Chemical Foundations

Cell Chemistry

Molecules are compounds The interaction of these molecules with each other determines how the cell works The types of interactions that molecules have with each other depend on the chemical properties of each of the molecules Understanding the types of interactions allows one to understand and predict the functions of the molecules

The Chemistry of Water

• The intracellular environment is aqueous• 70-80% of cellular weight is water• Water is the most abundant molecule in

biological systems• This is the medium in which the chemistry

of life happens

Water: How Does It Make You Feel?

• Hydrophilic

• Hydrophobic

• Amphipathic

I WATER I WATER I WATER Biomolecules are defined in part by how they relate to water.

Time to “Bond”

• Covalent BondsConnect atoms into a molecule: within molecule bonds

• Noncovalent Interactions

Stabilize groups of atoms into functional structure: within and between molecule interactions

– Ionic bond– Hydrogen bonds– van der Waals interactions– hydrophobic effect

Covalent Bonds

• Strong forces that hold atoms together into molecules• Form when atoms share (one pair or multiple pairs of ) electrons• Have fixed or specific geometric orientation

Polar Covalent Bonds

• What happens if one atom has a greater affinity for the electron?

Water: polar molecule

• Covalent BondsConnect atoms into a molecule: within molecule bonds

• Noncovalent Interactions

Stabilize groups of atoms into functional structure: within and between molecule interactions

– Ionic bond– Hydrogen bonds– van der Waals interactions– hydrophobic effect

Ionic Interactions

• Attractions between oppositely charged ions (cation+anion)• Do not have a specific geometry associated with them• Weaker than covalent bonds

Hydration shell

Hydrogen Bonds

• Interactions of a positively charge H atom in a molecular dipole with unpaired electrons from another atom

• This can occur within the same molecule or a different molecule

• Properties of water:– High melting/boiling points– Ability to interact with other

molecules

Hydrogen Bond

Potential Hydrogen Bond Interactions

• Solubility of uncharged substances in an aqueous environment largely depends on the ability of that substance to form H bonds with water

• Molecules with polar bonds that can easily form H bonds with water

• Charged molecules and ions that interact with the dipole in water

can dissolved in water

So, these molecules are hydrophilic (water liking)

(Ionic Interactions)

(Hydrogen Bond Interactions)

So how about nonpolar molecules?

These molecules are hydrophobic (water fearing)

• Non-polar molecules– Do not contain charged groups– Do not possess a dipole moment– Do not become hydrated

(do not interact well with water)− In biology, most common nonpolar molecules

are the hydrocarbons (C – C; C – H)

Hydrophobic Interactions

• Hydrophobic chemicals don’t form interactions with water– non-polar, uncharged

• H-bonds form between water molecules, excluding hydrophobic substances– hydrophobic

molecules end up clumped together

Van der Waals Interactions

• Weak, nonspecific attractive force created when two atoms approach each other closely

• Occurs in all types of molecules, both polar and nonpolar

• Particularly responsible for the cohesion between nonpolar molecules

• ↑Distance ↓Strength• Strength in numbers

• Covalent BondsConnect atoms into a molecule: within molecule bonds

• Noncovalent Interactions

Stabilize groups of atoms into functional structure: within and between molecule interactions

– Ionic bond– Hydrogen bonds– van der Waals interactions– hydrophobic effect

Done !

Polar vs. Nonpolar

Polar = parts are negatively charged and other parts are positively charged– This can be a formal charge (-) or (+)– This can be separation of charge but overall neutral

molecule.Nonpolar = no separation of charge (neutral)

- In biology, most common nonpolar molecules are the hydrocarbons- These molecules do not interact well with water

Amphipathic- molecule having a polar and a nonpolar part

Brief Summary

Relative Bond StrengthsBrief

Summary

Complementary shapes

Macro = large

Major Biological Molecules:ProteinsNucleic AcidsCarbohydratesLipids

How big is big?Molecular weightOxygen = 16, Carbon = 12

Carbon dioxide = 44Proteins - 5,000 to 150,000

Macromolecules

Chemical Building Blocks

Biological macromolecules formed by covalent bonds between monomers in a dehydration reaction– Proteins– Nucleic Acids– Polysaccharides

Phospholipids form the basic bilayer structure of biomembranes by non-covalent interactions

Biological macromolecules formed by covalent bonds between monomers in a dehydration reaction– Proteins– Nucleic Acids– Polysaccharides

MONOMERS POLYMER

polymerization

• Amino Acids Proteins• Nucleotides Nucleic Acids• Sugars Polysaccharides

Proteins

Each protein has an amino and a carboxyl group on it

C C

O

OH

R

H

N

Carboxyl Group (COOH)

Side Chain

Amino Group (H2N)

H

H

Amino acid

Proteins do most of the jobs in cellsAntibodiesEnzymesCarry oxygenTransportersStructure (cell cytoskeleton)and many, many more… There are 20 different types of amino acids

Proteins are made up of small subunits called amino acids

They can be hooked up in different orders to make a different protein

Sample words:andperformexplanationsupercalifragilisticexpialidocious

Sample proteinsInsulin - 51 a.aRubisco - hundreds of a.a.

Proteins as Words

ANALOGY: each amino acid is like a letter of the alphabet.

Words are constructed by putting together letters in different orders (and different lengths)

The 20 AAs:Alanine (A)Arginine (R)Aspartate (D)Asparagine (N)Cysteine (C)Glycine (G)Glutamate (E)Glutamine(Q)Histidine (H)Isoleucine (I)Leucine (L)Lysine (K)Methionine (M)Phenylalanine (F)Proline (P)Serine (S)Threonine (T)Tryptophan (W)Tyrosine (Y)Valine (V)

Amino AcidsThe amino acids can be grouped in terms of their chemical properties.−Ionized @ pH of 7 are the most hydrophilic−(+) Basic; (-) Acidic

Amino Acids

− Nonpolar side chain are hydrophobic and so poorly soluble in water− The larger the nonpolar side chain, the more hydrophobic the amino acid

Protein Conformation

• Primary structure: linear AA sequence• Secondary structure: folding of adjacent AAs into

3D shapes (α-helix, β sheets)– Hydrogen bonding

α-helix

β sheets

Protein Conformation

• Tertiary structure: overall conformation; domains– Non-covalent ionic interactions– Disulfide bridges

Protein Conformation

• Quaternary structure: multiple subunits (completely different polypeptide strings)

MONOMERS POLYMER

polymerization

• Amino Acids Proteins• Nucleotides Nucleic Acids• Sugars Polysaccharides

Reminder:

Four building blocks in DNAAdenineCytosineGuanineThymine

Four building blocks in RNAAdenineCytosineGuanineUracil

It’s amazing - isn’t it?Only 4 different building blocksmake up all of the code for us.

AND each of us is different eventhough there are only 4 types ofbuilding blocks.

What makes us different????

DNA (deoxyribonucleic acid)

RNA (ribonucleic acid)Nucleic Acids

Nucleotides

BaseO

5-C sugar

Common structure: phosphate + five carbon sugar + base

RNA DNA

How many types of base?

Nucleotides

BaseO

5-C sugar

Common structure: phosphate + five carbon sugar + base

AGC found in both DNA and RNA

T is found only in DNA

U only found in RNA

Nucleotides are hooked together through a phospodiester bond

Its all of the phosphodiester bondsthat make the phosphate backboneof nucleic acids

Water is lost during this reaction too!

Nucleotides Polymerization

MONOMERS POLYMER

polymerization

• Amino Acids Proteins• Nucleotides Nucleic Acids• Sugars Polysaccharides

Reminder:

Polysaccharides can be used:to store energy - glycogen, starch,

as protection - chitin (bugs)as support - cellulose (plants), and to make glycoproteins

PolysaccharidesThe building blocks of polysaccharides are simple sugars, or monosaccharidese.g. glucose, galactose, etc.

Disaccharides, Polysaccharides

• Glycosidic bonds ( C-O-C) link multiple sugars in a chain – water is lost in bond

formation

Cellulose

Long chains arrayed in parallel sheets for strength

Disaccharides- 2 monosaccharidesLactose= glucose + galactoseSucrose= glucose + fructose

Summary

Chemical Building Blocks

Biological macromolecules formed by covalent bonds between monomers in a dehydration reaction– Proteins– Nucleic Acids– Polysaccharides

Phospholipids form the basic bilayer structure of biomembranes by non-covalent interactions

Phospholipids• Biomembranes- large flexible sheets

– Boundries of cells and intracellular organelles– Assembled by non-covalent interactions

• Phospholipids are the primary building blocks of biomembranes

Amphipathic

• Saturated vs. Unsaturated– absence or presence of double bonds in carbon chain– affects melting point– affects the shape of fatty acids

Solid at room temp.

Trans fats: solid margarine sticks

Let’s name some things that each of the previousmolecules have in common and are different in terms of polymerization.

Lipids are not true macromolecules because they don’t undergo polymerization (but they are big!)

Similarities and Differences of Biological Macromolecules