Biochemistry Macromolecules, Proteins, Amino Acids 4

Amino Acids https://www.youtube.com/watch?v=G9BkFqVkQ-g 7 minutes 4

Introduction to Biochemistry Most biologically important macromolecules are: 1) proteins 2) polysaccharides (carbohydrates) 3) nucleic acids 4) Oils and fats All are polymers made via Condensation reactions and destroyed by Hydrolysis.

Amino Acid Properties are soluble in water They can act as either an acid or a base because they are Zwitterions (Zwi = 2 in German) have a positive & a negative charge Thus they are ionic and so: 1) Have high melting temperatures 2) Are solids (and colourless) 3) As they are ionic and charged they are soluble in water 4) Chemically they can behave as buffers 5) They are ALL chiral (except Glycine) therefore they are enantiomers

The asymmetry of their mirror images Amino Acids are optically active molecules or they have chiral carbons (4 DIFFERENT groups attached). One exception is the achiral glycine where the R-group is hydrogen). The asymmetry of their mirror images makes them non-superimposable. They are called enantiomers (anti - opposite)

Polypeptides and Proteins Proteins are polyamides made from 20 amino acids make proteins in humans. There are actually more than 700 amino acids counted so far. When formed by amino acids, each amide group is called a peptide bond (amide bond). Peptides are formed by condensation of the -COOH with the NH2 group of another amino acid. .

Acid-Base Behavior of Amino Acids 4

Amino Acids While their name implies that amino acids are compounds that contain an —NH2 group and a —CO2H group, these groups are actually present as —NH3+ and —CO2– respectively. How do we know this?

high melting point (when heated to 233°C ) Properties of aa’s Ex: glycine high melting point (when heated to 233°C ) soluble in water; not soluble in nonpolar solvent consistent with ions like this Not molecules like this – • • O H3NCH2C •• + O OH H2NCH2C •• • • Thus we know it is a zwitterion or dipolar ion

Acid-Base Properties of Glycine The zwitterionic structure of glycine also follows from considering its acid-base properties. Start with the structure of glycine in strongly acidic solution, say pH = 1, then ask the question, what would glycine look like? At pH = 1, glycine exists in its protonated form O OH H3NCH2C + •• • •

Acid-Base Properties of Glycine Now ask yourself "As base is added and the pH is raised, which is the first proton to be removed? typical carboxylic acid: pKa ~5 typical ammonium ion: pKa ~9 OOH H3NCH2C + The more acidic proton belongs to the COOH group. In fact, glycine is stronger than a typical carboxylic acid because the positively charged N acts as an electron-withdrawing group, making the H more likely to leave.

Acid-Base Properties of Glycine Now continue to raise the pH, and eventually the H+ attached to N can be removed. The pKa for removal of this proton is 9.60. This value is about the same as that for NH4+

The pKa of glycine is approx 6.0. Zwitterionic structure is neutral the pH is called isoelectric point. H+ gone in base H+ attaches in Acid The pKa of glycine is approx 6.0.

Protein Structure https://www.youtube.com/watch?v=gWM7S0Mpvtg All 4 structures 2 minutes Primary structure is the amino acid sequence. Ex: aa-aa-aa-aa-aa Secondary structure is how the amino acids in sequence fold up. Ex:a-helixes & b-sheets via H-Bonds. Tertiary the 3-D folding of the secondary structure. Also, disulfide bonds from cysteine form here Quaternary Final product, final structure, when all the subunits or polypeptides are brought together to make the whole thing.

1O Structure Consider a peptide with two amino acids AA1 AA2 20 x 20 = 400 different molecules AA1 AA2 AA3 20 x 20 x 20 (or 203 ) = 8000 different molecules For 100 amino acid protein the # of possibilities are: The total number of atoms in the universe is

2o structure: b-strands Inter-chain H-bonds

2o structure: a-helixes Intra-chain H-bonds https://www.youtube.com/watch?v=Q0NKorneE04 Alpha Structure 3 minutes

2o structure: a-helixes

3o 4o Structures 3o 4o HbA 22 tetramer Hb monomer (or myoglobin) (multimeric) Hb monomer (or myoglobin)

Enzymes Active (catalytic) site is a crevice which binds a substrate. 1500 enzymes have been found. Enzymes are proteins which act as catalysts(there may be 30,000 enzymes in a human. Active (catalytic) site is a crevice which binds a substrate. Lock & key metaphore.

Enzyme Inhibition

The Structure of DNA All life on earth uses a chemical called DNA to carry its genetic code or blueprint. In this lesson we be examining the structure of this unique molecule. {Point out the alligator’s eyes in the first picture.} By the way, can you make out what this is? *************************************************************** [The goal of this presentation is to introduce high school biology students to the chemical structure of DNA. It is meant to be presented in the classroom while accompanying the teacher’s lecture, under the control of the teacher.]

The Shape of the Molecule DNA is a very long polymer. The basic shape is like a twisted ladder or zipper. This is called a double helix. {Show students a model of the double helix. Explain what a spiral is and a helix is.}

The Double Helix Molecule The DNA double helix has two strands twisted together. We will take apart the DNA molecule to see how it is put together. First, we will look at one strand.

The teeth are nitrogenous 4 nitrogen bases. One Strand of DNA The backbone of the molecule is alternating phosphates and deoxyribose sugar The teeth are nitrogenous 4 nitrogen bases. Cytosine C Thymine T Adenine A Guanine G nucleotide deoxyribose {Point to the 3-D mode, if you have one, to show the parts as you discuss them.} phosphate bases

The teeth are the nitrogenous bases but why do they stick together? Two Stranded DNA Remember, DNA has two strands that fit together something like a zipper. The teeth are the nitrogenous bases but why do they stick together? {Point to the 3-D model to show the parts as you discuss them.}

Hydrogen Bonds The bases attract each other because of hydrogen bonds. Hydrogen bonds are weak but there are millions and millions of them in a single molecule of DNA. The bonds between cytosine and guanine are shown here with dotted lines C N O

Cis-Plantin https://www.youtube.com/watch?v=DbvCwd9XXtQ 2 minutes