Molecules of Life Chapter 3 Part 2

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

Proteins and Amino Acids An organic compound composed of one or more chains of amino acids Amino acid A small organic compound with an amine group (—NH3+), a carboxyl group (—COO-, the acid), and one or more variable groups (R group)

amine group carboxyl group valine Figure 3.15 Generalized structure of amino acids, and an example. Green boxes highlight R groups. Appendix V has models of all twenty of the common amino acids. valine Fig. 3-15, p. 44

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

Figure 3.16 Examples of peptide bond formation. Chapter 14 returns to protein synthesis. 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. 3-16a, p. 44

will be next. The chain is starting to 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. Figure 3.16 Examples of peptide bond formation. Chapter 14 returns to protein synthesis. Fig. 3-16b, p. 45

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

a Protein primary structure: Amino acids bonded as a polypeptide chain. Figure 3.17 Four levels of a protein’s structural organization. Fig. 3-17a, 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. Figure 3.17 Four levels of a protein’s structural organization. helix (coil) sheet Fig. 3-17b, 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 Figure 3.17 Four levels of a protein’s structural organization. Fig. 3-17c, p. 45

d Protein quaternary structure: two or more polypeptide chains associated as one molecule. Figure 3.17 Four levels of a protein’s structural organization. Fig. 3-17d, p. 45

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

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. Figure 3.18 Globin and hemoglobin. (a) Globin, a coiled polypeptide chain that cradles heme, a functional group with an iron atom. (b) Hemoglobin, an oxygen-transport protein in red blood cells. Fig. 3-18a, p. 46

alpha globin alpha globin beta globin beta globin Figure 3.18 Globin and hemoglobin. (a) Globin, a coiled polypeptide chain that cradles heme, a functional group with an iron atom. (b) Hemoglobin, an oxygen-transport protein in red blood cells. beta 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. Fig. 3-18b, p. 46

glutamic acid glutamic acid valine histidine leucine threonine proline Figure 3.19 Sickle-cell anemia’s molecular basis and symptoms. Section 18.6 explores evolutionary and ecological pressures that maintain this genetic disorder in human populations. A Normal amino acid sequence at the start of the hemoglobin beta chain. Fig. 3-19a, p. 47

valine histidine leucine threonine proline valine glutamic acid Figure 3.19 Sickle-cell anemia’s molecular basis and symptoms. Section 18.6 explores evolutionary and ecological pressures that maintain this genetic disorder in human populations. 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. 3-19b, p. 47

is a farm tool that has a crescent-shaped blade.) sickled cell 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 Figure 3.19 Sickle-cell anemia’s molecular basis and symptoms. Section 18.6 explores evolutionary and ecological pressures that maintain this genetic disorder in human populations. Fig. 3-19c, 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 Figure 3.19 Sickle-cell anemia’s molecular basis and symptoms. Section 18.6 explores evolutionary and ecological pressures that maintain this genetic disorder in human populations. 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. Fig. 3-19d, p. 47

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

3.5-3.6 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 ATP 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

base (adenine) sugar (ribose) 3 phosphate groups Figure 3.20 The structure of ATP. sugar (ribose) 3 phosphate groups Fig. 3-20, p. 48

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

base with a double ring structure thymine (T) 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 Figure 3.21 (a) Nucleotides of DNA. The four kinds of nucleotides in DNA differ only in their component base, for which they are named. The carbon atoms of the sugar rings in nucleotides are numbered as shown. This numbering convention allows us to keep track of the orientation of a chain of nucleotides, as shown in (b). Fig. 3-21, p. 48

hydrogen bonding between bases Figure 3.22 Models of the DNA molecule. covalent bonding in sugar– phosphate backbone hydrogen bonding between bases Fig. 3-22, p. 49

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