Amino acids and proteins - Chemistry study guide

What is the generalized structure of an amino acid?

There will be an amino group attached to a chiral carbon on the left side, with a hydrogen beneath the carbon, an r-group above the carbon, and finally a carboxyl group to the right

What is the handedness of an amino acid?

The carbon in the amino acid will be an alpha-carbon that also has L-isomerism

What are proteins?

Naturally occurring, unbranched polymer in which the monomer units are amino acids 

• second most abundant substance in cells next to water 

What are the building blocks of proteins?

Monomer units 

Which protein acts as a catalyst in reactions?

Catalytic protein 

Which protein recognizes and destroys foreign substances?

Defense protein

What kind of protein carries essential substances throughout the body

Transport proteins

What proteins transmit signals between tissues

Messenger proteins

What protein controls muscle movement?

Contractile proteins

What proteins provides structural components?

Structural proteins

Which proteins bind to small molecules to store for later use?

Storage proteins 

What is an alpha-amino acid?

Amino group and carboxyl group are attached to the same (alpha) carbon

How many amino acids are found in proteins?

20 amino acids

What is the only achiral amino acid?

Glycine

What are the four groups the amino acid side chains are classified into?

• 1.) Nonpolar amino acids

• 2.) Polar neutral amino acids 

• 3.) Polar acidic amino acids 

• 4.) Polar basic amino acids 

Where are nonpolar amino acids found in proteins?

Found on the interior parts of proteins

What is special about cysteine?

Only amino acid with sulfhydryl group

• can create a disulfide bond with another cysteine 

• needs an oxidizing agent 

What is a disulfide bond?

Where two sulfurs are involved in a bond the two cysteines bond together

How many carboxyl groups are found in polar acidic amino acids?

Both contain two carboxyl groups

How many amino groups are found in polar basic amino acids?

Two amino groups

What are essential amino acids?

Standard amino acids needed for protein synthesis that must be obtained from a dietary source 

List the essential amino acids.

• What amino acid is essential for babies but not for adults?

• Histidine 

• Isoleucine 

• leucine 

• lysine

• methionine

• phenylalanine

• threonine

• tryptophan

• valine

  • Arginine is needed for babies because it is required for growth

What are complete dietary proteins?

Protein that contains all the essential amino acids in the same relative amount that is needed by the body 

• this is protein from animal sources: meat, egg, milk and fish 

What are incomplete dietary proteins?

Protein that does not contain all the essential amino acids in the same relative is needed by the body 

• protein from plant sources: wheat, rice, oats, beans, peas and corn 

What is the limiting amino acids?

Amino acids that are missing

• Lysine - wheat, rice, oats and corn 

• Methionine - beans, peas 

• Tryptophan - beans, corn 

What are complimentary dietary proteins?

Two or more incomplete dietary proteins that when mixed provide adequate amount

What is the basic group in an amino acid?

• What is the acidic group? 

• The amine group is the basic group 

• The carboxyl group is the acidic group

What charges are present in an amino acid at neutral pH? (pH = 7.0)

• The carboxyl group loses a proton (hydrogen) so it will carry a negative charge 

• The amino group will gain a proton (hydrogen) so it will carry a positive charge 

What is a zwitterion?

Molecule that carries both a positive and negative charge so that the net charge on the molecule is zero 

What is the charge of an amino acid at acidic pH values? (low pH)

A positive charge

What is the charge of an amino acid at basic pH values? (high pH)

negatively charged

What is the charge of an amino acid at neutral pH values?

a net zero charge 

What are peptides?

• What are the prefixes associated with them?

Short, unbranched chains of amino acids 

• Di - two amino acids 

• Tri - three amino acids

• Oligo - 10-20 amino acids 

• Poly - more than 20 amino acids 

What is the N-terminus?

• What is the C-terminus?

The N-terminus is the start of a protein or polypeptide, referring to the free amine group located at the end of the polypeptide

• C-terminus is the end with the free carboxyl group 

What is a peptide bond?

It is the bond that connects amino acids

What type of bond is a peptide bond?

Amide bond

What reacts to form the amide bond?

The carboxyl group and amino group from the two different amino acids

What is the peptide backbone?

Alternating sequence of peptide bonds and the -CH groups

What are some examples of small peptide horomones?

• Oxytocin → synthesized in the pituitary gland → nonapeptide (has 9 amino acid residues 

• Vasopressin → same characteristics as oxytocin 

• Has the same general structure except on where the oxytocin and vasopressin are located on the 3 and atom

What is the function of oxytocin?

Regulates uterine contractions and lactation

What is the function of vasopressin?

regulates excretion of water by the kidneys; affects blood pressure

What are some examples of small peptide neurotransmitters?

Enkephalins → synthesized in brain → pentapeptide (5 amino acid residues)

What is the function of enkephalin?

binds to receptors in brain to reduce pain

What is an example of a small peptide antioxidant?

Glutathione → present in most cells → tripeptide 

What is the function of glutathione?

regulates redox reactions within the cell

What are proteins?

• What term is interchangeable with protein?

• How many amino acids do larger and small proteins contain?

Peptide that contains at least 40 amino acid residues 

• Polypeptide is a term that is interchangeable with protein '

• Larger proteins have 10K amino acid residues 

• Small proteins have between 40-100 amino acid residues 

What are proteins called that contain more than one peptide chain?

multimeric proteins 

What is the primary structure of a protein?

The order in which the amino acid residues are linked together 

What is the secondary structure of a protein?

Special arrangement of the protein backbone

What are the two main types of secondary structure?

• Alpha helix → secondary structure where a single peptide chain is shaped like a coil 

• Beta pleated sheet → secondary structure where fully extended segments of protein are held together by hydrogen 

Which structure is this?

Alpha helix

What structure is this?

beta pleated sheet 

What are the general characteristics of an alpha helix?

• Coil shape is maintained by hydrogen bonds 

• Coil twists in a clockwise direction 

• R-groups extend outward from the coil 

What are the general characteristics of a beta pleated sheet?

• Can be two different subunits, or within the same protein chain 

• forms a zigzag also bonded together by hydrogen 

What is the tertiary structure of a protein?

The overall 3D shape of the protein that results from the interactions between amino acid side chains

• The shape can be compared to a phone chain 

What causes the tertiary structure to occur?

results from the interactions between amino acid side chains

What types of interactions occur between the side chains of amino acid residues in a protein?

• Covalent disulfide bonds

• Electrostatic interactions

• Hydrogen bonding'

• Hydrophobic interactions

What is the quaternary structure of a protein?

The organization of various protein subunits

• found in only multimeric proteins

• contains an even number of subunits 

• held together by electrostatic interactions, hydrogen bonds, and hydrophobic reactions 

What types of proteins do not have quaternary structure?

In proteins that only have one subunit 

What happens during protein hydrolysis?

The peptide bond breaks in the presence of a strong acid or base and heat which produces free amino acids

What is complete hydrolysis?

Where all amino acids are broken and become free amino acids

What is partial hydrolysis?

Some peptide bonds will be left intact

What is protein denaturation?

Partial or complete disorganization of a proteins tertiary structure due to disruptions in the protein’s primary, secondary, and quaternary structure

What causes protein denaturation?

Disruptions in the proteins structure

What is the relationship between the shape of protein and its function

The shape of the protein regulates its function

What are some characteristics of denaturation?

o   Denaturation causes loss of biochemical ability

o   Some proteins can be re-folded → renaturation

o   renaturation is impossible for some proteins (like albumin in egg whites)

o   Denaturation causes decrease water solubility à curdling of milk (casein)

o   Cauterization – heat used to denature proteins à used to seal blood vessels

o   Perms – combination of denaturing and renaturing the disulfide bonds within hair proteins

What are the three main types of proteins?

• fibrous

• globular

• membrane 

What are the characteristics of fibrous proteins?

• It has an elongated shape with one dimension longer than the other

• simple, regular linear structures

• tend to aggregate

• water insoluble

What are the characteristics of globular proteins?

• has peptide chains that are folded into a spherical or globular shape

• hydrophobic side chains on the interior of the structure

• hydrophilic side chains on the exterior of a cell

• water soluble 

What are the characteristics of membrane proteins?

• protein that is found associated with the membrane of the cell

• most hydrophobic side chains are on the exterior of the molecule 

• water insoluble 

• fewer hydrophobic amino acid residues 

What type of protein shape is alpha-keratin?

Fibrous protein that functions as a protective coating

What is the shape of alpha-keratin?

Coiled-coil shape

• two alpha helix subunits that coil around each other

How does disulfide bonds affect the structure of the alpha-keratin?

It increases the rigidity of structure

• the harder the structure the more disulfide bonds 

What type of protein shape is collagen?

Triple helix made of glycine and proline

What increases the rigidity of the collagen?

The crosslinking of collagen fibrils 

What type of protein shape are hemoglobin and myoglobin?

Globular proteins

What is the function of hemoglobin?

Transports oxygen from lungs to tissues

What is the function of myoglobin?

oxygen storage molecule in muscles 

What is the shape of hemoglobin?

Tetramer → 4 subunits that contains a heme group

What is the shape of myoglobin?

Monomer → 1 subunit that contains only one heme group

True or false: Are proteins bonded together by ionic bonds?

False

What elements do all proteins contain?

• Hydrogen

• Carbon

• Nitrogen

• Oxygen

What are all proteins made up from?

Amino acids

What is the electron distribution of amino acids in proteins?

• polar

• nonpolar

• neutral

Are any of the standard amino acids chiral?

No, none of them are

How do standard amino acids differ from one another?

In the identity of the R group (side chain)

How is the protein backbone represented?