Amino acids
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| show | Amino group and carboxyl group
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| show | Amino acids represent building blocks for proteins, which are the most
abundant and functionally diverse molecules in the living system
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| show | 20
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| show | • Based on nature of their side chain groups
• Based on polarity
• Based on fate of carbon skeleton
(metabolic fate)
• Based on nutritional requirement
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| What is the role of the side chan (R) group in amino acids? | show 🗑
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| show | > Aliphatic side chains
>Hydroxyl side chains
>Sulphur side chains
>side chains containing acidic groups and their amides
> Basic group side chains
>Aromatic ring side chains
>Limo acid side chains
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| show | Organic compounds whose carbon atoms are linked in open chains, either straight or branched.
Eg:Glycine, Alanine, Valine, Leucine and Isoleucine
can either be branched or unbranched
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| show | Have an OH-
Eg:Serine, threonine and tyrosine
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| show | Cysteine and methionine
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| Examples of side chains containing acidic groups and their amides? | show 🗑
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| Examples of side chains containing basic groups? | show 🗑
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| Examples of side chains containing aromatic rings ? | show 🗑
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| Example of a side chain containing lmino acid | show 🗑
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| show | Even distribution of electrons
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| show | Uneven distribution of electrons
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| show | >Have no charge on R group
>hydrophobic (water hating)
> nonpolar side chain which does not gain or lose proton or participate in hydrogen or ionic bonds
> Stabilize tertiary & quaternary structure of protein by hydrophobic interactions
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| Where can you find non polar amino acids? | show 🗑
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| show | • Lmino acid
• Its side chain and α-amino nitrogen form a rigid five-membered ring structure
• Has a secondary amino group
• Unique geometry contributes to the formation of the fibrous structure of collagen
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| Properties of amino acids with polar side chains? | show 🗑
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| show | - attachment for Phosphate group in proteins
- Participate in hydrogen bonding in protein structure
- Attachment of carbohydrate moiety in glycoproteins
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| show | > Participate in hydrogen bonding in protein structure at alkaline pH
>Active site of many enzymes
> In proteins, the –SH group of two cysteine residues can be oxidized to form a disulfide bond (-S-S-)
>Stabilization of tertiary structure of proteins
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| What do the Amino acids with Amide groups do? | show 🗑
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| What do charged polar amino acids help stabilise? | show 🗑
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| show | > Dicarboxylic monoamino acids having negatively charged R group
>Proton donors
>At physiologic pH, the side chains of these amino acids are fully ionized containing a negatively charged carboxylate group (-COO-)
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| Properties of Amino acids with basic side chains? | show 🗑
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| What makes histidine different from other amino acids with basic side chains? | show 🗑
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| show | >Not synthesized in the body
> Should be taken in the diet.
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| show | >Arg, Val, His, Leu, Ile, Lys, Met, Phe, Thr, Trp.
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| show | Synthesized in the body from the 10 essential amino acids.
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| What are the 10 non essential Amino acids? | show 🗑
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| show | Gluogenic , Ketogenic or Glucogenic and Ketogenic
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| show | >Serve as precursor for the formation of glucose or glycogen
• Eg: Gly, Ala, Ser, Cys, Glu, Gln, Pro, His, Arg, Met, Val, Asp, An
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| show | >Precursor for the formation of acetyl CoA
• Eg: Leu & Lys
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| What are the glucogenic and ketogenic amino acids? | show 🗑
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| What type of behaviours do all amino acids exhibit | show 🗑
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| show | In an aqueous solution, amino acids contain weakly acidic α-carboxyl group and weakly basic α- amino groups (ionizable groups)
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| show | Each amino acid has a carboxyl group and a primary amino group (with an exception of Proline, which has a secondary amino group) and a distinctive side chain (“R group”) which is bonded to the α-carbon atom
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| show | In two reversible forms: Protonated (acidic) & deprotonated (conjugate base)
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| show | COOH
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| show | COO-
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| show | NH2
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| show | NH3+
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| What is meant by dissociation? | show 🗑
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| show | the carboxyl group is dissociated, forming negatively charged
carboxylate ion (-COO-), and the amino group is protonated (-NH3+)
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| What is the name of the linkage when amino or carboxyl groups are combined and what does this mean ? | show 🗑
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| show | The side chains
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| Key features of the 20 amino acids | show 🗑
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| show | pK values
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| What is pK Values | show 🗑
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| show | > pKa is defined as the pH at which an acid group is half dissociated
>pKa is the pH at which both protonated & deprotonated forms of an ionizable group are present at equal concentration
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| What is the pK of carboxyl groups? | show 🗑
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| What is the pK of amino groups? | show 🗑
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| At physiological pH of body fluids, what amino acid can act as buffer | show 🗑
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| Explain the buffering action of amino acids? | show 🗑
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| Why can histidine act as a buffer? | show 🗑
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| show | A peptide bond is formed when an amino group of one amino acid reacts with a carboxyl group of another amino acid by a covalent amide linkage
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| show | 1,2,3,4
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| show | >Sequence of chain of amino acids
>Primary structure is decided by the gene that codes for the protein
>In a protein/ polypeptide chain there is a free N-terminal end and other is a C terminal end
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| Secondary amino acids? | show 🗑
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| Tertiary amino acids? | show 🗑
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| show | >has two or more peptide chains forming subunits.
>It is stabilized by hydrophobic bonds, H- bonds and electrostatic bonds.
?Subunits may function independently of each other or may work co- operatively. E.g., Hemoglobin.
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| show | 153
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| show | >α - chain of hemoglobin – 141 amino acids
> β - chain of hemoglobin – 146 amino acids
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| What are the affects of alteration in primary structure of a protein? | show 🗑
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| Outline the alpha helix ? | show 🗑
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| Examples of proteins rich in α-helical structure? | show 🗑
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| show | Proline, disrupts the conformation of the α- helix, producing a bend (Because the peptide bond nitrogen of proline lacks a hydrogen atom to contribute to a hydrogen bond )
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| show | Because of its small size, also often induces bends in α –helices
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| show | Presence of large number of charged R groups or large number of bulky R groups (glu and trp) are not favorable for α –helix formation.
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| Outline B pleated sheets? | show 🗑
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| Two peptide segments are placed in the same direction what is this called ? | show 🗑
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| The peptide segments run in opposite directions what is this called | show 🗑
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| show | >Turns or bends refer to short sequences of amino acids that join the two units of secondary structure.
>A turn involves four amino acid residues, in which the first residue is hydrogen-bonded to the fourth
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| How many domains do polypeptides having more than 200 amino acids generally consist of | show 🗑
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| Where can you find amino acids with non polar and polar side chains | show 🗑
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| show | myoglobin
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| show | They are specialized group of proteins which facilitate the correct folding of proteins.
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| show | Covalent → disulfide bonds
Non-covalent bonds → hydrogen bond, hydrophobic interactions, ionic bonds
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| What are covalent bonds? | show 🗑
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| show | >Covalent linkage formed by the sulfhydryl group of each of two cysteine residues to form a Cystine residue
> A disulfide bond contributes to the stability of the 3D shape of the protein molecule and prevents it from denaturation in ECF compartment
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| show | Interaction between amino acids with nonpolar side chains
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| show | Hydrogen bonding is a special type of dipole-dipole attraction between molecules.It results from the attractive force between a hydrogen atom covalently bonded to a very electronegative atom such as a N, O, or F atom and another very electronegative atom.
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| show | Ions with opposite charges will attract one another creating an ionic bond.
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| show | > Loss of structure = denaturation
>2, 3 and 4 structure of proteins are destroyed during denaturation
> 1 structure of protein remains unaltered
>Change of physicochemical properties and biological activity occurs >
irreversible
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| show | > Physical: heat, vigorous mixing, x-rays, UV-radiation etc
> Chemical: Acids, alkali, organic solvents, salts of heavy metals etc
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| show | - Biological activity is lost
- Viscosity is increased
- Proteins become least soluble
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| m | show 🗑
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