Chemistry- Semester 2 Exam 3 Review

Amine

Nitrogen attached to hydrogen and R groups.

Hydrogen Bonding of Amines

• primary and secondary can form hydrogen bonds with themselves and with water molecules.

• tertiary amines lack an N-H bond, so they cannot hydrogen bond with themselves, but they can hydrogen bond with water.

Boiling Points of Amines

• primary amines and secondary amines have higher boiling points than tertiary amines of similar molecular mass (decreases from primary to secondary to tertiary)

• larger amines (longer carbon chains) have higher boiling points

Solubility of Amines

• insoluble with 4+ carbons

• nonpolar hydrocarbon chains decrease solubility.

Amines are…

• weak organic bases- accept protons (H)

• accept a proton in water

Neutralization of Amines

• reaction of amine with acid

• forms amine salt (ammonium salt) (N+ and Cl-)

Ammonium Salts

• ionic compounds with strong attractions between the positively charged ammonium ion and an anion (chloride)

• solids at room temperature, odorless, soluble in water

• amines are usually converted to their ammonium salt before being used as drugs

Heterocyclic Amines

cyclic organic compound with a ring of 5 or 6 atoms in which one or two are nitrogen atoms

Pyrrolidine

simplest five-atom ring (four C and 1 N)

Pyrrole

2 double bonds

Imidazole

2 N atoms and 2 double bonds

Piperidine

simplest 6 atom ring (5 C, 1 N)

Pyridine

1 N, 3 double bonds

Pyrimidine

2 N, 3 double bonds

Purine

imidazole + pyrimidine

Neurotransmitters

chemical compound that transmits an impulse from a nerve cell to a target cell.

Acetylcholine

• communicates between nervous system and muscle

• regulates muscle activation (contraction)

• degraded by hydrolysis to enable continual nerve transmission

Catecholamines

• include dopamine, norepinephrine, and epinephrine

• synthesize from amino acid tyrosine after it is converted to L-dopa

Serotonin

• helps us relax, sleep, think rationally

• well-being, calmness

Amides

• derivatives of carboxylic acids in which a nitrogen group (NH2) of a primary or secondary amine replaces the hydroxyl (OH) group of carboxylic acids

Amidation

• carboxylic acid reacts with ammonia or a primary or secondary amine

• forms amide

• requires heat

• tertiary do not react

• produces water

Naming Amides

• drop -oic acid (IUPAC) or -ic acid (common) from the carboxylic acid name and add the suffix amide

Boiling Point of Amides

• amides are not bases

• solid at room temperature

• higher boiling points than carboxylic acids

Solubility of Amides

• primary amides are more soluble than secondary amides, which are more soluble than tertiary amides

• more soluble than amines

• vs carboxylic acids- primary and secondary amides are comparable

• vs esters/ketones/aldehydes- tertiary are comparable

Amides Hydrolysis

• reverse of amidation

• water and an acid or a base split an amide

Amides Acid Hydrolysis

• requires heat + acid

• produces a carboxylic acid and an ammonium salt

Amides Base Hydrolysis

• requires base + heat

• produces amine (or ammonia) and carboxylate salt

Proteins

biomolecular polymers that contain many amide bonds, formed by joining amino acids.

Structural Proteins

• provide structural components

• collagen- in tendons and cartilage

• keratin- in hair, skin, wool, and nails

Contractile Proteins

• make muscles move

• myosin and actin contract muscle fibers

Transport Proteins

• carry essential substances throughout the body

• hemoglobin transports oxygen

• lipoproteins transport lipids

Storage Proteins

• store nutrients

• casein stores protein in milk

• ferritin stores iron in the spleen and liver

Hormone Proteins

• regulate body metabolism and the nervous system

• insulin regulates blood glucose levels

• growth hormone regulates body growth

Enzyme Proteins

• catalyze biochemical reactions in cells

• sucrase catalyzes hydrolysis of sucrose

• trypsin catalyzes hydrolysis of proteins

Protection Proteins

• recognize and destroy foreign substances

• immunoglobulins stimulate immune responses

Amino Acid Structure

contain an amino group (NH2), a carboxyl group (COOH), and a R group

Zwitterions

• neutral form of an amino acid

• at 7.4 pH

• protonated amino

• deprotonated carboxyl

Deprotonation

loss of a proton (H)

Protonation

gain of a proton (H)

Nonpolar amino acids

• contain alkyl groups, aromatic, benzene, many carbon atoms

Polar amino acids

• contain OH, SH, and amides

Polar Acidic Amino Acids

• have a carboxylic acid side chain

Polar Basic Amino Acids

• have an amine group

If pH decreases…

• carboxylic acid group gains a proton

• + net charge

if pH increases…

• a proton is lost from the amino group

• - net charge

• deprotonates

An amino acid exists as a…

neutrally charged zwitterion, at 7.4 pH (neutral pH)

Amino Acids- Acid Behavior

• when pH is low (or acidic), the carboxylate anion gains a proton

• + 1 charge

Amino Acids- Base Behavior

• when pH is high (or basic), the ammonium cation loses a proton

• -1 charge

Acid Behavior of Side Chains

• polar acidic amino acids have a deprotonated carboxylic acid side chain at 7.4 pH

• loses H

• COO-

Base Behavior of Side Chains

• polar basic amino acids have a protonated basic side chains at 7.4 pH

• NH+

N-terminus

start of a protein that contains the amine group

Peptide Bond

• an amide bond that forms when the COO- group of one amino acid reacts with the NH3+ group of the next amino acid

C-terminus

end of the protein that contains the carboxylic acid group

Naming Peptides

• begin with name of N-terminal amino acid

• change -ine and -ate endings to -yl

• c-terminal amino acid retains complete name

Primary Structure

• the sequence of amino acids held together by peptide bonds

Secondary Structure

• describes any regular folding patterns in the polypeptide backbone

• stabilized by hydrogen bonds between N-H of amide from one part of the protein and the C=O from carboxylic acid in another part

• alpha helix + beta sheet

Alpha Helix

• hydrogen bonds form between the oxygen of C=O group and hydrogen of N-H groups of amide bonds in the next turn of the helix

• R groups extend out of the helix

Beta Sheet

• two or more sections of a polypeptide folded in a pleated pattern

• hydrogen bonds between amide N-H of one strand and the C=O of another

• R groups project above and below the sheet

Collagen Structure

• triple helix

• three polypeptide chains woven together

• hydrogen bonds holds 3 together

• adds strength

Tertiary Structure

• folding of a single polypeptide as a result of interactions between

  • side chains in the polypeptide

  • side chains and the surrounding environment

Tertiary Structure: Disulfide Bonds

• covalent bonds that form between -SH groups of cysteine

• strongest type of interaction between two side chains

Tertiary Structure: Salt Bridges

• ionic attractions between ionized R groups of polar basic and polar acidic amino acids

• form between the carboxylate ion of an acidic side chain and the cation of a basic side chain

• very strong

Tertiary Structure: Hydrogen Bonds

• form between the H of a polar R group and the O or N of another polar amino acid

• weaker than disulfide bonds and salt bridges, but contribute to overall tertiary structure because there are many more hydrogen bonds

Tertiary Structure: Hydrophobic Interactions

• dispersion forces between two nonpolar R groups

• amino acids with nonpolar r groups are pushed away from the aqueous environment to form a hydrophobic center at the protein’s interior

Tertiary Structure: Hydrophilic Interactions

• occur between external aqueous environment and the R-groups of polar amino acid residues that are pulled to the outer surface of most proteins

Quaternary Structure

• biologically active proteins with two or more polypeptide chains or subunits

• not all proteins have a quaternary structure

Fibrous

• insoluble in water

Globular

• water soluble

• complex, spherical shapes

Protein Hydrolysis

• breaks the amide/peptide bond

• adds water

• occurs in the stomach when enzymes catalyze hydrolysis of proteins to give amino acids

• breaks up primary structure by breaking peptide bonds

Denaturation of Proteins

• occurs when changes disrupt the ineractions among residues that stabilize the 2, 3, 4 structures

• does not affect amind bond in primary structure

• causes protein to no longer be biologically active

Denaturation- Heat

• denatured above 50 degrees C

• disrupts hydrogen bonds and hydrophobic interactions among nonpolar residues

Denaturation: pH

• breaks hydrogen bonds

• disrupts ionic and salt bridges

Acidosis

• a proton is added to carboxyl, disrupting salt bridge

Alkalosis

• a proton is removed from the amine, disrupting the salt bridge

Denaturation: Organic Compounds

• isopropyl alcohol, ethanol

• disrupts hydrogen bonding

• used as disinfectants

Denaturation: Heavy Metal Ions

• Ag+, Pb2+. Hg2+ denature proteins by forming bonds with ionic residues or reacting with disulfide bonds

Denaturation: Agitation/Mechanical

• mechanical agitation stretches polypeptide chains until the stabilizing interactions are disrupted.

• hydrogen bonds and hydrophobic interactions disrupted

Enzymes

• biological catalysts

• increases rate of reaction by lowering activation energy required to start the reaction

• are globular proteins

• recognizes and binds a small group of reacting molecules (substrates)

• have a tertiary sturcture that includes a region called the active site where substrates bind to create a chemical reaction

Active Sites

contain specific amino acid residues that interact with functional groups of the substrate to form hydrogen bonds, salt bridges, and hydrophobic interactions

Absolute Enzyme

• catalyzes one type of reaction for one substrate

• urease catalyzes only the hydrolysis of urea

Group Enzyme

• catalyzes one type of reaction for similar substances

• hexokinase adds a phosphate group to hexoses

Linkage Enzyme

• catalyzes one type of reaction for a specific type of bond

• chymotrypsin catalyzes the hydrolysis of peptide bonds

Enzyme-Catalyzed Reactions

• combination of an enzyme and substrate forms an enzyme substrate complex

• the Es provides an alternative pathway for the reaction with lower activation energy

• within the active site, amino acid R groups catalyze the reaction to form an enzyme product complex

Lock-and-Key Model

• active site has a rigid, nonflexible shape

• enzyme binds only substrates that exactly fit the active site

Induced-Fit Model

• enzyme structure is flexible and adjusts to the shape of the active site in order to bind the substrate

• shape changes improve catalysis during reaction

Classification of Enzymes

• the name of an enzyme usually ends in -ase and identifies the reaction substrate

• describes function of enzyme

• can be common names

Oxidoreductases

• catalyze oxidation-reduction reactions

• gain of O, loss of H

Transferases

• catalyze the transfer of a functional group between two compounds

Hydrolases

• catalyze hydrolysis (addition of water) reactions

• add water to split a compound into two products

Lyases

catalyze the addition or removal of a group (without water)

Isomerases

catalyze the rearrangement (isomerization) of atoms within a substrate

Ligases

catalyze the joining of two substrates, using ATP

pH Dependence of Enzymes

• enzymes are most active at an optimal pH, where proper tertiary structure of the protein is maintained

• enzymes lose activity in a too low or too high pH

• changes in pH alter the acidic and basic side chains

• acidosis (making more acidic) and alkalosis (making more basic) are detrimental to the function of enzymes- can lead to denaturation

Temperature Dependence of Enzymes

• the optimal temperature for most proteins is 37 C

• enzymes show little activity at low temperatures

• denaturation occurs at high temperature and enzyme function is lost

Enzyme Concentration on Activity

• increasing enzyme concentration increases the rate of reaction

• binds more substrate with enzyme (since there is more enzyme)

Substrate Concentration on Activity

• increasing substrate concentration increases rate of reaction

• eventually saturates an enzyme with substrate to give maximum activity

• run out of enzymes for substrates to bind to

Regulation of Enzyme Activity

• rates of enzyme-catalyzed reactions are controlled by regulatory enzymes that

• increases the reaction rate when more of a particular substance is needed

• decreases the reaction rate when the substance is not needed

Regulation by Allosteric Enzymes

• allosteric sites are sites on the enzyme that is different from the active site

• binding to the allosteric site changes the shape of the active site

Positive Regulator (allosteric enzymes)

changes the shape of the active site to allow the substrate to bind more effectively

Negative Regulator (allosteric enzymes)

• changes the shape of the active site to prevent proper binding of the substrate

• decreases rate of reaction