Proteins Flashcards
structure of protein
- consist of elements carbon, hydrogen, oxygen, nitrogen and sulfur (in some cases)
- specific 3d conformation
- r groups
polypeptide definition
A linear sequence of
amino acids covalently joined together by peptide bonds
difference between fibrous and globular shape protein
ref to page 5
how are proteins classified
- simple protein - consist of only amino acid (albumin, globulins, histones)
- conjugated protein
- protein combined with non-protein component, cofactor
- cofactor aids protein function, can be inorganic or organic in nature
- organic cofactor tightly bound to a protein-> prosthetic group
(glycoprotein, chromoprotein, lipoprotein, flavoprotein, nucleoprotein)
types of amino acids?
essential amino acids - obtained through diet
non-essential amino acids - can be synthesised by body
derivatives - DNA does not code for them, modified after incorporation into polypeptide chain
note: both are impt, essential no more impt as non essential
structure of amino acid
carbon covalently attached to:
1. a basic amine group (–NH2)
2. an acidic carboxyl group (–COOH)
3. a hydrogen atom and
4. a variable group known as the R group which gives ‘uniqueness’ to the amino acid (also called the side chain)
properties of amino acid
- colourless and crystalline solids, relatively high mp
- able to form zwitterions
- able to act as buffer
- unique properties of R group -> R groups have important physical and chemical properties, which influence physical and chemical properties of amino acids and protein
How are zwitterions formed
- carboxyl group (–COOH) loses a hydrogen ion (H+), making it negatively charged (–COO-).
this hydrogen ion (H+) associates with the amine group (–NH2), making it positively charged (–NH3+).
resulting amino acid contains one positive charge and one negative charge, it is an electrically neutral, dipolar ion -> zwitterion
why are amino acids insoluble in organic solvents but soluble in water? (same as carbs)
amine and carboxyl group of amino acids can readily ionise
what is a buffer?
buffer: substance that can resist changes in pH in a solution when small amounts of an acid or alkali is added to it.
how are amino acids able to act as buffer
amino acids exist as zwitterions in aq medium -> amphoteric (both acidic and basic properties)
When acid is added, an amino acid (+H3N–RCH–COO-) takes up a hydrogen ion (H+) and becomes +H3N–RCH–COOH - the carboxyl group accepts the hydrogen ion.
When alkali is added, an amino acid (+H3N–RCH–COO-) loses a hydrogen ion and becomes H2N–RCH–COOi.e. the amine group loses a hydrogen ion which combines and neutralises the OH-
amphoteric is not amphiphatic(hydrophillic hydrophobic)
how are amino acids classified based on chemical properties
- amino acid with non-polar R groups
* R groups of amino acids are hydrocarbon in nature (C-C and C-H bonds)
* hydrophobic and unreactive
* localised in the interior, ie shielded from aq medium of the polypeptide as it folds into its 3D conformation - amino acid with polar R groups
* polar R groups (-OH and -NH) with no net charge
* hydrophillic - amino acids with charged R groups
* have negatively charged or positively charged R group -> hydrophilic
* Acidic amino acids have carboxyl group in R group -> net negative charge
* basic amino acids have amine group in R group -> net positive
what is a peptide bond
covalent bond formed between amine group of one amino acid and carboxyl group of the other.
process of formation of peptide bond -> condensation / dehydration rxn, water molecule eliminated
structure of polypeptide
- many amino acids joined together by peptide bonds in a specific linear amino acid sequence
- Each amino acid residue forms of two peptide bonds, linked to its neighbours in a head-to-tail fashion
- Each amino acid member in a polypeptide is now known as an amino acid residue
features of polypeptide:
* a free amine group, which marks the beginning of the polypeptide – the N terminus
* a free carboxyl group, which marks the end of the polypeptide – the C terminus
* R group (side chain) of each amino acid residue projects from the backbone of the polypeptide
property of polypeptide
- presence of the free amine and carboxyl group -> ability to buffer solutions, although not to as great an extent as free amino acids
- R groups of some amino acids can ionise -> additional buffering capacity, essential in biological systems, where small changes in pH can affect the functioning of enzymes and other proteins.
- variations in the length and the amino acid sequence of polypeptides contribute to
the diversity in the shape and biological functions of proteins
biuret test (principle, method, observation)
principle: biuret test detects peptide bonds, all proteins (NOT amino acids) give a positive result.
Nitrogen atoms in peptide bonds complexes with Cu2+ ions to give purple colouration.
method: Add equal volume of 5% potassium hydroxide solution to test solution.
Add 1% copper sulfate solution dropwise.
Mix the contents by shaking and leave for 3 minutes (no heating required)
observation:
purple / violet colour -> presence of peptide bonds
blue colour -> which is due to the copper sulfate solution indicates the absence of peptide bonds.
What is the primary structure of a protein?
the
1. unique number and
2. linear sequence of amino acids that constitute the polypeptide chain
how does primary sequence determine protein’s structure and function?
- much of the information necessary to specify how a polypeptide chain coils and folds into a specific 3D conformation + how each polypeptide chain will interact with another -> inherent the amino acid sequence
- The sequence of the amino acids in the protein influence the characteristics of a protein (not amino acid composition)
- size charge, polarity or hydrophobicity of amino acid R groups -> determine the type and location of bonds present at higher levels of organisation in the protein -> affect the ultimate 3D conformation hence function of the protein
e.g. sickle cell anaemia
secondary structure
- hydrogen bonds at regular intervals along polypeptide backbone -> regular coiling and folding of regions in polypeptide chain -> repeated patterns
- each hydrogen bond is formed between N-H group of one amino acid and C=O group of another amino acid (doesn’t involve R groups)
- each hydrogen bond is individually weak, but collectively serve to stabilise structure
- types of secondary structure: a-helix and b-pleated sheet
structure of a-helix
shape: extended spiral spring
nature of bonds:
- stabilised by intrachain hydrogen bonds,
which occur between C=O and N-H groups of
the peptide backbone
- hydrogen bond is formed between the O atom of the C=O group of an amino acid residue (nth) and the
H atom of the N-H group of another amino
acid that is situated four amino acid residues
(n
th + 4 residue) ahead in the linear
sequence.
The hydrogen bonds formed are parallel to
the main axis of the helix. In addition, all
C=O and N-H groups of the peptide
backbone can participate in hydrogen
bonding. Both features bring maximum
stability to the α-helix.
The α-helix makes one complete turn for
every 3.6 amino acids.
Fig. 15: α-helix viewed end-on.
R-groups are represented by filled circles
, whilst other atoms along the backbone
are represented by open circles
The R groups of the amino acid residues
project outside the helix, perpendicular to
the main axis (Fig. 15). This helps to prevent
steric interference with the polypeptide
backbone and with each other.
The chemical property of R groups, whether
hydrophilic or hydrophobic, will influence the
way the α-helix interacts with the surrounding
medium or other proteins.
Proline and hydroxyproline insert a kink
and disrupt the formation of the α-helix.
Amino acids with bulky R groups, e.g.
tryptophan, if present in large numbers can
also interfere with the formation of the α-helix.
E.g. of a protein with predominately α-helical
structure: keratin
Definition of a protein
polymers constructed from a set of 20 different amino acids encoded by DNA
What is a protein
Molecules made up of one or more polypeptide chains that has attained a stable, specific 3D conformation and is biologically functional
