| Question | Answer |
| What compounds do amino acids contain | Amino group and carboxyl group |
| What are Amino acids? | Amino acids represent building blocks for proteins, which are the most
abundant and functionally diverse molecules in the living system |
| How many amino acids are coded for by DNA | 20 |
| How can we classify amino acids? | • Based on nature of their side chain groups
• Based on polarity
• Based on fate of carbon skeleton
(metabolic fate)
• Based on nutritional requirement |
| What is the role of the side chan (R) group in amino acids? | ▪Determines the identity of different amino acids
▪Dictates the role of amino acid in a protein.
▪Determines the properties of amino acids in protein chains.
▪R –gps of certain amino acids crucial for the activity of enzymes
▪some acts as buffers. |
| What different types of side chains can you get with amino acids ? | > 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 |
| What are aliphatic side chain amino acids and give examples? | 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 |
| What are side chains containing hydroxyl groups and give examples? | Have an OH-
Eg:Serine, threonine and tyrosine |
| Examples of side chains counting sulphur atoms? | Cysteine and methionine |
| Examples of side chains containing acidic groups and their amides? | >Aspartate
>Glutamate
>Asparagine
>Glutamine |
| Examples of side chains containing basic groups? | Arginine lysine and histidine |
| Examples of side chains containing aromatic rings ? | Histidine, phenylalanine, tyrosine and tryptophan |
| Example of a side chain containing lmino acid | Proline |
| Define non-polar | Even distribution of electrons |
| Define polar | Uneven distribution of electrons |
| Properties of Amino acids with non polar side chains | >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 |
| Where can you find non polar amino acids? | >Side chains = in the interior of the protein molecule in an aqueous medium (hydrophobic effect)
>R group = In membranes, found on the outside surface of integral proteins, interacting with the lipid environment |
| What are the distinctive properties of proline? | • 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 |
| Properties of amino acids with polar side chains? | >Have an uneven distribution of electrons, such as acids and bases
>At physiologic pH, these amino acids have ‘zero net charge’
>possess groups such as hydroxyl, sulfhydryl and amide |
| What do the Amino acids with hydroxyl groups do? | - attachment for Phosphate group in proteins
- Participate in hydrogen bonding in protein structure
- Attachment of carbohydrate moiety in glycoproteins |
| What do the Amino acids with Sulfhydryl groups do? | > 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 |
| What do the Amino acids with Amide groups do? | > Side chains contain a carbonyl group and an amide group, both of
which can participate in hydrogen bonding in protein structure
>erve as a site of attachment of carbohydrate moiety in glycoproteins |
| What do charged polar amino acids help stabilise? | Stabilize tertiary & quaternary structure of protein by forming ionic bonds/ salt bridges. |
| Properties of Amino acids with acidic side chains? | > 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-) |
| Properties of Amino acids with basic side chains? | > Dibasic monocarboxylic acids
> The side chains of basic amino acids are Proton acceptors
> At physiologic pH, the R groups of Lysine and Arginine are fully ionized and positively charged |
| What makes histidine different from other amino acids with basic side chains? | > Weakly basic and uncharged at physiologic pH
> But when incorporated into protein, its R group can be either pos charged/ neutral ( depends on ionic environment provided by the proteins)
>Buffer= buffering role of proteins such as hemoglobin |
| What does essential amino acids mean? | >Not synthesized in the body
> Should be taken in the diet. |
| What are the 10 essential Amino acids? | >Arg, Val, His, Leu, Ile, Lys, Met, Phe, Thr, Trp. |
| What does non-essential amino acids mean? | Synthesized in the body from the 10 essential amino acids. |
| What are the 10 non essential Amino acids? | Gly, Ala, Ser, Cys, Asp, Asn, Glu, Gln, Tyr, Pro |
| How can we classify Amino acids by metabolic fate? | Gluogenic , Ketogenic or Glucogenic and Ketogenic |
| What are the glucogenic amino acids? | >Serve as precursor for the formation of glucose or glycogen
• Eg: Gly, Ala, Ser, Cys, Glu, Gln, Pro, His, Arg, Met, Val, Asp, An |
| What are the Ketogenic amino acids? | >Precursor for the formation of acetyl CoA
• Eg: Leu & Lys |
| What are the glucogenic and ketogenic amino acids? | > Precursor for both glucose and acetyl CoA.
• Eg: Phe, Ile, Trp, Tyr, Thr ( mnemonic is “PITTT) |
| What type of behaviours do all amino acids exhibit | Acid base property |
| In aqueous solution what do amino acids contain? | In an aqueous solution, amino acids contain weakly acidic α-carboxyl group and weakly basic α- amino groups (ionizable groups) |
| What does each amino acid contain? | 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 |
| How can each ionizable group of amino acid exist ? | In two reversible forms: Protonated (acidic) & deprotonated (conjugate base) |
| What is the protonated (Acid) form of the carboxyl group | COOH |
| What is the deprontonated (conjugate base) form of the carboxyl group | COO- |
| What is the deprontonated (conjugate base) form of the Amide group | NH2 |
| What is the protonated (Acid) form of the amide group | NH3+ |
| What is meant by dissociation? | The breaking up of a compound into simpler constituents that are usually capable of recombining under other conditions. |
| What happens at physiologic pH (approximately 7.4) to the carboxyl group and amino group? | the carboxyl group is dissociated, forming negatively charged
carboxylate ion (-COO-), and the amino group is protonated (-NH3+) |
| What is the name of the linkage when amino or carboxyl groups are combined and what does this mean ? | >Peptide linkaged
>Are not available for chemical reaction except for hydrogen bond formation |
| What dictates the role of an amino acid in in protein molecules | The side chains |
| Key features of the 20 amino acids | >15 amino acids have NEUTRAL R groups
2 amino acids, Asp & Glue have ACIDIC R groups
3 amino acids, Lys, Arg and His possess BASIC R groups
> The acidic and basic amino acid contain more ionizable group in its side chain |
| How can the dissociation behavior of different ionizable groups can be assessed ? | pK values |
| What is pK Values | “is the negative log. of dissociation constant of an acid Ka“
pKa = - log10Ka |
| What is pKa defined as ? | > 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 |
| What is the pK of carboxyl groups? | are much below pH 7.0, and since these carboxyl groups are in dissociated states at physiologic pH, they are considered as acidic groups |
| What is the pK of amino groups? | pK values of α - amino groups and the additional ionizable groups of lysine and arginine are much higher than 7.0 Moreover, these groups exist in fully protonated (undissociated) form at physiologic pH. |
| At physiological pH of body fluids, what amino acid can act as buffer | histidine
>pK value of histidine is relatively closer to the pH of the most biological fluids |
| Explain the buffering action of amino acids? | >Solutions of weak acids and their conjugate bases can resist pH change when strong acids or bases are added. They are called buffers
>All the acid/base groups of amino acids can exhibit buffering action
> Buffering action is maximum at pK values. |
| Why can histidine act as a buffer? | >only imidazole (C3N2H4) group of histidine can act as buffer
>This is because the pK value of the imidazole group is relatively closer to the pH of the most biological fluids |
| When is a peptide bond formed? | 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 |
| Different structures of amino acid | 1,2,3,4 |
| Primary amino acids? | >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 |
| Secondary amino acids? | >Local folding of polypeptide chains into helices or sheets
>Primary structure determines the secondary structure
> Maintained by hydrogen bonding
> Has : α – helix and β – pleated sheets |
| Tertiary amino acids? | >3D arrangement of all the amino acids in a single polypeptide chain.
> 1 stucturere determines the 3 structure
> 3D generates “domains” inproteins
>Domains are the fundamental functional and three-dimensional structural unit of the polypeptides |
| Quaternary amino acid? | >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. |
| How many amino acids are there in myoglobin | 153 |
| What is haemoglobin made up of | >α - chain of hemoglobin – 141 amino acids
> β - chain of hemoglobin – 146 amino acids |
| What are the affects of alteration in primary structure of a protein? | Alteration in primary structure of a protein may result in derangement of its biological activity |
| Outline the alpha helix ? | >Polypeptide chain is coiled around a central axis
> α-carbon, peptide N and carbonyl C form the backbone of the helix
>α - Helix structure = stabilized by H-bonds
> hydrogen bond is formed peptide bond and carbonyl oxygen= helical structure |
| Examples of proteins rich in α-helical structure? | α – keratin, Hemoglobin, myoglobin |
| Why does Proline not favor alpha helix of proteins? | 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 ) |
| Why does Glycine not favor alpha helix of proteins? | Because of its small size, also often induces bends in α –helices |
| Condition that may not be favourable for alpha helix formation? | 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. |
| Outline B pleated sheets? | >Form a zigzag or pleated pattern
> The peptide backbone of the β sheet is highly extended
> stability from hydrogen bonds between the C=O amide nitrogen of peptide bonds.
> H bonds are formed with adjacent peptide segments of the sheet |
| Two peptide segments are placed in the same direction what is this called ? | Parallael |
| The peptide segments run in opposite directions what is this called | Anti -parallel |
| Explain the loops and bends of amino acids? | >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 |
| How many domains do polypeptides having more than 200 amino acids generally consist of | two of more |
| Where can you find amino acids with non polar and polar side chains | > nonpolar side chains tend to be located in the interior of the polypeptide molecule where they associate with other hydrophobic amino acids
>In contrast, amino acids with polar side chains tend to be located on the surface of the molecule |
| Example of a tertiary structure | myoglobin |
| What is the role of chaperones? | They are specialized group of proteins which facilitate the correct folding of proteins. |
| What bonds stabilise to tertiary structure | Covalent → disulfide bonds
Non-covalent bonds → hydrogen bond, hydrophobic interactions, ionic bonds |
| What are covalent bonds? | > Sharing of electrons between two non metals
Covalent bonds are strong. Bond energy is relatively high, considerable energy must be expended to break covalent bonds.
> Specific enzymes are needed to break these bonds. |
| What are disulphide bonds? | >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 |
| What are hydrophobic interactions? | Interaction between amino acids with nonpolar side chains |
| What are hydrogen bonds? | 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. |
| What is ionic bonds? | Ions with opposite charges will attract one another creating an ionic bond. |
| Explain the denaturation of proteins? | > 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 |
| What are the causes of denaturation? | > Physical: heat, vigorous mixing, x-rays, UV-radiation etc
> Chemical: Acids, alkali, organic solvents, salts of heavy metals etc |
| Biological effects of denaturation | - Biological activity is lost
- Viscosity is increased
- Proteins become least soluble |
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