Biology 1020 lecture 5 Biological Molecules B

• 3D folded and coiled molecules - structure fits function
• 50% of the dry mass of cells
• 1+ polypeptides

• Provide support (keratin and collagen)
• Move cells, organelles ( muscles - actin and myosin)
• Assist chemical reactions (enzymes)
• Store amino acids (e.g. ovalbumin)
• Protect against disease (antibodies)
• Co-ordinate activities (hormones)
• Transport materials between cells (hemoglobin)
• Allow cells to detect and respond to stimuli-receptors on cell surfaces

• polymer: polypeptide
• monomer: amino acids
• ** 50-34000 amino acids long peptide

• central alpha carbon
• carboxyl and amino group
• side chain/variable groups - R group

• grouped based on properties of R groups at pH 7.2
• Uncharged
• - polar
• - uncharged

• Charged
• - Acidic
• - Basic

Amino Acids (ex. Aspartic or Glutamic acid): They have a carboxyl group on their side chain that can donate a H⁺

Amino Bases (ex. Lysine, Arginine, Histidine): They have a nitrogen group on their side chain that can accept H⁺

Non-Polar Amino Acids (ex. Tryptophan and Glycine): They have lots of hydrocarbon bonds that are non-polar on their side chains.

Polar Amino Acids (ex. Serine): They have hydroxides, disulfide, and/or NH₂-C=O group on side chain.

Amino acids are held together in polypeptides by peptide bonds formed via a dehydration reaction between the carboxyl and the nitrogen groups on the main backbone of the amino acid.

• Order and properties of amino acids determine shape
• Activity/function in a particular region (action site of protein)
• Other molecules bind/fit into a specific  space

• Starts to fold into shape as it is synthesized
• Physical interactions assist folding
• aqueous environment
• e.g. non-polar amino acids shielded from water
• parts of the chain brought close together

• Primary
• Secondary
• Tertiary
• Quaternary (most folded)

• Unique sequence of amino acids
• Determined by the gene sequence
• (Just the sequence of "beads" on a necklace. Amino acids).

• Coils or folds in polypeptide
• Hydrogen bonds between different parts of polypeptide backbone. O^-ve  H^+ve
• properties determined by mix of structure

α helix: Proteins rich in alpha helical structures tend to be fibrous and strong.

β pleated sheet: Proteins rich in beta sheets tend to stretch and recoil.

• Hydrophobic amino acids shield from water
• R groups close together for H bonding
• Disulfide bridges
• * Covalent bond. -S-S- cysteines

• 2+ polypeptide chains form one molecule.
• Can be Globular (e.g. hemoglobin, 2 beta and 2 alpha chains), or Fibrous (e.g. collagen - 3 polypeptides coiled)

• pH
• Solute Concentration
• Temperature

• Protein is denatured when it has lost proper 3D structure and loses function
• Denatured proteins can aggregate in harmful ways in cells.
• In some cases, the denatured protein can be renatured to a normal protein.

• Stressors such as heat can cause a protein to unfold
• Chaperonins assist the proper folding/refolding of other proteins.
• Chaperonin consists of a cap and a hollow cylinder

• Inherited blood disorder, Sickle-cell disease
• Single amino acid substitution in hemoglobin
• Glutamine-polar becomes Valine-non polar
• changes primary level to quarternary level

• Infectious proteins
• * Mammals
• * Fungi
• Abnormally folded, Not denatured by most denaturants such as heat, radiation, etc.
• Cause normal proteins to lose their structure
• - infectious

• DNA - Deoxyribonucleic Acid
• RNA - Ribonucleic Acid

• Synthesis of mRNA in the nucleus (transcription)
• Movement of mRNA into cytoplasm via nuclear pore
• Goes to ribosome. Synthesis of protein (translation)

Called Nucleotides: Nucleoside (nitrogenous base and pentose sugar) and phosphate.

• Single ringed
• Cytosine
• Thymine
• Uracil

• Double ringed
• Adenine
• Guanine

• Sugar-phosphate backbone
• - Covalent bond
• - OH on #3 carbon of one sugar
• - Phosphate on #5 carbon

• Nitrogenous bases as appendages
• Forms helix structures

• 2 polynucleotide spiral around an axis
• Backbones run in opposite directions
• => anti-paraellel
• 5'--> 3'
• 3'--> 5'
• H bonds between. Nitrogenous bases: A-T and G-C