Proteins Flashcards
What are proteins ?
macromolecular polypeptides.
• Makes up the muscles, tendons, organs, glands, enzymes, some hormones, blood proteins, immunoglobulin, bones, nails and hair.
• Needed for growth, repair and maintenance of cells
• Next to water, protein makes up the greatest portion of our body weight
10 functions of proteins and examples
1.Transport ( Hb and transferrin )
2. Mobility ( actin and myosin )
3. CNS ( laminitis , nerve growth factors )
4. Wound healing regeneration , energy and satiation
5. Fluid balance ( blood proteins )
6. Acid-base regulation ( Hb, albumin )
7.Hormones (insulin , growth hormones )
8. Enzymes (amylases and pepsin)
9. Immunity ( lysozyme, antibodies)
10. Structure ( collagen, keratin, elastin)
8 protein classifications based on function
- Structural
- Enzymes
- Hormones
- Respiratory
- Transport
- Contract.
- Storage
- Toxins
What are amino acids
• Chemical units or “building blocks” of proteins
What are “Essential Amino Acids”
• A.A that must be obtained from the diet
What are “Nonessential Amino Acids.”
• A.A that the body can synthesize from other sources than diet
3 applications of a.a
• Clinical Application -Slower, Longer-Acting Insulin Created by substituting Amino Acids in the year 2000
• Heavy metal poisoning: Sulphur group in cysteine binds heavy
metals
• Electrophoresis to identify different diseases: e.g. Crohn’s disease
(decreased serine and increased histidine), Sickle cell anaemia
9 essential a.a
1.Histidine
2.leucine
3. Isoleucine
4. Lysine
5. Methionine
6. Threonine
7.Phenylalanine
8. Valine
9. Tryptophan
6 conditionally non-essential
- Arginine (essential mainly in children )
- Cystine
- Glutamine
- Glycine
- Proline
- Tyrosine
5 non-essential a.a
Alanine
Asparagine
Aspartate
Glutamate
Serine
What are conditional a.a
Body cannot synthesize some a.a in sufficient quantities during certain stages/conditions. Hence they become conditionally essential.
e.g pregnancy, adolescent growth, or recovery from trauma
Structure of a.a
Each a.a has
• a carboxyl group
• a primary amino group (proline 2ry )
• & a distinctive side chain “R group”
• At physiological pH the carboxyl group is negatively charged (COO-) & the amino group (NH3+) is protonated
pH of anion and cation
Cation is low pH
Anion is high pH
Properties of a.a
• The α-carbon of a.a is a chiral carbon
(attached to 4 different groups-asymmetric centre)
• Optically active carbon atom except Glycine.
• They have the mirror image form: D & L isomerism
Known as enantiomers
D and L isomers and where are they formed
If Amino group is present on the right side of the asymmetric (a-carbon ) is known as D isomer
• All amino acid found in protein are of L-configuration.
• D-amino acids are found in some antibiotics and in
bacterial cell walls
(drug absorption and Handerson -Hasselbalch equation)
Classification 7 of amino acids present in proteins
- With Aliphatic Side Chains
- With Side Chains Containing Hydroxylic (OH) Groups
- With Side Chains Containing Basic Groups
- Containing Aromatic Rings
- With Side Chains Containing Sulfur Atoms
- With Side Chains Containing Acidic Groups /Their Amides
- Imino Acid
Abbreviation & symbols of a.a
• Each a.a has a 3 letter abbreviation and one-letter codes
Glycine Gly G Threonine Thr T
Alanine Ala A Cysteine Cys C
Valine Val V Tyrosine Tyr Y
Leucine Leu L Asparagine Asn N
Isoleucine Ile I Glutamine Gln Q
Methionine Met M Aspartic Acid Asp D
Proline. Pro P Glutamic Acid Glu E
Phenyl Aline Phe F Lysine Lys K
Tryptophan. Trp W Arginine Arg R
Serine. Ser S Histidine His H
What is proline
a secondary amine, but used in the biosynthesis of proteins - Proteinogenic (20 +1 amino acid )
When can amino acid side chains with hydroxyl group be phosphorylated
During post translational modification
What is Isoelectric point (pl)
the pH at which a particular molecule or surface carries no net electrical charge .
• The net charge is affected by pH of the environment & can become more (+)vely or (-)vely charged due to loss or gain of protons (H+).
4 applications of pl
• Separation of protein
• Solubilizing protein
• Isoelectric focusing
• Predict R group
Correlation between charge and pl
At a pH below their pI, proteins carry a net positive charge; above their pI they carry a net negative charge.
What is isoelectric focusing
• Proteins can be separated according to their isoelectric point using a technique called isoelectric focusing.
• To predict R group
How to calc pl for a.a with only one NH2 and one COOH group
the pI can be calculated from the pKa’s of this molecule.
Two pKa’s used are those of the two groups that lose and gain a charge from the neutral form of the amino acid.
How can 2 a.a be joined
covalently in a condensation reaction
These are amide linkages between the α-carboxyl group of one a.a and the α-amino group of the other.
• Side chain determines the property of protein
5 features of peptide bond
Peptide bonds are not broken in normal denaturing conditions.
– has a partial double bond character: (Shorter than a single bond )
–Is rigid (between C1 and N is always closer to 180 ) and planar (due to the delocalization of the electrons from the double bond)
–Exist in trans configuration
–Is uncharged but polar
prevents free rotation around the bond :between the carbonyl carbon and the nitrogen of the peptide bond. • Peptide bond is uncharged- neither accepts nor release protons. Generally peptide bond is not available for chemical reaction except for hydrogen bond formation. Polarity depends on the N-terminal amino group, C- terminal carboxy group and any ionized chains present in the side chain.
How peptide bonds named
• Free N terminal is written to the left • Free Carboxyl terminal to the right
• A.a are read from the N to C terminal
• A.a residue having the suffix “ine, an, ic, ate” are changed to “yl” except the c-terminal
Hw to determine amino acid comp of polypeptide
peptide bonds are cleaved and a.a are released , a.a is separated by cation-exchange chromatography.
Ninhydrin test
Positive tesr is purple coloured complex
Sequencing of the peptide from its N-terminal end
• Edman Degradation
How determine primary structure of protein by DNA sequencing
• If the nucleotide sequence is determined, from the genetic code it is possible, to translate the sequence of nucleotides into the corresponding a.a of that polypeptide.
Structure Organization of Proteins
• Mainly four organizational level
• Primary, Secondary, Tertiary, Quaternary.
• The complexity increases
• Ranges from simple proteins to multifunctional proteins
Primary structure (Iry)
• Sequence of a.a in a protein (joined by peptide bonds)
• Includes the location of disulfide bond
• Deviation and abnormality in the a.a sequence may result in improper folding and loss of normal function
Secondary structure
• The conformation of the polypeptide backbones of proteins
• Commonly they form a regular arrangements with a.a close to each other : arrangements are due to the partial double bond character of the peptide bond
• 2ndry structure includes α-helix, β-sheet and β-bend
• Hydrogen bonds and Vander Waals force stabilize the 2ndry structure mainly the α-helix
What is a helix
• A common motif in the IIry structure of proteins
• The α-helix is a right- or left-handed coiled conformation
• Resembles a spring, in which every backbone N-H group donates a H bond to the backbone C=O group of the a.a four residues earlier
( hydrogen bonding).
• Spiral structure
• Tightly packed, coiled polypeptide backbone core.
Side chain extend outwards
Stabilized by H bonding b/w
carbonyl oxygen and amide hydrogen.
Amino acids per turn - 3.6
Pitch is 5.4 A
Alpha helical segments are found in many globular proteins like
myoglobins, troponin- C etc.
• It has the lowest energy and is the most stable form (stability increases with hydrogen bond formation)
• Some a.a disturb the helix
• proline may insert a kink,
• charged a.a form ionic bond and disturb the arrangement
• bulk side chain a.a may also interfere
Describe Beta sheet (β-sheet)
Unlike the alpha helix β-chain are composed of two or more peptide chains (strands) or segments of peptide chain
• All the peptide bond component are involved in hydrogen bonding
• The hydrogen bond is perpendicular
• Hydrogen bonds may be inter or intra chain bonds
• They may be parallel (C–terminals on the same side or antiparallel (C-terminals on the opposite side) or mixed (both )
Describe b bends / reverse turns
Predominant protein type in globular proteins
• Compact structure
• Predominantly found in cytosol & surface of protein molecule
• Connect strands of anti-parallel β-sheets
• Contain mainly proline (kink), glycine (smallest a.a)
• Non repetitive secondary structure
• Some polypeptides may have a loop or coil and have less regular structure
(“random coil”)
Secondary structure
• Super secondary structure
• Combines all IIry structure & assembles together
• Side chains of adjacent IIry structure elements assemble close to each other & folds into a protein