Lecture 1: Amino acids- The building blocks of proteins Flashcards
know: - the basic structure of an amino acid - about the properties of the 20 naturally occurring amino acids found in proteins - how a polypeptide chain is formed
What is the general structure of the amino acid?
NH3 (amino) group and COOH (carboxyl) group bonded to an alpha carbon
What is the reaction which results in the formation of a dipeptide called?
dehydration reaction
removal of H2O
true or false; peptide bonds are a form of covalent bonding?
true
- a covalent bond forms between the (-H)N terminal of one amino acids and the (-OH) C- terminal of another amino acids
What is an R group?
- bonded to an alpha carbon
- determines the identity of the particular amino acid
What is a stereoisomer?
- same molecular formula
What kind of stereoisomer are amino acids?
- chiral : due to 4 different groups being bonded to the alpha carbon
- optical isomers
- non superimposable mirror images
How are amino acids classified?
- L/D classification ( the position of theAMINO group on the left or right side of alpha carbon determines the L or D designation)
- L: left
- D: right
What are the functions of proteins?
basic examples:
- enzymes
- antibodies
- receptors
- carriers
- hormones
- materials
- ) Enzymatic catalysis: eg. hexokinase: ATP -dependent phosphorilation of glucose
- ) Transport and Storage : hemoglobin (red blood cells; binds oxygen)
- ) Hormones: Insulin (regulates plasma glucose)
- ) Immune protection: Immunoglobulins, bind infectious organisms
- ) Gene regulation: transciption factors
- ) structural: collagen (provides tensile strength to skin and bones
- ) Contraction (actin and myosin)
- ) Receptors: neurotransmitters
What are proteins involved in? What are their generalized functions?
- cell structure
- movement
- storage
- transport
- nerve cell signalling
- blood clotting
- immune defence
What is a proteins distiguishing feature?
abbility to fold into specific patterns to form unique 3D structures
How much dry weight do proteins comprise of?
50%
Why is the protein structure important?
defines the important property of proteins, an abbility to recognize other molecules
What is a protein?
- have highly specific 3- dimensional structure
- consists of one or more polypeptide chains
- each polypeptide chain consists of a long chain of amino acids joined end to end in a linear sequence known as the PRIMARY STRUCTURE
What does it mean by primary structure?
- LINEAR chain of amino acids , as linked by peptide bonds
- sequence of amino acids is in accordance to the gene translated by ribosomes during protein synthesis
- determine the other levels of structure
- its sequence is critical to proper proteins functioning
What does it mean by secondary structure?
- characterized by the repetative organisation of the peptide bond
- the arrangement in space of the atoms in the peptide backbone
- have repetative interactions resulting from hydrogen bonding between amide N-H and the carbonyl groups of the peptide backbone
- the conformations of the side chains of amino acids ARE NOT PART OF THE SECONDARY STRUCTURE
- alpha helix, and beta pleated sheet (examples)
What does it mean by tertiary structure?
- includes the 3D arrangement of all the atoms in the protein
- including those in the side chain
- and in any other prostheic groups (other groups of atoms other than amino acids)
- refers to the complete 3D structure of a protein
What does it mean by Quaternary structure?
- association of two or more polypeptides to make up a protein
- the arrangement of the subunits with respect to each other
- interactions between subunits is mediated by non covalent interactions such as :
hydrogen bonds
electrostatic attraction
hydrophobic interactions
What factors affect the properties of amino acids?
- nature of the side chain
- ) polar and non polar nature of side chain
- ) presence of acidic or basic group
etc. .
How are amino acids classfied?
- according to two major criteria
- ) the polarity of the side chain
2. ) the presence of acidic or basic group on the side chain
What are the 4 groups of amino acids?
- ) non polar side chains
- ) electronically neutral/ polar side chain
- ) carboxyl groups in their side chain
- ) basic side chains
Describe the properties of glycine
- the smallest amino acid
- side chain -H
- the small side chain allows glycine to fit into small spaces thus providing CONFORMATIONAL FLEXIBILITY to proteins
True or false; Glycine is the only achiral amino acid?
true
What are the properties of proline
- has a side chain that is bonded to a nitrogen atom of its amino group
- this results into greater RIGIDITY to proteins
- and this can cause KINKS in the protein structure
Cysteine
- contains sulphydryl group (-SH)
- this is used to STABILIZE proteins by disulfide bonds
What does tyrosine, tryptophan and phenylalanine have in common?
they all absorb UV light which can be used to detect the proteins in the solution
What are the properties of amino acids?
- variable side chain
- zwitterion
- chiral
- acid base chemistry
What does the biological activity of a protein depend on?
- their chemistry
- their structure
Why does the charge of some amino acids alter with pH?
the presence of ionizable groups
What is an ionizable group?
- these groups convey positive and negative charged groups to proteins
- each ionizable group HAS PH VALUE AT WHICH EQUAL AMOUNTS OF CHARGED AND UNCHARGED FORMS EXIST
- this is known as pKa
what is the significance of the amino acid side chain?
- gives chemical and structural diversity:
- size
- charge
- shape
- chemistry
Amino acid side chains groups?
- acidic
- basic
- neutral polar
- neutral non polar
Why is cysteine so special? Describe its properties
- polar side chains consist of a thiol group (-SH-)
- which can react with OTHER Cysteine groups to form DISULFIDE BRIDGES in proteins during an OXIDATION REACTION
- thiol group can also lose a proton
- can form cross links
What is the effect of a carboxyl group in an amino acid side chain?
- negatively charged at neutral pH
- can lose a proton that’s why
( glutamate and aspartate)
What do the pKa values of amino acids depend on?
the environment, and can change significantly in the confines of the protein
What does pKa mean?
- the pH at which have equal amounts of protonated (charged) and non protonated forms (uncharged)
If an amino acid has a hydrophobic side chain, where does this amino acid tend to be found?
are usually located in the interior of the protein away from contact with water
hydrophilic side chain and polar side chain? where does amino acid orientate?
found usually on the exterior of the protein, in contact with water, where they can be hydrated by the surrounding aqueous environment
acid and basic side chain? where found on protein?
also on the exterior of the protein
give 3 examples of basic side chains?
positively charged; can gain a proton
Hist, Arg, Lys
give 3 examples of acidic side chains?
negatively charged side chains; because they can lose a proton H+
Asparitc ACID (Asp) Glutamic acid (Glu)
give 3 examples of neutral (uncharged side chain)l, polar side chains?
Ser (serine), Thr (threonine), Gln (glutamine)
give examples of neutral (uncharged side chain), non polar side chains?
aliphatic: Val (valine), ala (alanine), Ile (Isoleucine)
aromatic: Phe (phenylalanine)
What are neutral, polar side chains good for?
GOOD FOR H-BONDING
Ser, Thr through -OH group
Asn, Gln through C=O or NH2 groups
define isoelectric PI
The pH at which negative an positive charges on the protein are equal
