Chem test 3

What functional group do amines contain?

An amino group or substituted amino group.

What is the general formula for a primary (1°) amine?

RNH₂

What is the general formula for a secondary (2°) amine?

R₂NH

What is the general formula for a tertiary (3°) amine?

R₃N

How are amines named in the IUPAC system?

As alkanamines, with the number of the carbon bonded to nitrogen placed before the word "amine."

How are amines named in the common system?

As alkylamines.

How do amines behave in water?

As weak bases, forming alkylammonium ions.

What forms when amines react with acids?

Alkylammonium salts.

What are quaternary ammonium salts?

Ammonium salts with four organic groups bonded to nitrogen.

What are heterocyclic amines?

Cyclic compounds with at least one nitrogen atom in the ring.

What are alkaloids?

Natural plant products containing at least one heterocyclic ring.

What is cocaine?

An alkaloid that acts as an anesthetic.

What is morphine?

An alkaloid that acts as a strong analgesic (painkiller).

How are amides formed?

By reacting a carboxylic acid derivative (acid chloride or anhydride) with an amine or ammonia.

What does a reaction between an acid chloride and ammonia produce?

A primary (1°) amide.

What does a reaction between an acid chloride and a primary amine produce?

A secondary (2°) amide.

What does a reaction between an acid chloride and a secondary amine produce?

A tertiary (3°) amide.

What is an amide bond?

The bond between the carbonyl carbon and the nitrogen of the amine.

How are amides named in IUPAC nomenclature?

Replace "-oic acid" with "-amide."

What are the common names for methanamide and ethanamide?

Formamide and acetamide.

What happens during hydrolysis of an amide with strong acid?

Produces a carboxylic acid and an ammonium ion (or alkylammonium ion).

What happens during hydrolysis of an amide with a strong base?

Produces an amine and a carboxylate salt.

What are proteins made of?

Polymers of alpha amino acids joined by peptide bonds.

What happens during protein synthesis?

The aminoacyl group of one amino acid is transferred from tRNA to the amino group nitrogen of another amino acid.

What are neurotransmitters?

Chemicals that carry signals from a nerve cell to a target cell.

Are neurotransmitters inhibitory or excitatory?

They can be either.

What are catecholamines?

Dopamine, norepinephrine, and epinephrine.

What disease is linked to too little dopamine?

Parkinson's disease.

What is associated with too much dopamine?

Schizophrenia.

What is serotonin involved in?

Pain perception, body temperature regulation, sleep, and mood.

What does histamine do?

Causes allergy symptoms.

What do antihistamines do?

Block histamine, providing allergy relief.

What is GABA?

An inhibitory neurotransmitter involved in controlling aggression.

What is acetylcholine’s role?

It functions at the neuromuscular junction, sending signals from nerves to muscles.

What are enzymes?

Biological catalysts.

What do defense proteins do?

Act as antibodies responding to antigens.

What do transport proteins do?

Carry materials through the body.

Name two movement proteins.

Actin and myosin.

What are nutrient proteins?

Proteins like egg albumin and casein that serve as amino acid sources.

What distinguishes amino acids from each other?

Their R groups (side chains).

What makes an amino acid hydrophobic?

Nonpolar side chains.

What makes an amino acid hydrophilic?

Polar or charged side chains.

Are amino acids chiral?

All except glycine.

What form are naturally occurring amino acids usually in?

L-amino acids.

What is a peptide bond?

An amide bond between the α-carboxyl group of one amino acid and the α-amino group of another.

Which terminus has the free carboxyl group?

C-terminus.

Which terminus has the free amino group?

N-terminus.

What defines the primary structure of proteins?

The linear sequence of amino acids.

What two shapes are common in secondary structures?

α-helix and β-pleated sheet.

What maintains these structures?

Hydrogen bonds between amide nitrogens and carbonyl oxygens.

What is tertiary structure?

The 3D folding of a protein.

What interactions maintain tertiary structure?

Hydrophobic interactions, hydrogen bonds, ionic bridges, disulfide bonds.

When does a protein have quaternary structure?

When composed of more than one peptide chain.

What are glycoproteins?

Proteins with covalently bonded sugar groups.

What dictates a protein’s structure and function?

Its primary amino acid sequence.

What can a single amino acid change cause?

Drastic effects on folding and function.

What is myoglobin?

An oxygen storage protein in muscle.

What is hemoglobin?

A protein that transports oxygen in the blood.

What gives myoglobin and hemoglobin their oxygen-binding ability?

The heme group.

Why does fetal hemoglobin have greater oxygen affinity?

To allow oxygen transfer from mother to fetus

What causes sickle cell anemia?

A mutant hemoglobin gene

What is the most abundant blood protein?

Albumin (55%).

What percentage do α-globulins and β-globulins make up?

13% each.

What percentage does fibrinogen make up?

7%

What causes protein denaturation?

Heat or pH changes disrupting structure.

What is coagulation?

Clumping of denatured proteins, making them insoluble.

What are essential amino acids?

Amino acids that must be obtained from the diet.

What are complete proteins?

Proteins with all essential and nonessential amino acids.

Where does protein digestion begin?

In the stomach, with pepsin.

Which enzymes complete protein digestion in the small intestine?

Trypsin and chymotrypsin.

Primary 1°structure is

the sequence of amino acid residues along the polypeptide chain (or chains) from which the protein is made

Secondary 2° structure is

the orderly arrangements of amino acid residues found along a polypeptide chain, such as alpha helices or beta sheets. These arrangements are held together by extensive hydrogen bonding within them.

Tertiary 3° structure is

the complete and exact arrangement of the amino acids in a functioning protein (or protein subunit). It can usually be considered to be some precise arrangement of secondary structure elements, joined by short strands of polypeptide chain often called loops.

The naturally-occuring amino acids found in proteins are often divided into____ classes based on ________

four classes (nonpolar, neutral polar, acidic, basic), based primarily on how strongly their side chains interact with water

Nonpolar amino acids …

They contain…

also called hydrophobic amino acids, have side chains that interact only weakly with water through the dispersion force.

they contain Hydrocarbon groups and rings.Thioether (−CH2−SCH2 or −CH2−SCH3) groups. Hydrocarbon rings with an embedded NH group (not just an N atom)

Neutral polar amino acids …

They contain…

have side chains that interact strongly with water through dipole and hydrogen-bonding forces. are hydrophilic

they contain OH, SH and Amide groups.

Acidic amino acids have …

They contain…

acidic side chains that lose an H+ at physiological pH. The resulting anion interacts very strongly with water through the ion-dipole force. are hydrophilic

they contain Carboxylate (COO−) groups.

Basic amino acids have …

they contain…

basic side chains that easily gain an H+ at physiological pH. The resulting cation interacts very strongly with water through the ion-dipole force. are hydrophilic

they contain An ammonium (NH+ ,NH+2 or NH+3) group and A hydrocarbon ring with an embedded N atom (not an NH group)

An alpha helix forms when

the main chain of amino acid residues curls into a spiral

Alpha helices are held together by

how are the bonds formed?

hydrogen bonds, one per residue. The carbonyl oxygen in each residue forms a hydrogen bond with the amide −NH hydrogen 4 residues further along the protein backbone.

No side-chain atoms are involved.

The overall shape of the alpha helix is a ___. They typically contain about __ residues, but may be much longer.

cylinder ; 10

There are often ___ alpha helices in one protein. They may…

several ; bundle together to form elements of tertiary structure.

alpha helices are disrupted by changes in …

solvent, changes in pH, and increases in temperature.

A beta sheet forms when

straight sections of the main chain line up next to each other, like the planks in a wood fence, or the pencils in a box of pencils

beta sheets are held together by …

where is the bond formed?

hydrogen bonds, one per residue

The carbonyl oxygen in each residue forms a hydrogen bond with the amide −NH hydrogen in a neighbor chain. No side-chain atoms are involved.

The overall shape of the beta sheet is a ______. The overall size of the beta sheet depends on ___ and ___. The sheet may be mostly ______.

pleated rectangular sheet ; how many sections of main chain are in it, and how long each section is ; flat or gently curved

There are often ___ beta sheets in one protein. Like alpha helices, beta sheets may ____ to form various elements of _____.

several ; combine ; tertiary structure

Like all elements of secondary (or tertiary) structure, beta sheets are disrupted by changes in __________________.

solvent, changes in pH, and increases in temperature

Disulfide bonds can form between …

two cysteine residues

Salt bridges are the powerful _______ between ________ residues when they're close to each other

electrostatic attractions ; oppositely-charged charged amino acid

Hydrogen bonds can form between a residue with an __ or ___ atom that has a lone pair, and another residue with an __ atom bonded to an _ or _ atom

O or N ; H ; O or N

Enzymes are the _____ that make almost all _____ _____ possible

catalysts ; biochemical reactions

all catalysts, enzymes speed up the chemical reaction of other compounds. In the case of enzymes those other compounds are called the enzyme's ______.

substrates

The substrate binds to the enzyme's ______.

active site

Enzymes themselves, however, are almost always _____.

proteins

Enzymes are usually big, with a typical molecular weight of 50,000 g/mol

They are also usually globular — that is, the _____ chains from which they are made are folded up tightly into a very specific arrangement that is key to their function. If their tertiary structure is disrupted (e.g. by temperature or pH change), enzymes ___________.

polypeptide ; stop working.

Enzymes are usually extremely ____. Usually they catalyze a chemical reaction in one specific molecule and no others.

specific

Catalysts speed up chemical reactions, but they do not change whether they are ____ or not, and whether they ___ or ___ energy. Since they do not change the free energy of either reactants or products, they do not change the ____ of either.

possible ; absorb or release ; stability

Catalysts take part in chemical reactions, but are neither ____ nor ____. So if you write a chemical equation for a catalyzed reaction, the catalyst should in principle appear on ____ sides.

consumed nor produced ; both

enzymes end in …

-ase