U1 Chemistry of Life

PDF pgs. 172-201

4 elements required to build biological molecules (carbs, proteins, lipids, nucleic acids)

Oxygen (O)

Carbon (C)

Hydrogen (H)

Nitrogen (N)

Element in proteins and nucleic acids

Nitrogen (N)

Element in nucleic acids and some lipids

Phosphorus (P)

Smallest units of an element

Atoms made of protons (+) , neutrons (O), and electrons (-)

Trace elements

Elements required by an organism only in very small quantities (Fe, I, and Cu)

Isotopes & Radiometric dating

Atoms with same number of protons but different amount of neutrons

Radiometric dating = artifacts dated by examining the rate of decay of carbon-14 in it

Chemical bonds

Atoms of a compound are held by:

Ionic bonds

Covalent bonds

Hydrogen bonds

Ionic bonds

When electrons are transferred from one atom to another

Ions = the atoms become negatively or positively charged depending on which one lost or gained the electron

Covalent bonds

Nonpolar covalent bonds = electrons are shared equally between atoms

Polar covalent bonds = Electrons are shared unequally between atoms

Single covalent bond = 1 pair of electrons is shared between 2 atoms

Double covalent bond = 2 pairs of electrons are shared

Triple covalent bond = 3 pairs of electrons are shared

Bonds in water

Hydrogen bonds

Electrons are unequally shared (Oxygen is more electronegative) (polar)

Negative oxygen of one water is attracted to the positive hydrogens

Hydrogen bonds

Intermolecular attraction

Weak that form when H atom covalently bonded to an electronegative atom is also attracted to another electronegative atom

Strong in large numbers

Great solvent to dissolve things

Special properties of water molecules because of hydrogen bonds

Cohesion and adhesion

Surface tension

High heat capacity (takes more energy to increase temperature of water than others)

Expansion on freezing

Cohesion

Water’s strong tendency to stick together

Adhesion

Water’s tendency to stick to other substances

(ex: two glass cups stuck together by the film of water between them)

Capillary action

Water’s ability to rise up the roots, trunks, and branches of trees (up the xylem)

Works because of both cohesion and adhesion

Surface tension

Water molecules stick together because of cohesion and let light things sit atop the surface

Acidic solutions

If you dissolve an acid in water, it will release many hydrogen ions (H⁺)

Has lots of hydrogen ions

Basic solutions (Alkalines)

If you add it to water, it will release many hydroxide ions (OH^-)

Don’t release hydrogen ions (H⁺)

Slippery

pH scale

Measures the acidity or alkalinity of a solution

1 through 14

1 = acidic

7 = neutral

14 = basic

Formula for pH

pH = -log [H+]

H⁺ and pH have an inverse relationship

pH graphing/scaling

Logarithmic

pH = 3 is 10 times more acidic than pH = 4

1 pH increase = x10 decrease in hydrogen ion concentration

Organic compounds vs Inorganic compounds

Organic: Chemical compounds that contain a skeleton of carbon atoms surrounded by hydrogen atoms and other elements

Inorganic: Molecules that don’t have both carbon and hydrogen

Properties of carbon

Can bind with other carbons, N, O, and H

Monomers vs Polymers

Monomers: Individual parts that make up macromolecules that have chains of monomers

Polymers: Macromolecules that are made up of repeating monomers

Dehydration Synthesis (condensation reaction)

Forms polymers

Water molecule is lost to build a larger compound

Hydrolysis

Polymers broken down into monomers

Water is added to separate the two monomers

Carbohydrates

(CH2O)n —→ C, H, and O usually in a 1:2:1 ratio

Categorized as either monosaccharides, disaccharides, or polysaccharides

Saccharides = sugar

Monosaccharides

Simplest sugars and energy sources for cells

Most common: glucose, fructose, galactose, ribose, deoxyribose

Glucose (C₆H₁₂O₆)

Most abundant monosaccharide

6 carbon sugar

Used in cellular respiration to convert into energy and in photosynthesis for plant food

Structure: Either a 6-cabon ring with many OHs and Hs OR a straight-chain with a carbon backbone and Hs and OHs attached to the side

Fructose

Monosaccharide

Common sugar in fruits

Structure: Either a 6-carbon ring with some OHs OR a straight-chain with a carbon backbone with OHs and Hs attached to the side

How to number carbons on rings/chains

Rings: First carbon is attached to 2 Oxygens (glucose) OR CH₂OH which is to the bottom right of the lone oxygen (then clockwise)

Chains: First carbon is closest to the side with the double bond to O

Glycosidic Linkage

When 2 monosaccharides are joined by dehydration synthesis (-H of sugar combines with -OH from another sugar)

Creates a disaccharide

Common disaccharides

Maltose = two glucose molecules

Sucrose = table sugar

Lactose = in dairy products

Polysaccharides

Made of repeated units of monosaccharides (Branched or unbranched chains)

Common: Starch, cellulose, glycogen

Glycogen and Starch

Sugar storage molecules

Glycogen = sugar in animals

Starch = sugar in plants

Cellulose

Made of β-glucose

Function: structural support in cell walls of plants

Chitin

Polymer of β-glucose molecules

Structural molecule in walls of fungus and in the exoskeletons of arthropods (bugs)

Protein

Functions: structure, function, and regulation of tissues and organs

Monomers: Amino acids

Amino Acids

Monomers of proteins

Made of C, H, O, and N atoms

20 different common amino acids

Structure:

• Central carbon

• Amino group (-NH₂)

• Carboxyl group (-COOH)

• Hydrogen

• R-group

R-groups (side-chains) of amino acids

Vary in:

• Composition (C, H, O, N, and S)

• Polarity (polar, nonpolar)

• Charge (o, +, -)

• Shape (long, short, ring)

Affects whether it’s hydrophobic or hydrophilic

3 categories of amino acids

1) Hydrophobic (nonpolar & uncharged)

2) Hydrophilic (polar & uncharged)

3) Ionic (polar & charged)

Dipeptide

2 amino acids joined (carboxyl group to an amino group)

Joined by a peptide bond

Polypeptide

Made of a string of amino acids

1st stage before it is twisted and folded to make a 3D protein

New amino acids are always added on the carboxyl end of the chain

Peptide termini

N-terminus/amino terminus = end of the peptide with an amino group

C-terminus/carboxyl terminus = end with a carboxyl group

Generally, all peptides have an N- and C-terminus

Protein stages

1) primary structure - linear sequence of the amino acids

2) secondary structure - polypeptide twists

3) tertiary structure - folds 3D

4) quaternary structure (sometimes) - multiple polypeptide chain interactions to make a protein

Primary structure of a protein

Linear sequence of amino acids in a polypeptide chain

Secondary structure of a protein

Polypeptide:

• Twists (forms a coil called an alpha helix)

  • OR

• Zigzags (pattern called beta-pleated sheets)

Depends on the different R-groups interacting with each other

Tertiary structure of a protein

Far away amino acids interact with each other (because the helix or sheet structure brings different groups closer together)

Often locked into a stable 3D shape

• Hydrophobic amino acids are on the inside of the protein

• Hydrophilic are on the outside

• Covalent disulfide bonds between two cysteine amino acids stabilize it sometimes

Covalent disulfide bonds

A bond between two cysteine amino acids that sometimes occurs to stabilize the tertiary structure of a protein.

• Only cysteine and methionine have sulfur in their R-groups (and methionine is almost always the start amino acid)

Quaternary structure of a protein

Interaction between multiple different polypeptide chains (almost always in tertiary structure)

Incorrectly folded proteins

Only proteins that have folded correctly into a 3D structure can perform their intended function

Mistakes in amino acid chain can create nonfunctional, differently shaped proteins

Chaperone proteins (chaperonins)

Proteins that sometimes help other proteins fold properly and more efficiently

Lipids (elements, types, and function)

Consist of C, H, and O atoms in different ratios

Monomer: basically fatty acids (but technically lipids doesn’t have one)

Common examples: triglycerides, phospholipids, and steroids

Function: Structural components of cell membranes because they’re nonpolar, insulation, signaling, and energy storage

Triglycerides

Makes up fat storage in tissue

Made of a glycerol molecule (backbone) with 3 fatty acid chains attached to it

Fatty acid chain = Long chain of carbons where each carbon is covered in hydrogen with a carboxyl group end on one side

Saturated fatty acids

Hydrogens along its carbon chain or with a few gaps where double bonds replace a hydrogen

NO double bonds

Tend to form solids at room temp.

• Generally linear molecules to be tightly packed (butter)

Unsaturated (monounsaturated) fatty acids

One double bond in the carbon chain

Tend to be liquid at room temp. if cis-double bonds (solid if not)

• More kinked in structure so cannot pack as tightly (oil)

Unsaturated (polyunsaturated) fatty acids

Has many double bonds within the fatty acid

More double bonds = more unsaturation

Tend to be liquid at room temp. if cis-double bonds (solid of not)

• More kinked in structure so cannot pack as tightly (oil)

Cis-double bonds vs Trans-double bonds

Cis-double bonds = The hydrogens are either both above or both below the 2 double bonded carbons to which they are connected

• Cis-double bonds are more kinked in their structure (around a 30 degree bend)

Trans-double bonds = The hydrogens are on opposite sides of the chain where they attach to the 2 double bonded carbons

Phospholipids

2 fatty acid “tails” = hydrophobic

• Nonpolar —→ also don’t mix well with polar water

1 negatively charged phosphate “head” = hydrophilic

• - drawn to + end of water

Amphipathic molecule = 1 side is hydrophilic and 1 is hydrophobic

Cholesterol

Four-ringed molecule and lipid in some membranes

Function: Increases membrane fluidity EXCEPT at high temps where it holds things together instead

Also helps make certain hormones

Nucleic acids [elements, monomers, types]

Elements: C, H, O, N (line proteins) AND Phosphorus

Monomers: nucleotides

Types: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

DNA structure and function

Structure: Phosphate group, Adenine/Cytosine/Thymine/Guanine (nitrogenous base), and deoxyribose (5-carbon sugar without OH)

Function: Contains hereditary blueprints of all life

RNA structure and function

Structure: Phosphate group, Adenine/Cytosine/Uracil/Guanine (nitrogenous base), and ribose (5-carbon sugar including OH)

Function: Essential for protein synthesis

Elements in the 4 macromolecules

All contain C, H, and O

N = Proteins and nucleic acids

S = Proteins

P = Nucleic acids and sometimes lipids