

What does the trombone model illustrate about DNA replication?

<p>It shows the association of DNA polymerase complexes with helicase. (B)</p> Signup and view all the answers

Why does DNA synthesis on the lagging strand require more primers than on the leading strand?

<p>Because it synthesizes Okazaki fragments which need separate initiation. (C)</p> Signup and view all the answers

What role does proofreading play in DNA synthesis?

<p>It corrects errors like substitutions or deletions. (C)</p> Signup and view all the answers

Recent studies suggest that during lagging strand synthesis, what might happen more frequently than previously thought?

<p>DNA polymerase dissociates from helicase during synthesis. (A)</p> Signup and view all the answers

What advantage might the presence of a third DNA polymerase provide in the replisome?

<p>It increases efficiency in initiating Okazaki fragment synthesis. (D)</p> Signup and view all the answers

What is a common error that DNA polymerases can make during replication?

<p>They can add an incorrect base. (C)</p> Signup and view all the answers

Flashcards

DNA Replication

The process of creating two identical DNA molecules from one original molecule.

Replication Origin

A sequence of DNA where replication begins. Often rich in AT base pairs.

Helicase

An enzyme that unwinds the DNA double helix during replication.

Replication Bubble

A region of DNA where the two strands have separated and replication is taking place.

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Single-Strand Binding Protein

A protein that binds to single-stranded DNA, preventing it from re-pairing.

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Replication Forks

The points in the replication bubble where the DNA is unwound.

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DNA Polymerase

The enzyme that synthesizes new DNA strands during replication.

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Primer

A short RNA sequence that provides a starting point for DNA polymerase to attach nucleotides to.

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N-glycosidic Bond

A bond formed between the anomeric 1' carbon of a sugar and a nitrogenous base. This bond is essential for forming nucleosides, the building blocks of DNA and RNA.

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Anomeric Carbon

The carbon atom (C1') in a sugar molecule where the nitrogenous base attaches.

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Nucleoside

A molecule formed by joining a nitrogenous base to a sugar (ribose or deoxyribose).

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Nucleotide

A phosphate group attached to the 5' position of a sugar in a nucleoside. Nucleotides are the building blocks of DNA and RNA.

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Polynucleotide

A chain of nucleotides linked together by phosphodiester bonds. DNA and RNA are examples of polynucleotides.

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Phosphodiester Bond

A bond formed between the phosphate group at the 5' carbon of one nucleotide and the hydroxyl group at the 3' carbon of another nucleotide.

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5' end

The end of a polynucleotide chain where the 5' carbon of the sugar is not attached to another nucleotide.

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3' end

The end of a polynucleotide chain where the 3' carbon of the sugar is not attached to another nucleotide.

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DNA (deoxyribonucleic acid)

A type of nucleic acid that serves as the genetic material in most organisms. It carries the instructions for building and maintaining an organism.

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RNA (ribonucleic acid)

A type of nucleic acid involved in various cellular processes, including protein synthesis. It acts as a messenger, carrying genetic information from DNA to ribosomes.

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Pyrimidine

A type of nitrogenous base found in DNA and RNA. The three pyrimidines are cytosine (C), thymine (T) (found only in DNA), and uracil (U) (found only in RNA).

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DNA Melting

The process of DNA double helix separation due to the breaking of hydrogen bonds between the bases, typically caused by heat or changes in pH.

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Melting Temperature (Tm)

The temperature at which half of the DNA double helix is denatured (separated into single strands).

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What is cDNA?

cDNA is synthesized from mRNA using the enzyme reverse transcriptase. It lacks introns, making it suitable for expressing eukaryotic proteins in prokaryotic cells.

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What is reverse transcriptase?

Reverse transcriptase is an enzyme commonly found in RNA viruses. It allows synthesis of DNA from an RNA template.

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What is the role of the polyA tail in cDNA synthesis?

The polyA tail, located at the end of eukaryotic mRNAs, serves as a binding site for a primer used during cDNA synthesis.

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What is PCR?

PCR (Polymerase Chain Reaction) amplifies specific DNA fragments by producing numerous copies of the target sequence.

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What are primers in PCR?

Oligonucleotide primers, which are short DNA sequences, are used in PCR to initiate DNA synthesis. They bind to specific regions flanking the target sequence.

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What are the steps involved in PCR?

The PCR process involves three steps: denaturation, annealing and extension. Each step involves specific temperatures optimized for the reaction to proceed.

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Why are thermostable DNA polymerases used in PCR?

Thermostable DNA polymerases, like Taq polymerase, can withstand high temperatures required for PCR. They are essential for the repeated cycles of DNA amplification.

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What are automated thermocyclers?

Automated thermocyclers are devices that control and manage the temperature cycles needed for PCR reactions, simplifying the process.

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What are Okazaki fragments?

DNA synthesis on the lagging strand occurs discontinuously, resulting in short, newly synthesized DNA fragments called Okazaki fragments.

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How are Okazaki fragments joined?

Okazaki fragments are joined together by DNA ligase, creating a continuous DNA strand.

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How does replication differ on the leading and lagging strands?

The leading strand is synthesized continuously in the same direction as the replication fork movement, while the lagging strand is synthesized discontinuously in the opposite direction.

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What is the 'trombone' model of DNA replication?

The trombone model suggests a loop of DNA forms on the lagging strand as Okazaki fragments are synthesized, but recent research suggests this might not be entirely accurate.

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What types of errors can occur during DNA replication?

DNA polymerase can sometimes make mistakes during replication, resulting in insertions, deletions, or substitutions of nucleotides.

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How does DNA polymerase ensure accuracy during replication?

DNA polymerase possesses a proofreading function that helps minimize errors during replication, ensuring accuracy.

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What is the role of DNA polymerases in DNA replication?

DNA polymerases, crucial enzymes in replication, associate with the helicase throughout the replication process. These enzymes are responsible for synthesizing DNA using different template strands.

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How many DNA polymerases might be involved in replication?

Multiple DNA polymerase complexes can be associated with the helicase during replication, enhancing the efficiency of Okazaki fragment synthesis.

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What are the -10 and -35 sequences?

The -10 and -35 sequences are DNA motifs found in the promoter region of bacterial genes, essential for initiating transcription. They are recognized by the sigma factor of RNA polymerase, a crucial element in recruiting the polymerase to the promoter and initiating transcription.

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What are consensus sequences?

Consensus sequences represent the most common nucleotides found at each position in a set of similar DNA sequences. They are like averages that represent the most typical sequence for a particular motif.

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What is the significance of the -10 and -35 sequences in transcription initiation?

The -10 and -35 sequences, when spaced correctly, are sufficient to recruit the RNA polymerase holoenzyme to the promoter, initiating transcription. Variations in these sequences, and the presence of additional regulatory elements, can influence the rate of transcription.

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What is promoter strength and how does it affect transcription?

The strength of a promoter refers to its ability to attract RNA polymerase and initiate transcription. Variation in sequence creates promoters that are more or less actively transcribed.

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How do gene specific regulatory proteins influence transcription?

Gene-specific regulatory proteins are molecules that bind to DNA sequences near a promoter, either enhancing (activators) or reducing (repressors) the rate of transcription. They provide a mechanism for fine-tuning gene expression in response to cellular needs.

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How is the Lac operon regulated?

The Lac operon in E.coli is an example of a gene system controlled by both negative and positive regulation. The Lac repressor acts as a negative regulator, blocking transcription in the absence of lactose. The Catabolite activator protein (CAP) acts as a positive regulator when glucose levels are low, enhancing transcription in the presence of lactose.

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What is the role of the Lac repressor in the Lac operon?

Lac repressor is a regulatory protein that blocks the transcription of Lac operon genes by binding to the operator region in the absence of lactose. When lactose is present, it binds to the Lac repressor, causing a conformational change that prevents it from binding to the operator, thus allowing transcription.

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What is the role of CAP in the Lac operon?

The Catabolite activator protein (CAP) is a regulatory protein that enhances transcription of the Lac operon when glucose levels are low. It binds to the promoter region in the presence of cAMP, which is high when glucose is scarce. This binding increases the affinity of RNA polymerase for the promoter, leading to enhanced transcription.

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Study Notes

Nucleic Acid Structure

  • Nucleic acids are polymers of nucleotides
  • DNA and RNA are the two major types
  • DNA stores genetic information
  • RNA has various functions, including protein synthesis and gene regulation
  • Nucleotides consist of a monosaccharide, a nitrogenous base, and a phosphate group
  • Ribose is the sugar in RNA; deoxyribose is the sugar in DNA
  • Nitrogenous bases: purines (adenine, guanine) and pyrimidines (cytosine, thymine, uracil)
  • Purines and pyrimidines are attached to the anomeric carbon of the sugar. A sugar joined to a nitrogenous base is called a nucleoside
  • Nucleotides are formed when a phosphate group is attached at the 5' position of the sugar.
  • The names of nucleotides are usually abbreviated using the nitrogenous base followed by an indication of the number of phosphates present (e.g., ADP for adenosine diphosphate).
  • Phosphates are negatively charged
  • DNA forms a double helix, stabilized by base stacking and base pairing
  • RNA can form various secondary structures
  • DNA and RNA have different structural organizations in eukaryotic cells, the nucleosome is an important example

DNA Replication

  • DNA replication is semi-conservative, each new DNA molecule contains one original strand
  • Replication starts at replication origins, which are rich in A-T base pairs
  • Initiator proteins bind to replication origins
  • Helicase unwinds the DNA, forming a replication bubble
  • Single-strand binding proteins prevent the separated strands from re-annealing
  • Primase synthesizes RNA primers
  • DNA polymerase III synthesizes DNA in the 5' to 3' direction, extending from the 3' end of RNA primers
  • There are leading and lagging strands
  • Okazaki fragments are synthesized on the lagging strand
  • DNA polymerase I removes RNA primers and fills in the gaps
  • DNA ligase connects Okazaki fragments
  • DNA polymerase proofreads - the ability to remove incorrect bases, increasing the accuracy of replication to about 1 error in 10^6 or 10^7 bases

DNA Repair

  • DNA polymerase makes mistakes during replication
  • Depurination: loss of a purine base
  • Deamination: conversion of a base to a different base
  • Pyrimidine dimers: formation of covalent links between adjacent pyrimidines, e.g., thymine dimers, usually from UV light
  • Other base modifications: damage from ionizing radiation
  • Strand breaks: single-strand or double-strand breaks
  • DNA repair mechanisms include: proofreading, mismatch repair, base excision repair, nucleotide excision repair

Cancer

  • Cancer is a disease characterized by rapid proliferation of abnormal cells
  • Cancer cells do not respond to signals that normally control cell division
  • Cancer cells are not sensitive to normal pathways of cellular differentiation or programmed cell death (apoptosis)
  • Cancer cells can escape their normal environment and proliferate at foreign sites (metastasize)
  • Cancer is a genetic disease, resulting from multiple mutations in genes

Bacterial Transcription

  • Genes are transcribed into RNA using RNA polymerase
  • Transcription starts at the promoter, and stops at the terminator sequence
  • Promoters consist of consensus sequences (-10 and -35) that are recognized by RNA polymerase
  • Bacterial genes are often organized in operons; a single promoter controls expression of multiple genes
  • Genes transcription can be regulated by proteins that bind to specific regulatory regions of DNA
  • Transcription factors can act as activators to enhance transcription, and repressors to block it

Eukaryotic Transcription

  • Eukaryotes have three different RNA polymerases
  • Transcription initiation in eukaryotes is more complex due to chromatin structure and presence of several transcription factors
  • Transcription factors bind to the promoter, and other regulatory regions
  • Genes in eukaryotes are typically transcribed into single units, not operons
  • Eukaryotic genes contain introns that are removed by splicing before translation

RNA Processing

  • Primary transcript in eukaryotes must be processed to mature mrRNA. This process includes
  • Capping of 5' end: crucial for RNA stability and translation
  • Polyadenylation (addition of the poly A tail) at the 3' end: enhances stability and translation
  • Splicing: removal of introns - non-coding regions between coding regions, exons.

Translation

  • Decoding mRNA sequences to produce proteins occurs in ribosomes
  • tRNAs carry amino acids to the ribosome, matching to the mRNA codons using their anticodons
  • Aminoacyl-tRNA synthetases (aaRS): enzymes that link the correct amino acid to tRNA
  • Ribosomes synthesize proteins in the 5' to 3' direction, based on the mRNA codon sequence

Recombinant DNA Technology

  • Recombinant DNA technology is used to manipulate genes and create new organisms, such as cloning genes, over-expressing proteins, and creating transgenic organisms
  • Techniques like PCR, restriction enzymes, DNA ligation, plasmids, cloning
  • DNA sequencing is used to determine precise order of nucleotides
  • Methods for creating genomic libraries (e.g shotgun method)

Genome Sequencing

  • DNA sequencing is the process of determining the order of nucleotides in a DNA molecule
  • Shotgun sequencing: a method to create random fragments of the genome that are cloned an sequenced, then assembled into contigs, and ultimately into the full genome sequence
  • Genomic Annotation: process of identifying genes, regulatory elements, and other important regions of a sequenced genome. A process following genome sequencing
  • Methods to identify DNA or RNA sequences based on their known sequence
  • Tools for gene cloning: PCR, restriction enzymes, DNA ligase and plasmids

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Description

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