AP Bio Organic Chemistry

Organic Chemistry

study of carbon containing compounds; carbon forms the structural basis for proteins, carbohydrates, nucleic acids, and lipids (only few other elements make up macromolecules: H,O,P,N,Ca)

What is the key to carbon's versatality?

-Carbon has 4 valence electrons (valence of 4) for 4 covalent bonds; Can bond with 4 different atoms or can bond with other carbon atoms forming carbon skeleton
-Covalent bonds are stable and strong in aqueous solutions
-Can form single and double bonds
-Serves as an intersection that can branch in any direction
-Carbon skeleton can vary in 4 different ways
-Functional groups can make it nonpolar or polar like methyl vs. hydroxyl

Carbon Skeleton Variations

-Length, Double bonds/single bonds (location & #), Branching, Rings
-contributes to diversity of organic molecules

Hydrocarbons

-Simplest organic molecule; carbon skeleton surrounded by hydrogen
-Hydrophobic because of non-polar covalent bonds
-Store large amounts of energy
-Undergo reactions that release a large amount of energy

Functional groups

-Chemical attachments to the carbon skeleton other than hydrogen.
-Bring unique properties to molecules they’re attached to; this contributes to the diversity of organic molecules.
-Ex: Because of a small difference in functional groups, estradiol and testosterone are different which can have LARGE effects like the sexual characteristic of animal

Hydroxyl

-OH; found in carbohydrates; polar/hydrophillic

Carboxyl

-COOH; found in Amino Acids and proteins; polar/hydrophillic and acidic (releases H)

Amino

-NH2; found in amino acids and proteins; polar/hydrophillic and basic (accepts H)

Sulfhydryl

-SH; found in Proteins; polar/hydrophillic

Phosphate

--PO4; found in Proteins, nucleotides, phospholipids; Polar/hydrophilic

Carbonyl

-CO- and -COH; found in Carbohydrates; polar/hydrophillic

Methyl

CH3; nonpolar/hydrophillic

Ketone (Carboxyl)

carbonyl group that is in the MIDDLE of carbon skeleton

Aldehyde (Carboxyl)

carbonyl group that is on the END of carbon skeleton

ATP

-Adenosine Triphosphate; 3 Phosphate groups + Ribose sugar + Adenine (nitrogenous base)
-Before it is used for energy

ADP

-Adenosine Diphosphate; 2 Phosphate groups + Ribose sugar + Adenine (nitrogenous base)
-After it is used for energy; breaking of triphosphate bonds requires Hydrolysis, investment of H2O

Polymer

Large molecules made up of repeating subunits that are similar or identical in structure (Proteins, carbs, nucleic acids)

Monomer

Subunits of polymer

enzyme

Protein that catalyzes chemical reactions

Dehydration reaction/synthesis

-Forming covalent bonds; one monomer provides hydroxyl (-OH), the other provides hydrogen (H+) to make a water molecule
-Releasing water; Energy invested

hydrolysis

-Reverse dehydration reaction
-Breaking covalent bonds between monomers; water molecule breaks the bond as the hydroxyl bonds to one monomer and hydrogen bonds to the other
-Investing water; releasing energy

Carbohydrates

macromolecule including monosaccharides, disaccharides, and polysaccharides; serve as fuel and building material

Monosaccharides

-monomers of carbohydrates (AKA simple sugars)
-contains 1 carbonyl groups and multiple hydroxyl groups
-forms rings in aqueous solutions
-Function: Energy, makes up Carbon Skeleton structure, and Make up polysaccharides
-Variation because of location of functional groups (aldose vs. ketose) and length of carbon skeleton (3-7)
-Ex. glucose and fructose

Monosaccharides formula

alpha glucose

glucose going in the same configuration

beta glucose

glucose switching directions because of a difference in the location of the hydroxyl group on Carbon 1

Disaccharides

-two monosaccharides bonded together through glycosidic linkages
-Ex: Lactose (Milk), Maltose (Beer), Sucrose (table sugar)

glycosidic linkages

a covalent bond between 2 monosaccharides by dehydration reaction (# in name represents carbons being bonded)

Polysaccharides

-polymers of carbohydrates
-Storage Polysaccarides include starch and glycogen
-Structural Polysaccarides include cellulose and chitin

Starch

-Storage polysaccharide for storing sugars in plants
-made up of Alpha glucose (same direction every time)
-Carbons 1-4 forming glycosidic linkages
-Helical structure

Glycogen

-Storage polysaccharide in animals; Can only last about a day; Stored in liver and muscles
-made up of Alpha glucose (same direction every time)
-Carbons 1-4 & 1-6 (when branching) forming glycosidic linkages
-Helical Branched structure

cellulose

-Structural polysaccharide in plants
- makes up Cell wall of plant cells; Most abundant organic molecule on earth
-Carbons 1-4 form glycosidic linkages
-made up of Beta glucose (switching directions) because of a difference in the location of the hydroxyl group on Carbon 1
-Straight, allowing parallel molecules to bond with each other creating microfibrils
-Can’t be digested by humans (bc they can't break beta linkages) but it stimulates our digestive system through the stimulation of stomach lining which releases mucus (“fiber”)
-Symbioses in cow and termites: Both have microorganisms in their guts that can break down cellulose for them

Chitin

-Structural polysaccaride in anthropods and fungi
-make up exoskeleton of anthropods and cell walls of fungi
-Contains nitrogen group which makes it a unique carbohydrate

Lipids

General characteristic all lipids have in common: Hydrophobic, because of nonpolar covalent bonds; Consist mostly of hydrocarbons

Triglyceride (fats)

-Made up of 1 glycerol and 3 fatty acids
-held together by nonpolar covalent bonds
-An Ester bond formed through dehydration synthesis holds fatty acids to glycerol
-Function: Energy storage, also Cushions, Protects, Insulates

Saturated fats

-contains NO carbon double bonds in the fatty acids
-Straight; no kinks (double bonds)
-Solid at room temp
-Usually from an animal source
-Examples: butter, lard, coconut oil

Unsaturated fats

-1 or more double bonds between carbon
-Kinks/bends
-Liquid at room temp because of kinks (can't fit closely together)
-Usually a plant source
-Examples: Olive and canola oil

Phospholipids

-Amphipathic
- make up the Cell membrane/phospholipid bilayer
-made up of 2 Fatty Acids, 1 Glycerol, 1 Phosphate head
-Phosphate group: hydrophilic because it has a charge
-Fatty acid tails: hydrophobic because it has no charge

Amphipathic

molecule that has hydrophilic and hydrophobic regions

Explain how phospholipids form a bilayer in aqueous solutions.

The phosphate group will interact with the water because it is polar and so is water, and the nonpolar fatty acid tails will flip inwards. This creates a sandwich of phosphate groups on the outside and fatty acid tails on the inside.

Steroids

-Carbon skeleton consisting of 4 fused rings
-Functional groups attached to rings create variation between steroids
-Ex: Cholesterol, Testerone and Estrogen (steroid hormones)

Cholesterol

-Crucial steroid to animals
-In vertebrates, synthesized in liver and obtained from diet
-Maintain integrity of cell membrane, precursor from which other steroids are synthesized

Protein

biologically functional molecule that consists of one or more polypeptides folded and coiled in a 3D structure

Functions of Proteins

-Enzymatic Activity
-Communication of organisms activity (hormones)
-Antibodies/Protection
-Transport proteins (Transporting chemicals across the cell membrane)
-Synaptic Signaling (Neurotransmitters)

Amino Acids

-Monomers of Proteins
-Has a carboxyl group, amino group, R-group, and hydrogen bonded to a central carbon
-20 different amino acids

R-groups

give amino acids their unique properties that influence shape of protein

Peptide Bond

an Amino acid bond between a carboxyl and amino group via dehydration reaction; forms polypeptides

Groups of amino acids and defining elements/characteristics

1. Nonpolar R-groups (hydrophobic): contain hydrogen and carbon
2. Polar R-groups (hydrophilic): contain nitrogen and oxygen
3. Electrically Charged R-groups (hydrophilic): have a charge
- contains acidic (negatively charged) and basic (positively charged)

Make a connection between the amino acid sequence of a polypeptide and
the resulting function of the protein.

Each specific polypeptide has a unique linear sequence of amino acids, which means they also have unique side chains. The chemical nature depends on the kind and sequence of side chains, which in turn would impact the resulting function/shape of the protein.

Briefly describe two examples illustrating the importance of a protein's shape
in its ability to perform its function.

1. The exact shape between an antibody and a particular foreign substance on a flu virus that the antibody binds to and marks for destruction
2. Endorphin molecules or morphine molecules that fit into receptor molecules on the surface of brain cell in humans
-Producing euphoria and relieving pain

Primary level of Protein structure (structure and bonds)

-Sequence of amino acids
-Determined by genetic information (DNA)
-amino acids are held together by peptide bonds between the amino group of one amino acid and carboxyl group of another

Secondary Level of Protein Structure (structure and bonds)

-coils and folds that are patterned in protein
-result from Hydrogen bonding of the peptide backbone causing the amino acids to bend into repeating patterns (oxygen has partial negative, and hydrogen attached to nitrogen have a partial positive, so weak hydrogen bonds from that strengthen and shape protein)
-Alpha Helix: Polypeptide coils into a helix shape because of hydrogen bonding between every 4th amino acid
-Beta Pleated Sheet: 2 or more segments of the polypeptide bend sharply and lie parallel to each other, hydrogen bonds form between parts of these segments

Tertiary level of Protein structure (structure and bonds)

-Overall shape of a polypeptide resulting from the interactions between the R-groups of multiple amino acids
-Hydrogen bonds: between 2 polar R-groups
-Ionic Bonds: positively charged + negatively charged R-groups
-Hydrophobic interactions/Van der Waals bonds: nonpolar amino acids concentrate at the center of the protein due to hydrophobic tendencies and form very weak Van der Waals bonds
-Disulfide bridge: covalent bonds between the sulfhydryls of 2 cysteine AAs

Quaternary Level of Protein Structure (structure and bonds)

-Overall protein structure that results from the aggregation of 2 or more polypeptide chains
-same types of interactions that hold together tertiary structure contribute to quatenary
-globular proteins: roughly spherical shaped; usually hormone or enzyme; ex. hemoglobin
-fibrous proteins: straight, structural, woven; ex. collagen

Sickle Cell Disease

-Inherited blood disorder caused by the sub of one amino acid for the normal once at a particular position in the primary structure of hemoglobin (valine for glutamic acid)
-The abnormal hemoglobin tends to crystallize, deforming some cells into sickle shapes; normal RBC are disk shaped
-Clog tiny blood vessels, impeding blood flow and not carrying oxygen

Denaturation

-when protein loses its shape
-pH, salt concentration, temperature, or other environmental factors are altered, weak chemical bonds in protein may be destroyed (on every level but primary level)
-can go back because it still has primary structure

Chaparonins

Multi-protein complex that protects the polypeptide from environmental influences that may affect its folding

Nucleic Acid

polymers made up of monomers called nucleotides

2 types of Nucleic Acids

RNA and DNA

What two functions make DNA unique among molecules?

Provides directions for its own replication and directs RNA synthesis and through RNA, controls protein synthesis

What is the flow of genetic information in a cell?

-Synthesis of mRNA in the nucleus (transcription)
-Movement of mRNA into cytoplasm via nuclea pore which is part of nuclear envelope
-Synthesis of protein using information carried on mRNA (translation)

three components of a nucleotide

Nitrogenous base, pentose sugar, and 1 or more phosphate groups

Two families of nitrogenous bases

-Pyrimidines: 1 ring; Cytosine (C), Thymine (T), and Uracil (U)
-Purines: 2 rings; Adenine (A) and Guanine (G)

DNA (bases, sugars, strandedness, genes)

ATGC; Deoxyribose sugar; 2 strands; 100s of thousands of genes

RNA (bases, sugars, strandedness, genes)

AUGC; Ribose Sugar; 1 strand; 1 gene

What is the specific name for the bonds holding the nucleotides in a single strand together?

Phosphodiester Bonds

What makes up the backbone of a polynucleotide?

Pentose Sugar and Phosphate group

Which end of a strand is the 5’ end and which is the 3’ end?

-5’ is the end that is connected to the 5th carbon on the sugar
-3’ is the end that is the 3rd carbon on the sugar that is not connected to anything

What is the overall shape of a DNA molecule?

Double Helix

When describing the two strands of DNA, what does the term antiparallel mean?

The two strands of DNA run in different directions

What bases are complementary between DNA & RNA?