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Amino acids and Proteins (Lecture Notes), Lecture notes of Biochemistry

this contains discussion about amino acids and proteins

Typology: Lecture notes

2021/2022

Available from 06/16/2023

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CHEM 142_N (LECTURE) : PROTEINS
CHARACTERISTICS OF PROTEINS
Account for 15% of a cell’s overall
mass
Contain CHON/S(carbon, hydrogen,
oxygen, nitrogen, sulfur)
Nitrogen is always present in
protein, unlike in carbohydrates and
lipids
Nitrogen content: 15.4 %
Specialized proteins like casein and
hemoglobin contain phosphorus
and iron, respectively
Naturally occurring, unbranched
polymer
Monomer units: amino acids
I. AMINO ACIDS: THE BUILDING
BLOCKS FOR PROTEINS
An organic compound
Contains an amino group(-NH2)
and carboxyl group(-COOH)
amino acids found in proteins are
always a-amino acids
a-amino acids
-(-NH2) & (-COOH) are always
attached to a-carbon atom
General formula:
R-GROUP
-Aka amino acid side chain
-Distinguishes a-amino acids from
each other
-Vary in size, charge, acidity,
functional groups present, h-
bonding ability, chemical
reactivity
STANDARD AMINO ACID
- 20 a-amino acids found in
proteins
4 Classification Based On The Side-
Chain Polarity
1) NONPOLAR
2) POLAR NEUTRAL
3) POLAR ACIDIC
4) POLAR BASIC
ESSENTIAL AMINO ACID
- 9 amino acids
- Must be obtained from dietary
sources
COMPLETE DIETARY PROTEIN
-Protein that contains all essential
amino acids
- E.g. milk, meat, fish, eggs, soy
protein
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CHEM 142_N (LECTURE) : PROTEINS

CHARACTERISTICS OF PROTEINS

 Account for 15% of a cell’s overall mass  Contain CHON/S (carbon, hydrogen, oxygen, nitrogen, sulfur)  Nitrogen is always present in protein, unlike in carbohydrates and lipids  Nitrogen content: 15.4 %  Specialized proteins like casein and hemoglobin contain phosphorus and iron, respectively  Naturally occurring, unbranched polymer  Monomer units: amino acids I. AMINO ACIDS: THE BUILDING BLOCKS FOR PROTEINS  An organic compound  Contains an amino group(-NH 2 ) and carboxyl group(-COOH)  amino acids found in proteins are always a-amino acids a-amino acids

- (-NH 2 ) & (-COOH) are always attached to a-carbon atom General formula: R-GROUP

  • Aka amino acid side chain
  • Distinguishes a-amino acids from each other
  • Vary in size, charge, acidity, functional groups present, h- bonding ability, chemical reactivity STANDARD AMINO ACID
  • 20 a-amino acids found in proteins _4 Classification Based On The Side- Chain Polarity
  1. NONPOLAR_

2) POLAR NEUTRAL

3) POLAR ACIDIC

4) POLAR BASIC

ESSENTIAL AMINO ACID

  • 9 amino acids
  • Must be obtained from dietary sources COMPLETE DIETARY PROTEIN
  • Protein that contains all essential amino acids
  • E.g. milk, meat, fish, eggs, soy protein

CHIRALITY AND AMINO ACIDS

CHIRAL CENTER

  • Four different groups are attached to the a-carbon atom  19 of the 20 standard amino acids possess a chiral center  except GLYCINE: r-group is hydrogen FISCHER PROJECTION FORMULA ACID-BASE PROPERTIES OF AMINO ACIDS  Amino acids are charged species in both solid state and in a solution → both (-COOH) & (-NH 2 ) are present on the same carbon in a-amino acid In neutral solution… CARBOX YL GROUP Lose protons (H+ donator) AMINO GROUPS Accept protons (H+ acceptor) ZWITTER ION:
  • Molecule that has a positive charge on one atom, and a negative charge on another, but has no net charge = 0 o ISOELECTRIC POINT AND ELECTROPHORESIS ISOELECTRIC POINT
  • “no net charge” pH value for an amino acid solution AMINO ACIDS

ISOELECTRIC

POINT

POLAR &

NONPOLAR

BASIC Higher than 6. ACIDIC Lower than 4. ELECTROPHORESIS

  • Process of separating charged molecules based on their

CLASSIFICATION OF PROTEINS

based on how many PEPTIDE CHAIN PRESENT MONOMERIC Only one peptide chain present MULTIMERIC More than one peptide chain present based on CHEMICAL COMPOSITION SIMPLE Only amino acid residues are present CONJUGATED Non-amino acids (prosthetic) + peptide chains based on SHAPE FIBROUS Molecules are elongated shape; linear “Water-insoluble” GLOBULAR Molecules are folded into spherical or globular shape “Water-soluble” MEMBRANE protein that is found associated with a membrane system of a cell. “Water-insoluble” based on FUNCTION Class Function examples CATALYTIC

- catalyze biochemical reactions in the cells - Participate in metabolic reactions in the body Enzymes – biochemical catalyst Sucrase Trypsin DEFENSE Recognize and destroy foreign substances Immunoglobulins Antibodies TRANSPORT carry essential substances throughout the body Hemoglobin Lipoprotein MESSENGER Transmit signals to different parts of the body Insulin Glucagon Human growth hormone CONTRACTILE Move muscles Actin Myosin STRUCTURAL Provide structural component Collagen keratin TRANSMEMBRANE Control movement of small molecules and ion through the cell membrane STORAGE Store nutrients Ferritin myoglobin REGULATORY Control enzymatic actions rhodopsin NUTRIENT Nourish and provide immunological Casein Ovalbumin

protection for young PROTEIN HYDROLYSIS

  • a chemical reaction in which peptide bonds within a protein are broken through a reaction with water.
  • Complete hydrolysis produces free amino acids PROTEIN DENTURATION
  • partial or complete disorganization of a protein’s characteristic three-dimensional shape as a result of disruption of its secondary, tertiary, and quaternary structural interactions GLYCOPROTEINS
  • conjugated proteins that contain carbohydrates or carbohydrate derivatives in addition to amino acids.
  • Collagen and immunoglobulins are important glycoproteins LIPO PROTEINS
  • conjugated proteins that contain lipids and amino acids
  • plasma lipoprotein