How Subcomponents are Arranged in Biological Molecules (College Board AP Biology)

Directional Structure of Nucleic Acids

• DNA molecules are made up of two polynucleotide strands lying side by side, running in opposite directions; the strands are said to be  antiparallel
• Each DNA polynucleotide strand..
  • is made up of alternating deoxyribose sugars and phosphate groups bonded together to form the sugar-phosphate backbone
  • is said to have a 3’ (3 prime) end and a 5’ (5 prime) end
    • These numbers relate to which carbon atom on the pentose sugar could be bonded with another nucleotide
• Because the strands are antiparallel, one is known as the 5’ to 3’ strand and the other is known as the 3’ to 5’ strand
• The nitrogenous bases of each nucleotide project out from the backbone toward the interior of the double-stranded DNA molecule
• This gives the strand of DNA its directionality:
  • The nitrogenous base is always attached to carbon number 1
  • Carbon number 3 has a hydroxyl group (-OH) that can form bonds to adjacent nucleotides
  • The phosphate group always attached to carbon number 5

Diagram of nucleotides joined together in a strand

A single DNA polynucleotide strand showing 3 nucleotides in a sequence

How Nucleotide Structure Affects DNA Synthesis

• During DNA and RNA synthesis, the 3' and 5' ends of each nucleotide determine the direction in which new nucleotides are added to the growing strand
• The enzyme that catalyzes DNA replication
  • DNA polymerase can build the new strand in only one direction (5’ to 3’ direction)
  • This is due to enzyme specificity and the way that the substrate and enzyme fit together
• So one strand is synthesized continuously
  • But the other strand has to be synthesized in short sections and joined together
• This is a direct consequence of the directionality of nucleotides and their polymers DNA and RNA
• Replication is dealt with in detail in Topic 6.2

Complementary Base Pairing

• The 2 antiparallel DNA polynucleotide strands that make up the DNA molecule are held together by hydrogen bonds between the nitrogenous bases
• These hydrogen bonds always occur between the same pairs of bases:
  • The purine adenine (A) always pairs with the pyrimidine thymine (T) – 2 hydrogen bonds are formed between these bases
  • The purine guanine (G) always pairs with the pyrimidine cytosine (C) – 3 hydrogen bonds are formed between these bases
  • This is known as complementary base pairing

Base Pairing in DNA Diagram

Base pairing in DNA; A—T linked by 2 hydrogen bonds; C—G linked by 3 hydrogen bonds

The Double Helix

• DNA is not two-dimensional as shown in the diagram above
• DNA is described as a double helix
• This refers to the three-dimensional shape that DNA molecules form

DNA Base Pairing and the Double Helix Diagram

The classical double helix shape of a DNA molecule

Levels of Protein Structure

• There are 4 levels of structure in proteins, 3 of which are related to a single polypeptide chain and the fourth level relates to a protein that has 2 or more polypeptide chains
• Polypeptide or protein molecules can have anywhere from 3 amino acids (Glutathione) to more than 34 000 amino acids (Titan) bonded together in chains

Primary

• The sequence of amino acids bonded by covalent peptide bonds is the primary structure of a protein
• DNA of a cell determines the primary structure of a protein by instructing the cell to add certain amino acids in specific quantities in a certain sequence
  • This affects the shape and, therefore, the function of the protein
• The primary structure is specific for each protein (one alteration in the sequence of amino acids can affect the function of the protein)

Primary Protein Structure Diagram

The primary structure of a protein.
The three-letter abbreviations indicate the specific amino acid (there are 20 commonly found in cells of living organisms)

Secondary

• The secondary structure of a protein occurs when the weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds
• There are 2 shapes that can form within proteins due to the hydrogen bonds
  • α-helix
  • β-sheet
• The α-helix shape occurs when the hydrogen bonds form between every fourth peptide bond (between the oxygen of the carboxyl group and the hydrogen of the amino group)
• The β-sheet shape forms when the protein folds so that two parts of the polypeptide chain are parallel to each other enabling hydrogen bonds to form between parallel peptide bonds
• Most fibrous proteins have secondary structures (eg, collagen and keratin)
• The secondary structure relates only to hydrogen bonds forming between the amino group and the carboxyl group (the "protein backbone")
• The hydrogen bonds can be broken by high temperatures and pH changes

Secondary Protein Structure Diagram

The secondary structure of a protein with the α-helix and β-sheet shapes highlighted.
The magnified regions illustrate how the hydrogen bonds form between the peptide bonds.

Tertiary

• Further conformational change of the secondary structure leads to additional bonds forming between the R groups (side chains)
  • Hydrogen (these are between R groups)
  • Disulfide bridges (only occur between sulfur-containing amino acids)
  • Ionic (occurs between charged R groups)
  • Weak hydrophobic interactions (between nonpolar R groups)
• Proteins are sometimes helped to form their final 3D shape by associations with specialized proteins called chaperonins
• This level of structure is common in globular proteins

Tertiary Protein Structure Diagram

The tertiary structure of a protein with hydrogen bonds, ionic bonds, disulfide bridges and hydrophobic interactions formed between the R groups of the amino acids.

Quaternary

• Occurs in proteins that have more than 1 polypeptide chain working together as a functional macromolecule eg, hemoglobin
• Each polypeptide chain in the quaternary structure is referred to as a subunit of the protein

Quaternary Protein Structure Diagram

The quaternary structure of a protein.
This is an example of hemoglobin which contains 4 subunits (polypeptide chains) working together to carry oxygen.

Summary of Bonds in Proteins Table

Directional Structure of Carbohydrates

• Starch and glycogen are polysaccharides
• Polysaccharides are macromolecules that are polymers formed by many monosaccharides joined by glycosidic bonds in a condensation reaction to form chains. These chains may be:
  • Branched or unbranched
  • Folded (making the molecule compact which is ideal for storage eg. starch and glycogen)
  • Straight (making the molecules suitable to construct cellular structures e.g. cellulose) or coiled
• Starch and glycogen are storage polysaccharides because they are:
  • Compact (so large quantities can be stored)
  • Insoluble (so will have no osmotic effect, unlike glucose which would lower the water potential of a cell causing water to move into cells, cells would then have to have thicker cell walls - plants or burst if they were animal cells)

Starch

• Starch is the storage polysaccharide of plants. It is stored as granules in plastids (e.g. chloroplasts)
• Due to the many monomers in a starch molecule, it takes longer to digest than glucose
• Starch is constructed from two different polysaccharides:
  • Amylose (10 - 30% of starch)
    • Unbranched helix-shaped chain with 1,4 glycosidic bonds between α-glucose molecules
    • The helix shape enables it to be more compact and thus it is more resistant to digestion

Amylose – one of the two polysaccharides that is used to form starch (the storage polysaccharide in plants)

• Amylopectin (70 - 90% of starch)
  • 1,4 glycosidic bonds between α-glucose molecules but also 1,6 glycosidic bonds form between glucose molecules creating a branched molecule
  • The branches result in many terminal glucose molecules that can be easily hydrolysed for use during cellular respiration or added to for storage

Amylopectin – one of the two polysaccharides that is used to form starch (the storage polysaccharide in plants)

Glycogen

• Glycogen is the storage polysaccharide of animals and fungi, it is highly branched and not coiled
• Liver and muscles cells have a high concentration of glycogen, present as visible granules, as the cellular respiration rate is high in these cells (due to animals being mobile)
• Glycogen is more branched than amylopectin making it more compact which helps animals store more
• The branching enables more free ends where glucose molecules can either be added or removed allowing for condensation and hydrolysis reactions to occur more rapidly – thus the storage or release of glucose can suit the demands of the cell

Glycogen, the highly branched molecule used as a storage polysaccharide in animals and fungi