MCB 100 January 30 2019 Biological Macromolecules Proteins

MCB 100 January 30, 2019 Biological Macromolecules Proteins, Lipids, Polysaccharides and Nucleic Acids

Chemical Composition of an Escherichia coli Cell % Total Weight Organic Compounds Proteins Nucleic Acids RNA DNA Carbohydrates Lipids Miscellaneous % Dry Weight 15 50 6 1 3 2 2 20 3 10 8 6 Inorganic Compounds Water Ions and Minerals 70 1 3 Macromolecule = large molecule Polymer = a large molecule made of many smaller molecules stuck together in long chains

Proteins – polymers of amino acids held together by peptide bonds Lipids – amphipathic molecules that form the matrix of cell membranes – fatty acids and glycerol components are held together by ester bonds Polysaccharides (also known as complex carbohydrates) – polymers of sugars held together by glycosidic bonds Nucleic Acids – polymers of nucleotides held together by phosphodiester bonds

Biological Macromolecules Which one of the following statements about biological polymers is FALSE? A. B. C. D. Polysaccharides are hydrophilic. Bacterial flagella are made of DNA. All proteins contain nitrogen atoms. The genetic material in all cells contains phosphorous atoms. E. All proteins, lipids, polysaccharides and nucleic acids contain carbon atoms.

Proteins – polymers of amino acids held together by peptide bonds Lipids – amphipathic molecules that form the matrix of cell membranes – fatty acids and glycerol components are held together by ester bonds Polysaccharides (also known as complex carbohydrates) – polymers of sugars held together by glycosidic bonds Nucleic Acids – polymers of nucleotides held together by phosphodiester bonds

Amino Acids and Proteins are large globular molecules. There are many different types of proteins found in a typical cell and each type has a different function. Some proteins are found in the cytoplasm and others are embedded in the cell membrane. Some Functions of Proteins: - some act as part of the structure of the cell - many act as enzymes that catalyze biochemical reactions - others transport substances through the cell membrane - some regulate expression of genes or control other cell functions The function of a protein is determined by it’s solubility, shape and the three dimensional arrangement of organic functional groups on it’s surface.

2 -D Protein Gel Electrophoresis Gel electrophoresis is a way to separate large biological molecules like DNA fragments and proteins. In 2 -D protein gels each spot is a different type of protein molecule. Gels like this can be used to characterize the population of proteins present in a particular type of bacterial culture or in a particular type of plant or animal tissue.

Structure of amino acids All amino acids contain nitrogen in the form of an amino group. They also always have a carboxylic acid group. The amino groups and the carboxylic acid groups are involved in the formation of the bonds that join amino acids into long chains to make proteins.

Formation of a Peptide Bond • The formation of a peptide bond requires a free carboxylic acid group and a free amino group. • A molecule of water is produced when the two amino acids are joined. • Note how the dipeptide has a free amino group and a free carboxylic acid group. Another amino acid can be attached by the formation of another peptide bond.

Structure of an Oligopeptide • Since each amino acid has an amino group and a carboxyl group, a linear chain of great length can be made. • The oligopeptide shown is a pentapeptide (oligo = few, penta = 5) • Most proteins are chains of 100 – 1000 amino acids.

Proteins are linear chains of amino acids • Typical proteins consist of 200 – 400 amino acids, but some are smaller than this and others are larger. The key factor that determines the structure and ultimately the function of an enzyme is the sequence of amino acids found in the protein.

The Folding of a Protein to Its Final Shape Primary Structure: - The sequence of amino acids in the chain - Determined by the genetic information encoded in the m. RNA - Determines the final shape and function of the protein Secondary Structure: - Local folding of a protein chain - Alpha helix and Beta sheet are common motifs - Stabilized by interactions between backbone groups that are fairly close to each other in the primary sequence Tertiary Structure: - Final folding of a single protein chain to its globular form - Stabilized by interactions between groups on side chains that may be far apart in the primary sequence but close together in the final 3 -D shape Quaternary Structure: - The noncovalent attraction of two or more separate protein chains to form a functional unit - Stabilized by interactions between groups on side chains that may be far apart in the primary sequence but close together in the final 3 -D shape

Structure of a Typical Protein Lysozyme: an enzyme that breaks down bacterial & fungal cell walls

Protein Functions 1 Which ONE of the following statements about proteins and the roles of proteins in living organisms is FALSE? A. Enzymes are catalysts that make the chemical reactions of life go faster. Most enzymes are proteins. B. Most substances that enter or exit a living cell do so by passing through specific pores in the cytoplasmic membrane. The pores in a cell membrane are made of proteins. C. Living cells contain packets of information called "genes” that must be copied and passed on to the next generation of cells. Genes are made of proteins. D. On the outside surface of some bacterial cells there are rod-like structures called pili that help the bacteria stick to specific surfaces. Pili are made of proteins. E. Some bacteria produce toxins that can cause disease in humans. Many bacterial toxins are proteins.

AMINO ACIDS GROUPED BY TYPES OF SIDE CHAINS NON-POLAR (hydrophobic) Glycine Alanine Leucine Isoleucine Valine Proline AROMATIC (mostly hydrophobic) Phenylalanine Tyrosine Tryptophan POLAR (hydroxyl or amide groups) Serine Threonine Asparagine Glutamine SULFUR CONTAINING Methionine Cysteine ACIDIC Aspartic acid Glutamic acid BASIC Lysine Histidine Arginine

Amino Acids Which one of the following amino acids has a basic side chain? A. Cysteine D. Lysine B. Valine C. Asparagine E. Phenylalanine

Amino Acids Which one of the following amino acids has a basic side chain? A. Cysteine D. Lysine B. Valine C. Asparagine E. Phenylalanine CH 2 CH 2 – NH 2 | H 2 N – COOH | H

Protein Structure Which one of the following statements about protein structure is TRUE? A. The backbone chain of a typical protein has many branch points that lead to side chains that are several amino acids long. B. Proteins are rich in phosphorous atoms because every amino acid contains at least one phosphate. C. The side chains of some amino acids are hydrophobic while other amino acids have hydrophilic side chains. D. All proteins have quaternary structure because every protein is composed of several peptide chains. E. The first amino acid in any protein chain is an Alanine.

DNA – Protein Interactions Some DNA-binding proteins are involved with the regulation of gene expression. A zinc-finger is a motif or fold seen in some DNA binding proteins. Functional groups on the alpha helices of the protein stick to functional groups in the major groove of the DNA double helix. Zinc finger-DNA. Note three alpha helices pointing into the major groove, each recognizing 3 bp of DNA. The Zinc binding domain is a structural element for protein folding, not directly involved in DNA binding. From: kahn@biochem. umd. edu

Above: Hemoglobin Right: Cell Membrane Structure

Antigen-Antibody Complex

The Active Site of a Serine Protease From: www. researchgate. net/profile/Rima_Chauduri