AP Biology Unit 1: Biochemistry

# of chemical elements required for life

25

What four elements make up 96% of living matter?

Carbon, Hydrogen, Oxygen, Nitrogen

Special Properties of Water

Cohesion/Adhesion, Universal Solvent, Lower Density when Solid, High Specific Heat Capacity, Heat of Vaporization

Cohesion & Adhesion

H-bonding between H2O molecules gives water surface tension.

H-bonding between H2O and other substances causes capillary action and meniscus.

Universal Solvent

Water!! due to its polarity, polar H2O molecules surround + and - ions

Hydrophillic

Polar and attracted to H2O

Hydrophobic

Non-polar and deterred from H2O

Ice

H bonds form a crystal. This ensures water bodies don’t freeze solid.

Specific Heat

H2O resists change in temperature due to Hydrogen bonds. Takes a lot to heat it up and a lot to cool it down. Water moderates temperatures on Earth.

Heat of Vaporization

Organisms rely on heat of vaporization to remove body heat (i.e. sweating, panting)

Cellular Regulation

Water regulates cells, donates H+ when too few, absorbs H+ when too much.

Electronegativity

The measure of an atom’s ability to attract a shared electron pair when it is participating in a covalent bond.

Ionic Bond - Electronegativity

When the electronegativity difference between two atoms is greater than 1.7.

Polar Covalent Bond - Electronegativity

When the electronegativity difference between two atoms is greater than 0 and less than 1.7

Nonpolar Covalent Bond - Electronegativity

When the electronegativity difference between two atoms is 0.

Molecule’s Biological Function

Determined by the types of bonds between its atoms, and its overall shape and polarity.

Hybridization

A modification of the valence orbitals that changes the orientation of the valence electrons. VSEPR models are useful to predict molecular shape.

Physical Properties of Water (4)

Colourless, Tasteless, Odourless, Good solvent

Intermolecular bonds

Chemical bonds between molecules.

Includes: London Dispersion Forces, Dipole-dipole forces, Hydrogen Bonds

London Dispersion FOrces

• Weakest intermolecular bond

• exists between all atoms and molecules

• only IMF between noble gas atoms and nonpolar molecules

• formed by temporary unequal distribution of electrons at random

Dipole-dipole Forces

• holds polar molecules to eachother

• positive dipole of one molecule attracted negative dipole of another

• stronger than LDF, weaker than H-bond

Hydrogen Bonds

• Strongest intermolecular bond

• very strong dipole-dipole bonds between positive H ion of one molecule to negative F, O, or N atom of another polar molecule

• like WATER

Van Der Waals Forces

LDF, D-D, H-Bond

Water’s uniqueness

• from hydrogen bonds and angular shape

• more substances dissolve in water than in any other liquid

• its polarity makes it excellent at dissolving, since other polar molecules can attach to it

Soluble

Any substance that dissolves in another substance

Insoluble

Substances that dissolve very little in other substances

Miscible

Soluble in eachother

Immiscible

Insoluble in eachother

Aqueous (aq)

Molecule or ion dissolved in water

Ice Floats Explanation

As water freezes, the hydrogen bonds between the molecules spread the molecules further apart, making it less dense than water, thus it floats.

What is the remaining 4% of living matter composed of?

Phosphorousi, Calcum, Sulfur, Potassium

Cell Chemical Composition

72% H2O

25% carbon compounds

3% salts

Carbon Compounds (4)

Carbohydrates, Lipids, Proteins, Nucleic Acids

Hydrocarbons

• Combinations of C & H

• nonpolar

• hydrophobic

• stable

• minimal attraction between molecules

• gas at room temp

• monkeys eat peeled bananas

Isomer

Molecules with the same molecular formula but different structures/shapes.

Different chemical properties and biological functions.

Functional Groups

• Parts of organic molecules that are involved in chemical reactions

• gives organic molecules distinctive properties

  • hydroxyl

  • cabonyl

  • carboxyl

  • amino

  • sulfhydryl

  • phosphate

Hydroxyl

-OH

Organic compounds with OH are alcohols.

Names typically end in -ol (ethanol)

Carbonyl

C=O

O double bonded to C

Aldehyde - if at the end of molecule

Ketone - if in the middle of molecule

Carboxyl

-COOH

C double bonded to O and single bonded to OH

Acids (Fatty, amino, etc)

Amino

-NH2 (could be NH3 if ionized)

Compounds are amines

(amino acids)

NH2 acts as vase, ammonia picks up H+ from solution

Sulfhydryl

-SH

S bonded to H

Thiols

Stablizes the structure of proteins

Phosphate

-PO4

P bound to 4 O (one is double bonded!! since it breaks octet rule)

Connects to C through an O

Lots of O means lots of negative charge and highly reactive

Transfers energy between organic molecules (ATP, GTP)

Macromolecules

Small organic molecules joining together to form larger molecules.

4 Major Classes

• carbohydrates (starch, sugar)

• lipids (fat, oil, wax)

• proteins (hemoglobin)

• nucleic acids (DNA, RNA)

Polymer

Long molecules built by linking repeating similarbuilding blocks (monomers) in a chain through covalent bonds!

Of the major classes of macromolecules only complex carbohydrates, proteins, and nucleic acids are polymers.

Digestion/Hydrolysis

Breaks down polymers using H2O and reverse dehydration synthesis,c leaving off one monomer at a time

Requires enzymes and releases energy.

Always results in smaller molecules

Catabolic Reaction

Macromolecules broken down into their constituent smaller subunits

Dehydration Synthesis / Condensation

Forms a covalent bond between two subunits by removing H+ from one monomer and PH- from another to free up space for a bond, which consequently produces water. This absorbs energy and will always create a bigger molecule.

Anabolic Reaction

Large molecule produces from smaller subunits.

(Dehydration synthesis)

Enzymes

Biological catalysts, which speed up chemical reactions without becoming consumes in the process.

They also possess special structures which recognize which covalent bonds must be created or broken.

Carbohydrates

Composed of CHO

Function: Energy, energy storage, raw materials, structural materials

Monomer: sugars

Examlples: Glucose, Sucrose, Fructose

Separated into Monosaccharides, Oligosaccharides and Polysaccharides

Sugars

Most names end in -ose

Classified by number of carbons (3C is triose, 5C is pentose…)

Functional groups determine function

Structure: 5C and 6C sugars form rings in solution

Monosaccharides

Simples monomer sugars

Example glucose

Disaccharides

2 monomers

Example sucrose

Polysaccharides

Large polymers of sugars

Costs little energy to build

Easily reversible = release energy

Complex carbohydrates, which are monosaccharide polymers composed of several hundred thousands of monosaccharidesubunits held together by glycosidic linkage

Function:

• Energy storage

  • starch (plants)

  • glycogen (animals) (in:

  • liver and muscles)

• Structure

  • cellulose (plants)

  • chitin (arthropods and fungi)

Example starch: glucose goes down to potatoes while they’re growing, is stored as starch (bc its harder for microbes to break down) this is insurance that it will at least have offspring next year even if it isn’t harvested this year

Linear Polysaccharide

Slow release

Starch (plant)

Branched Polysaccharides

Fast release

Glycogen (animal)

More sites for enzymatic

Digesting Polysaccharides

Starch is easy to digest because all the oxygen bonds go down. Cellulose is hard to digest because some up some down

Cellulose

Most abundant organic compound

Herbivores evolved a mechanism to digest cellulose

Most carnivores have not, which is why they rely on meat for energy and nutrients

Cellulose = undigestible roughage

Cow can digest cellulose well, thus no need for other sugars.

Gorilla can’t digest cellulose well, must add another sugar source like fruit to diet

Also herbivores have helpfulbacteria living in their digestive systems that help digest cellulose rich meals

Saccharide

Sugar

Pentose/Hexose Sugars

5C - Ribose, Ribulose

• Ribose - RNA, ATP

• Ribulose - Photosynthesis

6C - Glucose, Galactose, Fructose

• Glucose - Energy Source

• Galactose- Energy Production

• Fructose - Fruits

Found in Ring state when dissolved in water

a-glucose

hen hydroxyl group at Carbon 1 lies below plane of ring

B-glucose

When hydroxyl group at Carbon 1 lies above plane of ring

Oligosaccharides

Sugars containing two or three simple sugars attached to one another by covalent bonds called glycosidic linkage

Sucrose

Oligosaccharide made up of a-glucose and a-fructose

Glycosidic Linkage

Covalent bonds holding monosaccharides to one another

Formed by condensation reactions

Lactose

Oligosaccharide made up of a-glucose and a-galactose

Maltose

Found in whole grains and root veggies

Sucrose

Found in fruits, nuts, sweet peas

Starch

An energy storage polysaccharide made of two polysaccharides amylose and amylopectin, which are insoluble in water. This is because they form coils due to the angles that their glycosidic linkages form at.

In order to break down chemically stored energy, heterotrophs possess enzymes that can ultimately breakdown (hydrolyze) amylose and amylopectin to individual glucose molecules, which cells can t

Amyloplast

Primariliy found in roots, tubers, and seeds (like potatoes, carrots, rice, wheat).

It synthesizes and stores starch granules

Glycogen

Storage molecule used by animals. Similar to amylopectin but with more branches.

Cellulose

Most abundant organic substance on Earth.

Molecules have a straight shape, which means it can more easily form Hydrogen bonds with hydroxyl groups, which produces microfibrils, which become touch insoluble cellulose fibres that are used in cell walls.

Indigestible for humans! because we can’t digest beta glucose subunits in cellulose. Other animals (cow, sheep, rabbits) have symbiotic bacteria and protists in digestive tract which produces enzymes that break beta glucose linkages.

It is still useful in our diets because the cellulose fibres (aka roughage) pass through our digestive system undigested and gently scrape the walls of the large intestine, stimulating intestinal cells into mucus secretion, which lubricates feces. They also keep feces moist with water.

Chitin

Second most abundant organic molecule found in nature

Insects and Crustaceans use it for their exoskeleton.FUngi use it for their cell wall. We use it for medical applications like contact lenses and touch yet biodegradable stitches that decompose as a wound heals.

Similar to cellulose, but has a nitrogen containing group attached to the second carbon position.