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What compounds do amino acids contain
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What are Amino acids?
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Amino acids

QuestionAnswer
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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Created by: RachelOayo
 

 



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