1. Molecules of Life
Chapter 3 Part 2

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

3. 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)

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

20. 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

21. 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

22. 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

23. 3.7 Nucleic Acids
Some nucleotides are subunits of nucleic acids such as DNA and RNA
Some nucleotides have roles in metabolism

24. 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

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

26. 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

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

28. 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

29. 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

30. 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

31. 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

32. Summary: Organic Molecules in Living Things