BIOCH 200

Biochemistry

The scientific discipline that seeks to explain life at the molecular level.

Most Common Elements

• (H)Hydrogen

• (C)Carbon

• (N)Nitrogen

• (O)Oxygen

• (P)Phosphorus

• (S)Sulfur

Essential Ions

• (Na)Sodium

• (Mg)Magnesium

• (Cl)Chlorine

• (K)Potassium

• (Ca)Calcium

Trace Elements

• (B)Boron

• (F)Fluorine

• (Al)Aluminum

• (Si)Silicon

• (V)Vanadium

• (Cr)Chromium

• (Mn)Manganese

• (Fe)Iron

• (Co)Cobalt

• (Ni)Nickel

• (Cu)Copper

• (Zn)Zinc

• (Ga)Gallium

• (As)Arsenic

• (Se)Selenium

• (Mo)Molybdenum

• (Sn)Tin

• (I)Iodine

Major Classes Of Biomolecules

• Amino Acids

• Carbohydrates

• Nucleotides

• Lipids

Directionality

All covalent bonds are in the same orientation

Hydrogen Bonds

Non-covalent bonds where a hydrogen is shared between two electronegative atoms

Hydrogen Bond Donor

Strongly electronegative atom covalently attached to the hydrogen

Hydrogen Bond Acceptor

Electronegative atom with an appropriate (hybridized) lone pair

Water H-Bond Stucture

• ~3 per molecule

• 2A:2D

H₃O⁺ H-Bond Structure

• 4 per molecule

• 1A:3D

Van der Waals Interactions

• Dipole-dipole interactions

• London dispersion forces

Dipole-Dipole Interactions

Between polar non-charged groups

London Dispersion Forces

Between nonpolar molecules

Bond Strength

Covalent > Ionic > Hydrogen > Van der Waals

The Hydrophobic Effect

Non-polar compounds tend to associate with each other in aqueous environments

Amphiphilic/Amphipathic

Structures that have both non-polar and polar regions

Nucleotide

• Phosphate

• Sugar

• Nitrogen-containing aromatic base

Cytosine

Thymine

Adenine

Guanine

Uracil

Thymine and Uracil H-Bond Structure

• 6 per molecule

• 4A:2D

Nucleoside

• Base

• Sugar

Adenine + Ribose

Adenosine

Adenine + Deoxyribose

Deoxyadenosine

Guanine + Ribose

Guanosine

Guanine + Deoxyribose

Deoxyguanosine

Cytosine + Ribose

Cytidine

Cytosine + Deoxyribose

Deoxycytidine

Thymine + Deoxyribose

Deoxythymidine

Uracil + Ribose

Uridine

Nucleic Acids

Polymers of nucleotides linked by phosphodiester bonds

Phosphoester

Link carbons to phosphate groups

Phosphodiester

Link two carbon atoms to one phosphate group

Phosphoanhydride

Link two phosphates to each other

A260nm/A280nm for Pure DNA

1.95

Zwitterion

A neutral ion with an equal number of positive and negative charges

• Alanine

• Ala

• Aliphatic

• Hydrophobic

• Valine

• Val

• Aliphatic

• Highly hydrophobic

• Branched

• Leucine

• Leu

• Aliphatic

• Highly hydrophobic

• Branched

• Isoleucine

• Ile

• Aliphatic

• Highly hydrophobic

• Branched

• Phenylalanine

• Phe

• Aromatic

• Highly hydrophobic

• Tryptophan

• Trp

• Aromatic - heterocyclic

• HydrophobiC

• Methionine

• Met

• Aliphatic

• Hydrophobic

• Sulfur-containing - thioether

• Proline

• Pro

• Aliphatic - distinctively cyclic

• Hydrophobic

• Glycine

• Gly

• Achiral

• Weakly Polar

• Very small - flexible

• Serine

• Ser

• Polar - uncharged

• Contains hydroxyl group

• Threonine

• Thr

• Polar - uncharged

• Contains hydroxyl group

• Tyrosine

• Tyr

• Weakly polar - uncharged

• Aromatic

• Contains hydroxyl

• pKa 10.5

• Cysteine

• Cys

• Polar - uncharged

• Sulfur containing - thiol group

• pKa 8.5

Cystine

• Disulfide bond between two cysteine sidechains

• Occurs in oxidizing environments

• Asparagine

• Asn

• Amide containing

• Polar

• Glutamine

• Gln

• Amide containing

• Polar - noncharged

• Histidine

• His

• Can be acidic or basic at pH 7

• Polar - charged/uncharged

• pKa 6.0

• Aspartate

• Asp

• Negatively charged at pH 7

• Very polar

• pKa 4.0

Aspartic Acid

Aspartate at pH 1

• Glutamate

• Glu

• Negatively charged at pH 7

• Very polar

• pKa 4.0

Glutamic Acid

Glutamate at pH 1

• Lysine

• Lys

• Positively charged at pH 7

• Contains amino group

• Very polar

• pKa 10.0

• Arginine

• Arg

• Positively charged at pH 7

• Very polar

• pKa 12.5

Peptide/Oligopeptide

• Larger number of amino acids

• Often synthetic

Polypeptide

• Long chain of amino acids

• Usually natural

Protein

Large polypeptide(s) with a biological function

Primary Structure

Sequence of amino acids in a polypeptide

Secondary Structure

Local folding of the polypeptide backbone

Tertiary Structure

Arrangement of all atoms in a single polypeptide

Fibrous Proteins

• Insoluble

• Long protein filaments

• Structural or connective

Globular Proteins

• Soluble

• Compact structures with nonpolar cores and polar surfaces

Ion Pairs/Salt Bridges

Electrostatic interactions between closely-positioned formal charged groups

Disulfide Bonds/Bridges

Covalent bonds between closely-positioned cysteines

Domain

Polypeptide segment folded into a single structural unit with a hydrophobic core

Motif

Region of polypeptide with a recognizable 3D shape

Prosthetic Group

• Non-peptide component that is permanently incorporated into a protein

• Provide structure and functional chemical groups

Heat breaks

• H-bonds

• Hydrophobic interactions

Changes in pH Break

• Salt bridges

• H-bonds

Salt Breaks

• Salt bridges

• Ion pairs

Detergents Break

Hydrophobic interactions

Quaternary Structure

Proteins comprised of more than one polypeptide chain (subunit)