DNA Structure and Chromosomes Notes

The Structure of DNA & Chromosomes

Learning Objectives

  • Explain the importance of nucleic acids as biological messages.

  • Discuss hydrogen bonding between complementary base pairs and what it means to be complementary.

  • Diagram antiparallel DNA and label the 5’ and 3’ carbons along the DNA.

  • Explain why the double stranded formation of DNA is energetically favorable.

  • Diagram the organization of chromosomes in a somatic cell and explain their importance in heredity.

  • Diagram the organization of chromosomes to base pairs.

  • Explain the function and importance of the chromatin remodeling complex.

Genes

  • The primary protein sequence is generated from genes.

  • The order of amino acids is determined by genes.

Nucleic Acids and Genetic Information

  • Life depends on storing, retrieving, and translating genetic instructions.

  • Nucleic acids specialize in storing, transmitting, and using genetic information.

  • DNA = deoxyribonucleic acid.

    • Deoxyribo refers to the ribose sugar lacking a hydroxyl/oxygen at the 2’ carbon.

    • Nucleic refers to the molecule's presence in the nucleus.

    • Acid refers to the phosphate group that gives DNA acidic properties.

Nucleotides & Nucleic Acids

  • Nucleotides are subunits of nucleic acids.

  • Nucleotides consist of a phosphate group, a sugar, and a base.

  • Phosphodiester bonds link nucleotides together, forming the sugar-phosphate backbone.

DNA Building Blocks

  • DNA is made of four nucleotide building blocks: Guanine (G), Cytosine (C), Adenine (A), and Thymine (T).

  • DNA (and RNA) are always written 5’ to 3’.

  • Strands have directional polarity.

Base Pairing

  • Base pairing occurs via hydrogen bonds, leading to the double helix structure.

  • Examples of hydrogen bonds: C=O---HN, NH---O=C, NH---N, N---HN.

DNA Bases

  • Purines: Adenine (A) & Guanine (G).

  • Pyrimidines: Cytosine (C) & Thymine (T).

  • Complementary base pairing: purines pair with pyrimidines by hydrogen bonds.

Base Pairing Details

  • Thymine (T) pairs with Adenine (A) via two hydrogen bonds.

  • Cytosine (C) pairs with Guanine (G) via three hydrogen bonds.

  • These pairings are antiparallel.

Questions about Base Pairing

  • Which base pair is strongest?

  • Why can’t Adenine and Thymine form three hydrogen bonds?

  • Why can’t Thymine pair with Guanine?

Double-Stranded DNA

  • The two polynucleotide chains in double-stranded DNA (dsDNA) are held together by hydrogen bonding between the bases.

  • Bases point inward from the sugar-phosphate backbone.

  • DNA has a sugar-phosphate backbone.

  • It's energetically favorable because the bases are hydrophobic, and the sugar-phosphate backbone is hydrophilic.

  • Structure contributes to DNA replication.

Energetics of Base Pairing

  • Complementary base pairing (A + T and G + C) is energetically favorable.

  • Pairing a purine with a purine or a pyrimidine with a pyrimidine would alter the width of the dsDNA.

Antiparallel Strands

  • For complementary base pairing to occur (two hydrogen bonds between A and T, and three hydrogen bonds between G and C), the two strands must run in opposite orientations, which is antiparallel.

  • The antiparallel strands then twist around each other to form a double helix.

Double Helix Formation

  • DNA forms a double helix with 10 base pairs per turn.

  • The DNA double helix is energetically favorable.

  • Van der Waals interactions between stacked base pairs also support the structure.

DNA as Information

  • Information is encoded in the order of the nucleotides - A, C, G, & T.

  • This is a biological alphabet that is used as information for life.

  • Different nucleotide sequences carry different biological messages, but the molecule always looks the same.

DNA's Role in Protein and RNA Production

  • Transcription and translation are key processes.

  • Both protein and RNA have important functional roles in cells.

  • DNA serves as the carrier of biological information to produce RNA and protein.

DNA Packaging Challenge

  • The human genome contains approximately 3 billion base pairs.

  • This equates to 2 meters (6.5 feet) of DNA.

  • It needs to fit in a cell nucleus that is only ~5 micrometers wide (1/12th of the diameter of the tip of a needle).

  • This is equivalent to fitting 24 miles of extremely fine thread into a tennis ball.

Chromosomes

  • 2 meters of DNA in the nucleus in our cells is parceled out into chromosomes.

  • 23 pairs in somatic cells (any cell that is not a reproductive cell).

  • Each chromosome in a pair is inherited - one from the mother and one from the father.

  • They carry the same genes but differ in their sequence, leading to unique traits.

  • Example: Chromosome 9 contains the gene for ABO blood type.

  • The total genetic information carried in an organism’s chromosomes is referred to as the genome.

DNA Packaging with Histones

  • DNA is wrapped around a protein called a histone, reducing DNA length by ~1/3.

  • The histone/DNA complex is called a nucleosome.

  • Nucleosomes contain DNA wrapped around a protein core of eight histone molecules.

Nucleosome Core Details

  • An individual nucleosome core particle consists of a complex of eight histone proteins (two molecules each of histones H2A, H2B, H3, and H4) along with a segment of double-stranded DNA, 147 nucleotide pairs long, that winds around this histone octamer.

  • All four of the histones have a high proportion of positively charged amino acids (lysine and arginine).

  • The positive charges on the histones bind tightly to the negatively charged sugar–phosphate backbone of DNA.

Chromatin Structure

  • The nucleosomes are packed on top of one another in a condensed structure called chromatin or chromatin fiber.

  • Chromatin fibers are folded into a series of loops.

  • Loops are condensed to form chromosomes.

DNA Packaging During Cell Division

  • Packaging stops at the fiber level unless a cell is undergoing cell division (mitosis).

DNA Packaging in Cell Division

  • Interphase DNA is in a “loose” chromatin state.

  • During Mitosis, chromatin is condensed into chromosomes, which is important for the proper division of chromosomes into daughter cells.

Chromatin Remodeling

  • Changes in nucleosome structure allow access to DNA, enabling gene expression.

  • DNA is tightly packed into chromatin, but the structure of this chromatin needs to change to allow access to genes in response to cellular needs.

  • Chromatin remodeling complexes use energy from ATP hydrolysis to loosen the DNA and push it along the histone octamer.

  • The complex can also make DNA less accessible.

Histone Tails and Gene Expression

  • Each histone molecule within the core particle has one end that sticks out from the particle. These ends are called N-terminal tails (H3 tail).

  • They play an important role in higher-order chromatin structure and gene expression.

  • Cells control gene expression by modifying these tails with small chemical groups, such as acetyl groups.

Summary

  • DNA is a double-stranded structure composed of nucleic acids (deoxyribonucleic acid) whose bases are complementary to one another.

  • Adenine base pairs with Thymine (2 hydrogen bonds).

  • Guanine base pairs with Cytosine (3 hydrogen bonds).

  • DNA strands have polarity, a 5’ and a 3’ end.

  • In double-stranded DNA, the two strands run anti-parallel to one another.

  • DNA is organized in the cell by wrapping around histones to form a nucleosome (eukaryotic cells).

  • DNA is further packaged into chromatin fibers and loops in the nucleus (eukaryotic cells).

  • DNA accessibility is controlled by altering nucleosome structure and histone modification (eukaryotic cells).