Proteins and Amino Acids

Proteins Overview

• Proteins have a significant role in the structure, catalysis, movement, transport, and hormones in the body

Protein Functions

• Structure: Collagen and keratin are key elements of the skin, bone, hair, and nails
• Catalysis: Enzymes, proteins, speed up virtually every reaction in living systems
• Movement: Muscles use myosin and actin proteins
• Transport: Delivers oxygen from the lungs to cells, and carries molecules across cell membranes with hemoglobin and other proteins
• Hormones: Hormones such as, insulin, oxytocin, and human growth hormone are proteins
• Protection: Fibrinogen causes blood clots to form; antibodies are proteins used by the body to fight diseases
• Storage: Delivers nutrients to newborn infants and birds by storing casein in milk and ovalbumin in eggs
• Regulation: Proteins can regulate the expression of genes, along with when the gene expression occurs
• Proteins are grouped into two types: fibrous and globular proteins

Amino Acids

• Amino acids consist of an amino group and a carboxyl group

Alpha-Amino Acids

• The amino group sits on the carbon close to the carboxyl group in an alpha-amino acid
• While alpha-amino acids are often displayed in their non-ionized form, they are most accurately represented as zwitterions (internal salt)

Chirality of Alpha-Amino Acids

• With the exception of glycine, all protein-derived amino acids have at least one stereocenter (the alpha-carbon) and are chiral
• The vast majority of alpha-amino acids have the L-configuration at the alpha-carbon

Protein-Derived Alpha-Amino Acids

• Nonpolar side chains each ionizable group is shown with highest concentration for pH 7.0
• Alanine (Ala, A)
• Glycine (Gly, G)
• Isoleucine (Ile, I)
• Leucine (Leu, L)
• Methionine (Met, M)
• Phenylalanine (Phe, F)
• Proline (Pro, P)
• Tryptophan (Trp, W)
• Valine (Val, V)

Polar Side Chains (occurs at pH 7.0)

• Asparagine (Asn, N)
• Cysteine (Cys, C)
• Glutamine (Gln, Q)
• Serine (Ser, S)
• Threonine (Thr, T)
• Tyrosine (Tyr, Y)

Acidic Side Chains (occurs at pH 7.0)

• Aspartic acid (Asp, D)
• Glutamine acid (Glu, E)

Basic Side Chains (occurs at pH 7.0)

• Arginine (Arg, R)
• Histidine (His, H)
• Lysine (Lys, K)
• The alpha-amino group is primary for 19 out of 20 amino acids; for proline, it is secondary
• Each alpha-carbon (excluding glycine) is a stereocenter
• Isoleucine (left) and threonine (right) contain a second stereocenter

Ionization vs. pH

• An amino acid's net charge varies depending on the solution's pH
• The amino acid is present as a zwitterion in the aqueous solution

Strong Acid

• Applying a strong acid (like HCl) to a solution to lower the pH to 0 causes the acid to give a proton to the zwitterion's -COO-, turning it positive

Strong Base

• When a strong base like NaOH is added to the solution to raise the pH to 14, a proton is transferred from the NH3+ group, producing a negative ion from the zwitterion

Isoelectric Point

• Isoelectric point, or pI, is the pH level at which a sample of amino acids has an equal number of positive and negative charges

Peptides

• Proteins consist of long chains of amino acids connected by amide bonds
• A special name for the amide bond between the alpha-carboxyl group and the alpha-amino group of separate amino acids is a peptide bond (or peptide linkage)

Peptide Polymers

• Peptide is a short polymer of amino acids joined by peptide bonds and are classified based on their number of amino acids
  • Dipeptide: two amino acids
  • Tripeptide: three amino acids

Polypeptide Macromolecule

• Polypeptide: many amino acids
• Protein: biological macromolecules that have at least 30 to 50 amino acids
• The name "residues" refers to individual units of amino acid

Writing Peptides

• Written peptides start from left to right, beginning with the free -NH3+ group and end with the free -COO- group
  • C-terminal amino acids in the chain’s end have the free -COO- group
  • N-terminal amino acids are located at the end of the chain and has the free -NH3+ group
• C-terminus and N-terminus are alternative names, respectively

Aromatic Amino Acids

• Aromatic rings are found in phenylalanine, tryptophan, and tyrosine
• Tryptophan is a precursor to serotonin neurotransmitters

Phenylalanine and Tyrosine

• Phenylalanine and tyrosine are precursors to norepinephrine and epinephrine, both of which are stimulatory neurotransmitters

Hydroxylation

• The hydroxylation of proline, lysine, and tyrosine, coupled with tyrosine iodination results in uncommon amino acids

Protein Properties

• Peptides written from the N-terminal to C-terminal.
• Peptide bonds are created from multiple amino acid chains

Peptide Bonds

• Typically, a carbonyl group bonded to an N-H group is a peptide bond in the body
• Linus Pauling found out that peptide bonds between amino acids are planar and have about 40% double bond character to the C-N bond

Protein Characteristics

• Proteins have an isoelectric point, pl, and behave as zwitterions
• There is no net charge at its isoelectric point
• A net negative charge exists when the bases are more acidic
• A positive net charge exists when bases are more basic

Structure

• The hemoglobin pI is 6.8, as it has about the same number of acidic/basic side chains
• The pI of serum albumin is 4.9, as it holds more acidic side chains
• Water solubility is lowest when pH = pI, that is when the structure is at its isoelectric point

Protein Structure Levels

• Proteins have four levels to their structure that can consist of multiple polypeptide chains
• Primary structure: Polypeptide chain amino acids, read from the N-terminal through the C terminal
• Secondary structure: The conformation of amino acids in localized regions of a polypeptide chain. This occurs in alpha helix, beta-pleated sheet, and random coil
• Tertiary structure: The arrangement of atoms in a polypeptide chain with three-dimensions
• Quaternary structure: The spatial relationship and interactions between subunits in a protein that has more than one polypeptide chain

Possible Chains

• With 20 protein-derived amino acids, the amount of polypeptide chains is extremely long
• There are 400(20 x 20) possible chains for dipeptides,
• There are 8000(20 x 20 x 20 )possible chains for tripeptides
• For a chain of n amino acids, there is 20n possible chains available
• For a protein of 60 amino acids, the possible protein chains would be 1078, greater than the numbers of atoms

Human Insulin

• Human insulin: two polypeptide chains, 51 amino acids in total, connected by two interchain disulfide bonds
• There are differences in insulin for humans and animals

Differences Between Insulins

• Human chains from Table 21.2 is:
• A chainpositions 8-9-10 is -Thr-Ser-Ile
• B Chain position 30 is -Thr
• Animal/Cow chains from Table 21.2 is:
• A chain positions 8-9-10 is -Ala-Ser-Val
• B Chain position 30 is -Ala
• Hog chains from Table 21.2 is:
• A chain positions 8-9-10 is -Thr-Ser-Ile
• B Chain position 30 is -Ala
• Sheep chains from Table 21.2 is:
• A chain positions 8-9-10 is is -Ala-Gly-Va
• B Chain position 30 is -Ala

Vasopressin and Oxytocin

• Vasopressin and oxytocin: both nonapeptides with different biological functions
  • Vasopressin: an antidiuretic hormone
  • Oxytocin: affects childbirth, stimulates uterine contractions and contraction in the muscles of the breast to aid in milk secretion

Secondary Structure

• Occurs with conformations of amino acids in localized regions of a polypeptide chain
• Common types are a-helix and B-pleated sheet

Alpha-Helix

• This is a type of secondary structure in which a section of the polypeptide chain coils into a spiral and is usually right-handed

Beta-Pleated Sheets

• Consists of two polypeptide chains or sections of polypeptide chains that are next to each other such that they align parallel to each other and can be either parallel or anti-parallel

Considerations for a Section of Alpha-Helix

• Six atoms form within a peptide bond while in the same plane,
• Bonded N-H groups point in the same directing, parallel to the helix axis,
• Bonded C=O groups point in the opposite direction, parallel to the helix axis,
• Hydrogen is bonded to a four amino acid bond between the C=O group of the chain and the N-H group,
• Groups of R point up from the helix

Beta-Pleated Sheet Elements

• Six atoms from inside the polypeptide form in the same plane,
• Bonds from C=O and H-N group point in the same direction with one another to be near enough to undergo hydrogen bonding,
• Groups of R are above and below the plane to alternate the chains

Random Coil

• A random coil has no organized structure

Globular Proteins

• Globular proteins contain all three kinds of secondary structure: a-helix, β-pleated sheet, and random coil

Collagen Triple Helix

• Collagen is made up of three chains of repeating amino acids linked together in a triple helix

Tertiary Structure

• Governs the conformation of a complete polypeptide chain Tertiary Structures is stabilized in 4 ways:
• Through covalent bonds, the formation of disulfide bonds between cysteine side chains
• The connection between side chains of polar groups as for the groups -OH of serenity and the amino acid Threonine
• As a good example, we can see the attraction of NH3+ with -COO- of aspartic acid

Cysteine and Disulfide

• Cystine has a group -SH, which can be oxidized to an bond of -S-S
• In nonpolar side chains, it can be seen that the Chains of phenylketonuria and isoleucine have Hydrophobic interactions

Forces of Proteins

• Forces such as hydrogen bonds, metal and ion coordination, disulfide bonds are forces to stabilize proteins

Hemoglobin and Tertiary Structure

• Hemoglobin is produced of proteins with hydrophobic interactions, the bonds of water molecules on the coordination and disulfide bonds

Quaternary Structure

• Polypeptide chains arrange themselves in noncovalently bonded aggregations

Structure

• Individual groups are contained in units with iron and consist of interaction/ Hydrogen bonds, salt bridges
• Adult structure: formed of two proteins alpha(141), beta(146)
• Fetal structure: two alpha and two gamma; greater oxygen capacity than alpha

Quaternary Structure of Proteins

• The structure of heme is made of molecules with carbon, hydrogen, nitrogen, carboxyl groups connected with an Fe(II) ion complex
• In membrane proteins: the presence of nonpolar components makes Interactions with chains of lipids possible on the outer surface of the membrane in quaternary interactions

Denaturation

• When the native confirmation of chains of amino acids has been destroyed through chemical/physics changes, the chains denature; some bonds can reform.
• Globular proteins have their hydrogen, globular proteins destroyed with the result of coagulation and precipitation may take place. - Heat agents can be denaturing + When 70% of acids ( Alcohol groups) penetrates bacterial chains; chains coagulate and the organism dies + If Groups -SH are created through the reactions of 2-Mercaptoethanol (HOCH2CH2SH) + If bonds are broken when interacting with transition ions of materials like cadmium, lead or mercury
• 6Maqueous urea: bonding is destroyed