Molecules of Life Chapter 3 Part 2

3.5 Proteins – Diversity in Structure and Function  Proteins are the most diverse biological molecule (structural, nutritious, enzyme, transport, communication, and defense proteins)  Cells build thousands of different proteins by stringing together amino acids in different orders

Proteins and Amino Acids  Protein An organic compound composed of one or more chains of amino acids  Amino acid A small organic compound with an amine group (—NH 3 + ), a carboxyl group (—COO -, the acid), and one or more variable groups (R group)

Amino Acid Structure

Fig. 3-15, p. 44 amine group carboxyl group valine

Polypeptides  Protein synthesis involves the formation of amino acid chains called polypeptides  Polypeptide A chain of amino acids bonded together by peptide bonds in a condensation reaction between the amine group of one amino acid and the carboxyl group of another amino acid

Peptide Bond Formation

Fig. 3-16a, p. 44

A DNA encodes the order of amino acids in a new polypeptide chain. Methionine (met) is typically the first amino acid. B In a condensation reaction, a peptide bond forms between the methionine and the next amino acid, alanine (ala) in this example. Leucine (leu) will be next. Think about polarity, charge, and other properties of functional groups that become neighbors in the growing chain.

Fig. 3-16b, p. 45

C A peptide bond forms between the alanine and leucine. Tryptophan (trp) will be next. The chain is starting to twist and fold as atoms swivel around some bonds and attract or repel their neighbors. D The sequence of amino acid subunits in this newly forming peptide chain is now met–ala–leu–trp. The process may continue until there are hundreds or thousands of amino acids in the chain.

Fig. 3-16a, p. 44 A DNA encodes the order of amino acids in a new polypeptide chain. Methionine (met) is typically the first amino acid. B In a condensation reaction, a peptide bond forms between the methionine and the next amino acid, alanine (ala) in this example. Leucine (leu) will be next. Think about polarity, charge, and other properties of functional groups that become neighbors in the growing chain. Stepped Art

Fig. 3-16b, p. 45 D The sequence of amino acid subunits in this newly forming peptide chain is now met–ala–leu–trp. The process may continue until there are hundreds or thousands of amino acids in the chain. C A peptide bond forms between the alanine and leucine. Tryptophan (trp) will be next. The chain is starting to twist and fold as atoms swivel around some bonds and attract or repel their neighbors. Stepped Art

Animation: Peptide bond formation

Levels of Protein Structure  Primary structure The unique amino acid sequence of a protein  Secondary structure The polypeptide chain folds and forms hydrogen bonds between amino acids

Levels of Protein Structure  Tertiary structure A secondary structure is compacted into structurally stable units called domains Forms a functional protein  Quaternary structure Some proteins consist of two or more folded polypeptide chains in close association Example: hemoglobin

Levels of Protein Structure

3.6 Why Is Protein Structure So Important?  When a protein’s structure goes awry, so does its function

Fig. 3-17a, p. 45

a Protein primary structure: Amino acids bonded as a polypeptide chain.

Fig. 3-17b, p. 45

b Protein secondary structure: A coiled (helical) or sheetlike array held in place by hydrogen bonds (dotted lines) between different parts of the polypeptide chain. helix (coil) sheet

Fig. 3-17c, p. 45

c Protein tertiary structure: A chain’s coils, sheets, or both fold and twist into stable, functional domains such as barrels or pockets. barrel

Fig. 3-17d, p. 45

d Protein quaternary structure: two or more polypeptide chains associated as one molecule.

Fig. 3-17, p. 45 a) Protein primary structure: Amino acids bonded as a polypeptide chain. helix (coil)sheet b) Protein secondary structure: A coiled (helical) or sheetlike array held in place by hydrogen bonds (dotted lines) between different parts of the polypeptide chain. barrel c) Protein tertiary structure: A chain’s coils, sheets, or both fold and twist into stable, functional domains such as barrels or pockets. d) Protein quaternary structure: two or more polypeptide chains associated as one molecule. Stepped Art

Just One Wrong Amino Acid…  Hemoglobin contains four globin chains, each with an iron-containing heme group that binds oxygen and carries it to body cells  In sickle cell anemia, a DNA mutation changes a single amino acid in a beta chain, which changes the shape of the hemoglobin molecule, causing it to clump and deform red blood cells

Globin Chains in Hemoglobin

Fig. 3-18a, p. 46

alpha globin heme A Globin. The secondary structure of this protein includes several helices. The coils fold up to form a pocket that cradles heme, a functional group with an iron atom at its center.

Fig. 3-18b, p. 46

alpha globin beta globin B Hemoglobin is one of the proteins with quaternary structure. It consists of four globin molecules held together by hydrogen bonds. To help you distinguish among them, the two alpha globin chains are shown here in green, and the two beta globin chains are in brown.

Animation: Globin and hemoglobin structure

Molecular Basis of Sickle Cell Anemia

Fig. 3-19a, p. 47

valinehistidineleucinethreonineproline glutamic acid A Normal amino acid sequence at the start of the hemoglobin beta chain. glutamic acid

Fig. 3-19b, p. 47

valinehistidineleucinethreonineprolinevalineglutamic acid B One amino acid substitution results in the abnormal beta chain of HbS molecules. The sixth amino acid in such chains is valine, not glutamic acid.

Fig. 3-19c, p. 47

C Glutamic acid carries a negative charge; valine carries no charge. This difference changes the protein so it behaves differently. At low oxygen levels, HbS molecules stick together and form rod-shaped clumps that distort normally rounded red blood cells into sickle shapes. (A sickle is a farm tool that has a crescent- shaped blade.) sickled cell normal cell

Fig. 3-19d, p. 47

Clumping of cells in bloodstream Circulatory problems, damage to brain, lungs, heart, skeletal muscles, gut, and kidneys Heart failure, paralysis, pneumonia, rheumatism, gut pain, kidney failure Spleen concentrates sickle cells Spleen enlargement Immune system compromised Rapid destruction of sickle cells Anemia, causing weakness, fatigue, impaired development, heart chamber dilation Impaired brain function, heart failure D Melba Moore is a celebrity spokesperson for sickle-cell anemia organizations. Right, range of symptoms for a person with two mutated genes for hemoglobin’s beta chain.

Animation: Sickle-cell anemia

Proteins Undone – Denaturation  Proteins function only as long as they maintain their correct three-dimensional shape  Heat, changes in pH, salts, and detergents can disrupt the hydrogen bonds that maintain a protein’s shape  When a protein loses its shape and no longer functions, it is denatured

Key Concepts: Proteins  Structurally and functionally, proteins are the most diverse molecules of life  They include enzymes, structural materials, and transporters  A protein’s function arises directly from its structure

3.7 Nucleic Acids  Some nucleotides are subunits of nucleic acids such as DNA and RNA  Some nucleotides have roles in metabolism

Nucleotides  Nucleotide A small organic molecule consisting of a sugar with a five-carbon ring, a nitrogen-containing base, and one or more phosphate groups  ATP A nucleotide with three phosphate groups Important in phosphate-group (energy) transfer

ATP

Fig. 3-20, p. 48 base (adenine) sugar (ribose) 3 phosphate groups

Fig. 3-20, p. 48 base (adenine) sugar (ribose) 3 phosphate groups Stepped Art

Nucleic Acids  Nucleic acids Polymers of nucleotides in which the sugar of one nucleotide is attached to the phosphate group of the next RNA and DNA are nucleic acids

RNA  RNA (ribonucleic acid) Contains four kinds of nucleotide monomers, including ATP Important in protein synthesis

DNA  DNA (deoxyribonucleic acid) Two chains of nucleotides twisted together into a double helix and held by hydrogen bonds Contains all inherited information necessary to build an organism, coded in the order of nucleotide bases

Four Nucleotides of DNA

Fig. 3-21, p. 48 adenine (A) base with a double ring structure thymine (T) base with a single ring structure 3 phosphate groups sugar (deoxyribose) guanine (G) base with a double ring structure cytosine (C) base with a single ring structure

Animation: Nucleotide subunits of DNA

The DNA Molecule

Fig. 3-22, p. 49 covalent bonding in sugar– phosphate backbone hydrogen bonding between bases

3.7 Key Concepts: Nucleotides and Nucleic Acids  Nucleotides have major metabolic roles and are building blocks of nucleic acids  Two kinds of nucleic acids, DNA and RNA, interact as the cell’s system of storing, retrieving, and translating information about building proteins

Summary: Organic Molecules in Living Things

Video: Effects of trans fats