Molecular Biology: DNA Structure and Function
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Questions and Answers

What is primarily responsible for holding the two antiparallel strands of DNA together in a double helix?

  • Phosphodiester linkages between adjacent nucleotides.
  • Covalent bonds between complementary bases.
  • Hydrophobic interactions between the sugar-phosphate backbones.
  • Hydrogen bonds between complementary bases. (correct)

Why do A-T and G-C base pairs have almost identical dimensions in a DNA double helix?

  • Purines always pair with purines, and pyrimidines always pair with pyrimidines.
  • A purine always pairs with a pyrimidine, ensuring consistent width. (correct)
  • The number of hydrogen bonds that form between A-T and G-C pairs are the same.
  • The sugar-phosphate backbone dictates the dimensions of the base pairs.

In a DNA double helix, what is the significance of the antiparallel arrangement of the two strands?

  • It positions the 5' and 3' ends of both strands at the same end of the helix.
  • It ensures that the sugar-phosphate backbones are equidistant from each other.
  • It allows for stronger covalent bonds between the bases.
  • It enables optimal hydrogen bond formation between complementary bases. (correct)

What type of chemical linkage connects a nucleotide to the next nucleotide in a single strand of DNA?

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

What is the approximate diameter of a DNA double helix?

<p>20 Å (D)</p> Signup and view all the answers

Which of the following scientists are credited with the discovery of the molecular structure of DNA?

<p>James Watson, Francis Crick, and Maurice Wilkins (A)</p> Signup and view all the answers

What key experimental technique provided crucial data for Watson and Crick's DNA structure model?

<p>X-ray Diffraction (B)</p> Signup and view all the answers

What was the significant shift in understanding of DNA structure proposed by Watson and Crick?

<p>The bases pair in an anti-parallel fashion within the double helix. (C)</p> Signup and view all the answers

Who correctly predicted that the DNA molecule comprised of two chains, each with a phosphate-sugar backbone on the outside and hydrogen bonded bases on the inside?

<p>J. Michael Creeth (C)</p> Signup and view all the answers

When did Maurice Wilkins show a diffraction pattern of DNA at a scientific meeting in Naples?

<p>1951 (D)</p> Signup and view all the answers

When did Watson and Crick propose a double helix formed by pairing of A-T and C-G in an anti- parallel fashion?

<p>1953 (A)</p> Signup and view all the answers

When was The Nobel Prize in Physiology or Medicine awarded to James Watson, Francis Crick and Maurice Wilkins for their discovery of the molecular structure of DNA?

<p>1962 (D)</p> Signup and view all the answers

In what year did R.E.F.is at last making the correct connection between structures A and B?

<p>February 23 &amp; 24, 1953 (B)</p> Signup and view all the answers

What type of bond connects the nucleotides in a single strand of DNA?

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

Which carbon in the deoxyribose sugar is directly bonded to a nitrogenous base?

<p>1' carbon (C)</p> Signup and view all the answers

Which of the following is a pyrimidine?

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

In a nucleotide, which phosphate group is incorporated into the polynucleotide chain?

<p>Alpha ($\alpha$) phosphate (A)</p> Signup and view all the answers

What is the difference between a nucleoside and a nucleotide?

<p>A nucleotide contains a phosphate group, while a nucleoside does not. (D)</p> Signup and view all the answers

Which of the following is unique to RNA nucleotides compared to DNA nucleotides?

<p>Ribose sugar (B)</p> Signup and view all the answers

If a DNA sequence contains 30% adenine, what percentage of cytosine will it contain?

<p>20% (D)</p> Signup and view all the answers

How many hydrogen bonds are formed between adenine and thymine?

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

What is meant by the term 'antiparallel' concerning the strands in a DNA double helix?

<p>The two strands run in opposite directions (5' to 3' and 3' to 5'). (D)</p> Signup and view all the answers

What is the primary consequence of DNA's complementary base-paired structure in the context of DNA manipulation?

<p>It ensures that separated DNA strands can only reassemble in one specific, predictable way (DNA hybridization). (C)</p> Signup and view all the answers

How does the complementary base-pairing of DNA contribute to the process of DNA replication?

<p>It provides a template for accurate DNA duplication, ensuring that only the correct complementary sequence is synthesized. (D)</p> Signup and view all the answers

What is a direct result of over- or under-winding DNA?

<p>Torsional stress, providing potential energy for strand separation (D)</p> Signup and view all the answers

What is supercoiling in DNA primarily a consequence of?

<p>Untwisting or over-twisting the double helix. (B)</p> Signup and view all the answers

How does supercoiling affect the overall state of a DNA molecule?

<p>It relieves the stress caused by over- or under-twisting of DNA. (A)</p> Signup and view all the answers

In what type of DNA molecule is supercoiling most evident?

<p>Covalently closed circular molecules of DNA. (A)</p> Signup and view all the answers

What effect does supercoiling have on the physical structure of DNA?

<p>It compacts the DNA, reducing its overall volume. (D)</p> Signup and view all the answers

Why do thermodynamically unstable DNA molecules tend to become more stable?

<p>To achieve a lower energy state and relieve internal stress. (D)</p> Signup and view all the answers

Which structural feature contributes to localized rigidity in a DNA strand?

<p>A run of adenine bases (D)</p> Signup and view all the answers

Which of the following is a characteristic of DNA sequences with alternating purines and pyrimidines?

<p>Increased flexibility and ability to twist (D)</p> Signup and view all the answers

What condition favors the formation of A-DNA over B-DNA?

<p>Low hydration levels (C)</p> Signup and view all the answers

In which scenario does A-DNA play a significant role?

<p>RNA strand double helix formation (C)</p> Signup and view all the answers

What structural feature is characteristic of B-DNA under hydrated conditions?

<p>A spine of hydrogen-bonded water molecules in the minor groove (B)</p> Signup and view all the answers

What unusual structural characteristic defines Z-DNA?

<p>Left-handed double helix (B)</p> Signup and view all the answers

What conformational change in guanine or cytosine bases is necessary for the formation of Z-DNA?

<p>Rotation from the <em>anti</em> to the <em>syn</em> configuration (C)</p> Signup and view all the answers

What is the biological significance of the syn and anti conformations of nucleobases?

<p>They allow bases to be positioned either over the sugar or away from it, affecting helix structure. (C)</p> Signup and view all the answers

What primary structural feature results from the tight packing of nucleotide base pairs in DNA?

<p>Base stacking and a twist in the double helix (A)</p> Signup and view all the answers

What is the approximate width of the major groove in B-DNA?

<p>12 Å (A)</p> Signup and view all the answers

How do DNA binding proteins interact specifically with DNA?

<p>By forming direct hydrogen bonds with the nucleotides in the major and minor grooves (A)</p> Signup and view all the answers

What technique is used to determine the precise position of atoms in a DNA molecule for comparison with the Watson & Crick model?

<p>X-ray crystallography (B)</p> Signup and view all the answers

What is a key difference between the DNA structures observed via X-ray crystallography and the original Watson & Crick model?

<p>Base-pairs are not 'flat' and they are sometimes slightly twisted (C)</p> Signup and view all the answers

Why are the major and minor grooves important for protein-DNA interactions?

<p>They expose the nucleotides, allowing proteins to make specific contacts. (D)</p> Signup and view all the answers

Which type of interaction, besides hydrogen bonding, contributes to the binding of proteins to DNA?

<p>Electrostatic interactions with the charged phosphates (B)</p> Signup and view all the answers

Flashcards

DNA nucleotide composition

A DNA nucleotide consists of a sugar, phosphate, and nitrogenous base.

Types of DNA bases

The four types of DNA bases are adenine (A), thymine (T), cytosine (C), and guanine (G).

Double helix structure rules

DNA double helix follows base pairing rules and anti-parallel orientation for stability.

3D structure of B-DNA

B-DNA is the most common form, with a right-handed helix, major and minor grooves.

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Major and minor grooves

The major and minor grooves of DNA provide binding sites for proteins and enzymes.

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DNA supercoiling

DNA supercoiling is the over- or under-winding of the DNA helix, regulated by topoisomerases.

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Topoisomerases

Enzymes that regulate DNA supercoiling by cutting and rejoining DNA strands.

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Watson and Crick discovery

Watson and Crick proposed the double helix structure of DNA in 1953, based on earlier studies.

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Complementary Base Pairing

The pairing of A with T and C with G through hydrogen bonds in DNA.

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Antiparallel Strands

The two polynucleotide chains run in opposite directions (5' to 3').

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Phosphodiester Linkages

Covalent bonds that form the backbone of the DNA strand, linking phosphate and sugar.

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Hydrogen Bonds in DNA

Weak bonds that hold complementary bases together, A with T has 2, C with G has 3.

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DNA Double Helix Dimensions

The diameter of the double helix is approximately 20Å, with each base pair being ~11Å wide.

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Base stacking in DNA

Base stacking describes the interaction between adjacent nucleotide bases in DNA that leads to a stable, twisted structure.

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Major groove

The major groove is a wider region of DNA, approximately 12Å, allowing binding interactions with proteins.

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Minor groove

The minor groove is a narrower region of DNA, approximately 6Å, involved in molecular interactions.

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DNA binding proteins

Proteins that interact with DNA at major and minor grooves to facilitate various biological functions.

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Electrostatic interactions in DNA

Interactions between charged phosphates in DNA and proteins facilitate binding and recognition.

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X-ray crystallography

A technique used to determine the atomic structure of DNA by analyzing diffraction patterns of crystals.

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Watson and Crick model

The proposed structure of B-DNA by Watson and Crick, which closely aligns with real DNA structure.

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Structural perturbations in DNA

Slight deviations in DNA structure from the ideal model that still maintain functionality.

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DNA hybridization

DNA hybridization is the process where separated strands reanneal in a complementary manner.

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Faithful DNA copying

DNA can be copied accurately because each strand leads to only its complementary sequence.

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RNA transcription

DNA can be copied into RNA through base pairing, creating a complementary strand.

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Torsional stress in DNA

Over- or under-winding DNA causes torsional stress, which provides energy for strand separation.

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Supercoiling

Supercoiling results from twisting DNA, relieving torsional stress during over- or under-twisting.

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Covalently closed circular DNA

Supercoiling is most evident in covalently closed circular DNA molecules, which can relieve stress efficiently.

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Relaxed versus supercoiled DNA

Relaxed DNA has fewer twists, while supercoiled DNA is more compact and stressed.

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Thermodynamic comfort

Molecules seek stability; uncomfortable twisted DNA aims to become thermodynamically stable.

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Run of adenines

A sequence of adenine bases that provides localized rigidity due to ring-stacking overlap.

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Purines and pyrimidines

Purines (A, G) and pyrimidines (C, T) alternate for flexibility, allowing twisting.

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A-DNA vs B-DNA

A-DNA is less hydrated, while B-DNA is more hydrated with a 'spine' of water in the minor groove.

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Z-DNA

A left-handed DNA structure formed from specific sequences, like GCGCGC, possibly impacting gene expression.

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Anti and syn configuration

Refers to the orientation of bases; anti is away from the sugar, syn is over the sugar.

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Hydration's role in B-DNA

B-DNA's structure is influenced by hydrogen-bonded water molecules present in its minor groove.

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Base flipping in Z-DNA

In Z-DNA, bases flip between anti and syn configurations, creating its distinct structure.

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Commonality of B-DNA

B-DNA is the most prevalent structural form of DNA found in cellular contexts.

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DNA Double Helix

Structure of DNA formed by two antiparallel polynucleotide strands.

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Nucleotide

Building block of DNA, consisting of a base, sugar, and phosphate.

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Phosphodiester Bond

Covalent bond connecting nucleotides in a polynucleotide chain.

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Purines

Double-ring nitrogenous bases in DNA: adenine (A) and guanine (G).

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Pyrimidines

Single-ring nitrogenous bases in DNA: cytosine (C), thymine (T), uracil (U).

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Sugar-Phosphate Backbone

The backbone of DNA formed by alternating sugar and phosphate groups.

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Nucleoside

A base linked to a sugar, without a phosphate group.

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RNA vs DNA

RNA contains ribose sugar; DNA contains deoxyribose sugar.

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Five Nitrogenous Bases

The five bases in nucleic acids: A, T, C, G (DNA); U (RNA).

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Study Notes

DNA Structure I & II

  • DNA structure is a double helix formed by the pairing of A-T and C-G.
  • The pairing follows a specific rule of complementarity.
  • A pairs with T, and G pairs with C.
  • These base pairs have the same dimensions.
  • The two polynucleotide chains are antiparallel.
  • The double helix consists of two complementary and antiparallel strands.
  • Nucleotides are linked by phosphodiester bonds forming a polynucleotide chain.
  • Each polynucleotide chain has a sugar-phosphate backbone consisting of alternating sugar and phosphate groups.
  • The major groove is approximately 12Å wide.
  • The minor groove is approximately 6Å wide.
  • DNA binding proteins interact with DNA through electrostatic interactions with charged phosphates.
  • The major and minor grooves are regions where DNA binding proteins make direct and specific contact with nucleotides through hydrogen bonds.
  • DNA can untwist/overtwist creating supercoiling.
  • Supercoiling is regulated by enzymes called topoisomerases.
  • Topoisomerases are important to maintain the proper supercoiling of DNA.
  • There are different forms of DNA, such as A-DNA, B-DNA, and Z-DNA.
  • B-DNA is the most common form of DNA in cells.
  • DNA can be "melted" (strands separated).
  • DNA can be copied into DNA (duplicated) faithfully.
  • DNA can be copied into RNA.

Learning Objectives

  • Describe the composition of a DNA nucleotide.
  • Identify the types of DNA bases.
  • Explain the rules followed by a DNA double helix to form a stable structure.
  • Detail significant features of the 3-D structure of B-DNA.
  • Define the major and minor grooves of a DNA double helix.
  • Explain DNA supercoiling and its regulation by topoisomerases.
  • Describe the differences between the major structural forms of DNA.

Nobel Prize in Physiology or Medicine (1962)

  • James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize for their study of DNA molecular structure which solved a major biological riddle.
  • Their discovery helped tremendously in solving the most important of all biological riddles.

Watson and Crick (1953) Model of DNA

  • Watson and Crick proposed a double helix formed by pairing A-T and C-G in an anti-parallel fashion.
  • This was a significant shift from previous ideas.
  • The bases were proposed to be on the outside of the helix.

X-Ray Diffraction Studies of DNA

  • Wilkins and Rosalind Franklin provided key X-ray diffraction patterns that Watson and Crick used.
  • These patterns suggested a helical structure.
  • Wilkins showed a diffraction pattern of DNA at a scientific meeting in 1951.
  • Their work showed how important the X-ray data was for determining the DNA's structure.

DNA Nucleotides

  • DNA (and RNA) are made of nucleotide building blocks.
  • Nucleotides comprise a base, a sugar (deoxyribose), and a phosphate.
  • There are four nitrogenous bases: adenine (A), guanine (G), cytosine (C), and thymine (T).
  • Different bases have a unique structural configuration (purine or pyrimidine).
  • The phosphate closest to the sugar is the alpha (α) phosphate.

Nucleosides and Nucleotides

  • Base + sugar = nucleoside
  • Nucleosides are named for their bases: Adenine—adenosine; Cytosine—cytidine; Guanine—guanosine; Thymine—thymidine; Uracil—uridine.
  • Nucleoside + phosphate = nucleotide

Complementary DNA Nucleotide Pairing

  • The bases of one strand are complementary to the bases in the other strand.
  • A pairs with T, and G pairs with C, forming hydrogen bonds.
  • A = T base pairs have the same dimensions as G = C base pairs..
  • The two chains are antiparallel with respect to their 5´and 3´ends.

3D Structure of B-DNA

  • Sugar-phosphates form the backbone of the DNA molecule.
  • The backbone is held together by phosphodiester linkages.
  • Sugar-phosphate backbones run antiparallel to each other.
  • Complementary base pairing aligns one purine with one pyrimidine.
  • A pairs specifically with T, forming two hydrogen bonds.
  • C pairs with G, forming three hydrogen bonds.
  • The diameter of the molecule is ~20Å.
  • Nucleotide base pairs create gaps between the sugar-phosphate backbones exposing nucleotides.
  • Base-pair stacking creates gaps between the sugar-phosphate backbones and provides the twist, causing slight distortions to the helix.
  • The dimensions of the base pairs are ~identical.

Topoisomerases

  • Supercoiling is regulated by enzymes called topoisomerases.
  • Topoisomerases change the supercoiled state of DNA in 2 ways: by cutting one or both strands.

Topoisomerases and Disease

  • Topoisomerases are important in several diseases like scleroderma, lupus, and cancer.

Topoisomerases as Clinical Targets

  • Some antibiotics inhibit prokaryotic topoisomerases (e.g., DNA gyrase).
  • Some anti-cancer drugs inhibit eukaryotic topoisomerases.

Different Forms of DNA

  • DNA can exist in different forms like A-DNA, B-DNA, Z-DNA.
  • B-form is the most common in cells.
  • A-DNA and Z-DNA have different structures and may have different functions.

Real DNA

  • Real DNA can deviate from a perfect Watson-Crick double helix.
  • Bases in sequences can rotate; this can distort the helix.
  • Certain runs of adenines cause significant ring-stacking overlap causing rigidity.
  • Alternating purines and pyrimidines are flexible and can twist more.

Summary of DNA

  • DNA has a complex structure with various forms.
  • DNA structure is important in many biological processes.

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DNA Structure I & II PDF

Description

Test your knowledge on the fundamental aspects of DNA, including the double helix structure, base pairing, and historical discoveries. This quiz covers critical concepts such as the chemical linkages within DNA and the significance of its antiparallel arrangement. Perfect for students studying molecular biology or genetics.

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