Lecture 3: Macromolecules
Proteins & Nucleic Acids

Proteins are Made up of Exactly 20 Types of Amino Acids

• The proteins in our bodies are made of 20 different amino acids strung together like beads on a string.
• All 20 have a part in common: a central carbon attached to a carboxyl, an amino and a hydrogen atom.
• The differences between the 20 types are in the side groups that can be designated as R.

	Note the amino (NH2), carboxyl (COOH) and hydrogen groups (H) which are found on all amino acids. The differences in amino acids are in the 20 different types of R groups.
Basic Amino Acid Structure
Formation of a Peptide Bond	Two amino acids can combine, with the carboxyl of one attaching to the amino group of the other. Water is removed. This process also requires energy in the form of ATP.

Proteins are Amino Acids Linked Together by Peptide Bonds

• In proteins the carboxyl group (COOH) of one amino acid attaches to the amine group (NH2) of the next to form a peptide bond.
• The reaction requires ATP
• Water is removed
• Protein chains are not branched
• Note that the R groups stick out to the side of the protein chain
• Each protein has a terminal amino group on one end and a terminal carboxyl on the other end

The Side Groups of Proteins can be Hydrophobic or Hydrophilic

• The 20 different R groups fall naturally into 2 classes, those that like water (hydrophilic) and those that hate water (hydrophobic).
• Hydrophobic side groups are nonpolar (no partial charges): attracted to lipids or to other hydrophobic groups
• Hydrophilic side groups are polar: side group has a partial + charge at one end and a partial - charge at the other: attracted to water
• Some hydrophilic side groups are charged: these are sensitive to pH
• Carboxyls (COOH) can lose H ion, become negatively charged
• Amines (NH2) can take up a H ion, become positively charged
  
  

  Phenylalanine	Valine
  Two hydrophobic amino acids
  Lysine	Serine
  Two hydrophilic amino acids

  
  
• The hydrophobic amino acids are likely to be imbedded in other hydrophobic structures, such as the interiors of membranes or the hydrophobic side groups of another part of the same protein.
• To cross a membrane a protein must have a stretch of 20 to 25 amino acids which are mostly hydrophobic.
• Click to view all 20 amino acids

The Shapes of Proteins are Determined by Hydrogen Bonding and by the Numbers and Sequence of the Side Groups

• Primary structure of a protein is the sequence of amino acids. Each protein has a unique sequence determined by the genetic code (no substitutions allowed)
• Secondary structure of a protein is caused by regular hydrogen bonding between carbonyl and amino groups of the protein (see text fig. 5.20). This H-bonding causes the protein to coil and fold in various ways
  • alpha helix: spiral structure common in fibrous proteins (hair)
  • beta pleated sheat: H-bonding between adjacent parallel strands of protein (silk)
• Tertiary structure: caused by bonding between amino acid side groups. Types of bonds (see fig. 5.22):
  • ionic (between carboxyls & amines)
  • hydrophobic
  • disulfide
  • H-bonds
• Quaternary structure: produced by binding of 2 or more protein subunits together to form a functional unit
  • Example: hemoglobin if formed by association of 2 alpha and 2 beta chains

Protein Properties are Determined by their Shapes

• A typical protein will have 200 to 1000 amino acids. A molecule this big can bend into millions of different shapes, but only one is correct
• Proteins will not function unless folded into proper shape. Like any machine, the parts must be in the right positions before it can work
• Many proteins have"active sites" produced by side groups brought together by folding
• Protein shape is disrupted by many agents, especially heat- this is called denaturation
• Heat sterilizes by denaturing proteins of bacteria and viruses

Proteins Do Most of the Work of the Cell

• Every cell has thousands of different types of proteins, each specialized to do a certain job
• Some proteins are structural: control shape of cells and bind cells together
  • Example: collagen- binds all of the cells of the body together
• Chemical reactions of the cell are controlled by protein enzymes
• Protein pumps move things across the cell membrane
• Proteins give mobility:
  • Muscles
  • Flagella
  • "Molecular motors"
• Defend the body against foreign invaders: antibodies
• Receptors: required for signalling in endocrine and nervous systems

Nucleic Acids are the Molecules of Heredity

• Two major types: DNA & RNA
• Both types have code which specifies the sequence of amino acids in proteins
• DNA = archival copy of genetic code, kept in nucleus, protected
• RNA = working copy of code, used to translate a specific gene into a protein, goes into cytoplasm & to ribosomes, rapidly broken down
• RNA is a molecule with a single strand
• DNA is a double strand (a double helix; helix = spiral) held together by hydrogen bonds between the bases (A always bonds to T; C always bonds to G)

The Building Blocks for Nucleic Acids are Nitrogen Bases, Sugars and Phosphate

• DNA and RNA are made of nucleotides strung together like beads
• Nucleotides also have other functions in energy transfer and as signal molecules.
• Nucleotides are made from 3 components: a nitrogen base (purine or pyrimidine), a 5 carbon sugar (ribose or deoxyribose) and 3 phosphates.

Nitrogen Base Purine or Pyrimidine	Nucleoside Base + Sugar	Nucleotide Base + Sugar + 3 Phosphates
Adenine (purine)	Adenosine	Adenosine triphosphate
Guanine (purine)	Guanosine	Guanosine triphosphate
Cytosine (pyrimidine)	Cytidine	Cytidine triphosphate
Thymine (pyrimidine)	Thymidine	Thymidine triphosphate
Uracil (pyrimidine)	Uridine	Uridine triphosphate

• There are 5 important nitrogen bases. They are usually given a one letter code: adenine = A; guanine = G; cytosine = C; thymine = T; uracil = U.
• The bases A, C, G and T are found in DNA.
• In RNA the bases are A, C, G and U, that is T is replaced by U.
• These bases, in groups of 3, are the basis of the genetic code; sugar and phosphate make up the backbone

Guanine (G)	Adenine (A)
Cytosine (C)	Thymine (T)	Uracil

• The nitrogen bases are ring compounds with nitrogen in the rings.
• Those with 2 rings are called purines, while those with a single ring are known as pyrimidines.
• In DNA the 2 strands of the helix are held together by hydrogen bonds between the A and T, and between the C and G bases.
• A nucleotide looks like this:

Adenosine Triphosphate (ATP: the energy currency of the cell)

• ATP is used in almost all energy transactions of the cell
• Useful energy is stored in the4 bonds between the phosphate groups

Summary of Biological Macromolecules:

Macromolecule	Building Blocks	Functions
Polysaccharides	Sugars	Energy storage (4 Cal/gm) Structure (cell walls, exoskeletons)
Lipids: triglycerides	Fatty acids, glycerol	Energy storage (9 Cal/gm)
Lipids: phospholipids	Fatty acids, glycerol, phosphate, polar groups	Cell membranes
Proteins	Amino acids: 20 types	Cell structure Enzymes Molecular motors (muscle, etc) Membrane pumps & channels Hormones & receptors Immune system: antibodies
Nucleic Acids: DNA	4 Bases: A, C, G, T Deoxyribose sugar, phosphate	Storage of hereditary information (genetic code)
Nucleic Acids: RNA 3 types: m-RNA t-RNA r-RNA	4 Bases: A, C, G, U Ribose sugar, phosphate	Protein synthesis: m-RNA: working copy of genetic code for a gene t-RNA & r-RNA: translation of the code

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