BIOCH 200 - Introductory Biochemistry

Iron (Fe)

• Important trace element.

  • Binds oxygen.

  • Moves electrons (especially through the electron transport chain).

Biomolecules!

• H₂O, CO₂, NH₃, O₂, N₂ → turn into amino acids (monomer), carbohydrates (monomers), nucleotides (monomers), lipids (not monomers.

• In its poly- form, amino acids are proteins, carbohydrates are polysaccharides, and nucleotides are nucleic acids.

• Polysaccharides → ribosomes, chromatin, membranes, etc.

Biomolecules Flowchart

Monomers

• Is a molecule that can be covalently bonded to other identical/similar molecules to form a polymer.

  • i.e. Amino acids, nucleotides, monosaccharides.

• The start and end always in a polymer → b/c of covalent bonds.

Amino Acids

• Soluble in water.

Carbohydrates

• Soluble in water.

Nucleotides

• Soluble in H₂O.

• Phosphorous tail and nitrogen base attached to a sugar base.

Lipids

• Is not soluble in water.

Carbohydrates — Key Features

• General formula: (C • H₂O)ₙ; unbranched carbon chain where n ranges from 3–9.

• Structure in solution: Typically exists in a ring structure.

• Functional groups: n − 1 hydroxyl groups and always 1 carbonyl group.

• Carbonyl details: Carbonyl group can be an aldehyde or ketone, usually on carbon 1 or 2; polyhydroxy aldehydes and ketones.

Biomolecules

• Oxygen – red.

• Carbon – grey/black.

• Hydrogen – white.

• Nitrogen - blue.

• S – yellow.

• P – orange.

Organic Compounds

• A carbonyl group is simply C=O.

• Memorize!

Functional Groups

• Nitrogen/oxygen groups: Amino group (amine) and hydroxyl group (alcohol).

• Sulfur and carbonyl groups: Sulfhydryl group (thiol) and carbonyl group (aldehydes and ketones).

• Carboxyl groups: Carboxyl/carboxy; carboxylic acid (H) and carboxylate (conjugate base).

Linkages in Biochemical Compounds

• Will be described as a linkage when reactions occur.

• Under most biological conditions, carboxylic acids exist as carboxylate anions.

• When you see “POP” it is a phosphoanhydride.

Acyl Group

• Formation: Formed by removing one or more hydroxyl groups from an oxoacid (typically a carboxylic acid) during attachment to another molecule.

• Structure: Carbonyl group (C=O) bonded to an alkyl group.

• Function: Only formed when two molecules are linked together.

Linkages: Esters

• Linkage between carboxyl group and a hydroxyl group.

• A condensation reaction and a dehydration reaction.

• H₂O is formed as a byproduct.

Linkages: Amides

• Linkage between a carboxyl group and a amino group.

• Dehydration reaction and condensation reaction.

Polymer

• Monomer that is part of a polymer.

• They have “directionality” - all covalent bonds are in the same orientation.

Residue

• Monomer which is a part of a polymer.

• Is not a monomer itself.

Monomers and Polymers

• Amino acids → protein.

  • Has a peptide bond.

• Nucleotides → nucleic acids.

  • Has a phosphodiester bond.

Electronegativity & Dipoles

• Electronegativity: Some atoms pull electrons stronger than others.

  • Least → most electronegative: H, C, S, N, O.

• Bond effect: Covalent bonds between atoms with different electronegativities create a permanent dipole.

Hydrogen Donor

• A hydrogen bonded to an electronegative atom (i.e. O, N, or S).

Hydrogen Acceptor

• A lone pair of electrons associated with an electronegative atom.

  • Must have a lone pair (O, N).

Hydrogen Bond

• H-bond interaction is almost double the length of the covalent bond ∴ weaker bond.

• Each H₂O molecule can form 4 H-bonds, two as donors and 2 as acceptors.

Ice

• In ice each water molecule forms 4 H-bonds.

• Hydrogen bonds in ice are most stable than hydrogen bonds in water.

Acid–Base Behavior of Water

• Bonding: ~3 H-bonds per water molecule on average.

• Roles: Forms 2 H-bonds as an acceptor and 2 as a donor.

• Acid–base: Acts as a weak acid by sharing (not fully giving away) its H as a donor; acting as a weak base means the H is not fully given away.

Non-Covalent Interactions

• Electrostatic forces: Ionic interactions (− ↔ +); NEVER called an ionic bond; generally stronger.

• Hydrogen bonds: Dipole–dipole interactions.

• Van der Waals: Lack H in their bonds; include dipole–dipole interactions and LD forces.

• Charge nature: Hydrogen bonds and van der Waals interactions are non-covalent associations between neutral molecules; no full ± charge, but form δ⁺/δ⁻.

Dipole-Dipole Interactions

• Between polar non-charged groups.

• Weaker than H-bonds.

London Dispersion Forces

• Between nonpolar molecules.

• Weaker than dipole-dipole interactions.

  • Exhibited by all molecules.

Hydrophobic Effect

• The tendency of water to minimize its contacts with nonpolar substances, thereby inducing the substances to aggregate.

  • Important in LD forces.

• Will involve LDF.

• Effect is always based on water’s whims.

• These are hydrophobic interactions.

Bond Strength in Biological Molecules

• An interaction may be weak.

• However, if there is a high amount of LD forces, they become strong together.

H-Bond Donors/Acceptors

• Donors: N-H, O-H, and S-H (S not as strong).

• Acceptors: -O-, -N-, and -S- (S not as strong).

Hydrophobic Effect - Shell

• Layer of constrained water molecules.

• A shell of water forms around the non-polar molecules.

  • Unhappy H₂O molecules.

• Water loves to make/break H-bonds.

The Hydrophobic Effect - Entropy

• Scattered non-polar molecules: Less favourable for water; lower entropy due to constrained water.

• Grouped non-polar molecules: More favourable for water; higher entropy.

• Mechanism: In water, non-polar compounds are forced to associate together.

• Result: Less water is consumed; water shoves them together, increasing entropy.

Amphipathic

• Molecules experience hydrophilic interactions and the hydrophobic effect.

• Used for bigger molecules (amphiphilic).

Micelle

• Water shoves fatty acids into a spherical structure.

• Aggregate to position polar parts close to water and nonpolar together away from water.

• Self-assembling to a bilayer.

T2 Phage Structure

• T2 phage is a virulent bacteriophage (virus) that infects Escherichia coli.

• DNA is contained in the head. A protein coat forms the head, collar, and tail.

• DNA is high in phosphorus (P), while the protein coat is relatively high in sulfur (S).

Hershey–Chase Experiment

• Bacteriophages were labeled with sulfur to track protein or with phosphorus to track DNA, then allowed to infect cells.

• After centrifugation, sulfur-labeled protein was not found in cells, while phosphorus-labeled DNA was found in cells.

Nucleotides and Their Polymers

• Involved in nearly every facet of cellular life.

• Storage and decoding of genetic information: DNA and RNA.

• Act as enzymes: RNA.

Pyrimidine

• Smaller but longer name and must have two N’s in the ring.

• All have a carbonyl at C2.

• Uracil and thymine have carbonyls at C2 and C4; thymine has a methyl group at C5.

• All bases are aromatic and heterocyclic.

Purines

• Smaller word larger molecule.

• There are 4 N’s in the molecule.

• There are no oxygens in adenine.

• All bases are aromatic and heterocyclic.

Resonance

• Describes delocalized electrons when bonding cannot be shown by a single Lewis structure.

• Occurs when electrons flow through neighboring π-systems; involves π-electrons or certain lone pairs.

• Delocalization stabilizes molecules but reduces H-bonding capacity; resonance lone pairs cannot accept H-bonds.

Lone Pairs in Resonance & H-Bonding

• Lone pairs involved in resonance cannot accept hydrogen bonds.

• In aromatic rings, an N with two single bonds and an H has its lone pair involved in resonance, while an N with one single and one double bond has a lone pair not involved in resonance.

• When N is bonded to a C that is double bonded to O, the N lone pair is involved in resonance.

• When N is bonded to a C that is double bonded to N, the N lone pair is involved in resonance.

Ribonucleic Acid (RNA)

• Polymer of G, A, C, U.

• Sugar portion is ribose + heterocyclic.

• C5’ is the only carbon atom not part of the ring structure.

• At C2 there’s an -OH group.

Deoxyribonucleic Acid (DNA)

• Polymer of G, A, C, T.

• Sugar potion is deoxyribose.

• There is no OH at the C2 position - literally lacking a oxygen.