1. Chapter 3 Molecules of Life

2. 3.1 Fear of Frying Organisms consist of the same molecules
Different arrangements impact function
Trans and cis fats are good examples
Cis fats: most naturally occurring fats
Trans fats: unhealthy fats found mostly in partially hydrogenated vegetable oils
Trans fats: linked to diabetes, heart attacks, and atherosclerosis in humans

3. Trans Fats: An Unhealthy Food
O OH C
H—C—H
O OH C
H—C—H
H—C
C—H
H—C—H H
oleic acid
elaidic acid
has a trans bond:
C—H
H—C—H
H—C—H H
has a cis bond:
Figure 3.1 Trans fats, an unhealthy food. Double bonds in the tail of most naturally occurring fatty acids are cis, which means that the two hydrogen atoms flanking the bonds are on the same side of the carbon backbone. Hydrogenation creates abundant trans bonds, with hydrogen atoms on opposite sides of the tail.

4. 3.2 Organic Molecules Carbon is the backbone of life and can form:
Four covalent bonds with other atoms
A variety of structures, including rings and chains
Polar and nonpolar bonds
“Organic” means that a compound consists mostly of carbon and hydrogen
These and many other elements are present in nonliving things as well, just at different proportions

5. Modeling Organic Molecules
The structure of an organic molecule controls its function
Chemical structure can be represented in four different ways
Structural formula
Simplified carbon ring structures
Ball-and-stick models
Space-filling models

6. Representing Structures of Organic Molecules
Structural model of an organic molecule
Each line is a covalent bond
Two lines are double bonds
Three lines are triple bonds
Figure 3.3 Modeling an organic molecule. All of these models represent the same molecule: glucose.
glucose

7. Carbon Ring Structures Are Represented as Polygons
Carbon atoms are implied
Figure 3.3 Modeling an organic molecule. All of these models represent the same molecule: glucose.
glucose
glucose

8. Ball-and-Stick Models
Show positions of atoms in three dimensions
Elements are coded by color
Black =
Red=
Gray=
Figure 3.3 Modeling an organic molecule. All of these models represent the same molecule: glucose.
glucose

9. Space-Filling Models Show how atoms sharing electrons overlap glucose
Figure 3.3 Modeling an organic molecule. All of these models represent the same molecule: glucose.
glucose

10. 3.3 Molecules of Life—From Structure to Function
Functional groups are important for molecules of life
Bond an atom or small molecular group to a carbon in an organic compound
Impact chemical properties such as acidity or polarity
Impart chemical behavior of molecules of life

11. Important Functional Groups
Table 3.1 Some Functional Groups in Biological Molecules

12. Important Functional Groups
Table 3.1 Some Functional Groups in Biological Molecules

13. Assembling Complex Molecules
Monomers
Small organic molecules used as subunits to build larger molecules (polymers)
Simple sugars, fatty acids, amino acids, and nucleotides
Polymers
Larger molecules that are chains of monomers
May be split and used for energy
Complex carbohydrates, lipids, proteins, and nucleic acids

15. What Cells Do to Organic Compounds
Metabolism
Activities by which cells acquire and use energy to construct, rearrange, and split organic molecules
Allows cells to live, grow, and reproduce
Requires enzymes (proteins that increase the speed of reactions)
Two important reactions: condensation and hydrolysis

16. Condensation
Cells build a large molecule from smaller ones by this reaction
An enzyme removes a hydroxyl group from one molecule and a hydrogen atom from another. A covalent bond forms between the two molecules, and water also forms.
Figure 3.6 Metabolism. Two common reactions by which cells build and break down organic molecules are shown.

17. Hydrolysis (Hydro-lysis)
Cells split a large molecule into smaller ones by this water-requiring reaction.
An enzyme attaches a hydroxyl group and a hydrogen atom (both from water) at the cleavage site.
Figure 3.6 Metabolism. Two common reactions by which cells build and break down organic molecules are shown.

18. 3.4 Carbohydrates The most abundant biological molecules
Carbon, hydrogen, and oxygen in a 1:2:1 ratio
Used for structural materials, fuels, and for storing and transporting energy
Simple carbohydrates
Monosaccharides = 1 sugar
Carbon backbone with carbonyl and hydroxyl function groups
Soluble in water

19. Carbohydrates in Biological Systems
Short chain carbohydrates
Oligosaccharides = a few monosaccharides
Disaccharides like lactose and sucrose have two sugar units
Complex carbohydrates
Polysaccharides = 100s or 1000s of sugars
Straight or branched chains
One or many types of monosaccharides
Three of the most common: cellulose, starch, and glycogen

20. Oligosaccharides determine blood type

22. Cellulose
Figure 3.8 Three of the most common complex carbohydrates and their locations in a few organisms. Each polysaccharide consists only of glucose subunits, but different bonding patterns result in substances with very different properties.
Cellulose is the main structural component of plants. Above, in cellulose, chains of glucose monomers stretch side by side and hydrogen-bond at many —OH groups. The hydrogen bonds stabilize the chains in tight bundles that form long fibers. Few types of organisms can digest this tough, insoluble material.

23. Starch
Figure 3.8 Three of the most common complex carbohydrates and their locations in a few organisms. Each polysaccharide consists only of glucose subunits, but different bonding patterns result in substances with very different properties.
Starch is the main energy reserve in plants, which store it in their roots, stems, leaves, seeds, and fruits. Below, in starch, a series of glucose monomers form a chain that coils up.

24. Glycogen
Glycogen functions as an energy reservoir in animals, including people. It is especially abundant in the liver and muscles. Glycogen consists of
highly branched chains of glucose monomers.
Figure 3.8 Three of the most common complex carbohydrates and their locations in a few organisms. Each polysaccharide consists only of glucose subunits, but different bonding patterns result in substances with very different properties.

25. 3.5 Lipids Fatty, oily, or waxy organic compounds
Vary in structure but always hydrophobic
Fatty acids are present in most lipids
A long hydrophobic hydrocarbon tail with a hydrophilic carboxyl head
Saturated fatty acids have straight tails with single bonds (solid fats)
Unsaturated fatty acids have crooked tails with double bonds (liquid fats EXCEPT trans fat)

26. Fatty Acids
hydrophilic “head” (acidic
carboxyl group)
hydrophobic
“tail”
Figure 3.10 Fatty acids. A The tail of stearic acid is fully saturated with hydrogen atoms. B Linoleic acid, with two double bonds, is unsaturated. The first double bond occurs at the sixth
carbon from the end, so linoleic acid is called an omega-6 fatty acid. Omega-6 and C omega-3 fatty acids are “essential fatty acids.” Your body does not make them, so they must come from food.
A stearic acid (saturated)
B linoleic acid (omega- 6)
C linolenic acid (omega-3)

27. Fats
Lipids with one, two, or three fatty acids bound to the same glycerol head
Triglycerides have three tails
Most abundant and richest energy sources in vertebrates
Ex: Butter
Veg. Oil

28. Triglycerides The three fatty acid tails of a triglyceride are
head
tails
The three fatty acid tails of a triglyceride are
attached to a glycerol head.
Figure 3.11 Lipids with fatty acid tails.
A: The three fatty acid tails of a triglyceride are attached to a glycerol head

29. Phospholipids
Lipids with two hydrophobic hydrocarbon tails bound to a hydrophilic phosphate-containing head
Arranged into two layers to form the lipid bilayer of cell membranes

30. Lipids with Fatty Acid Tails
head
tails
The two fatty acid tails of this phospholipid are attached to a phosphate-containing head.
Figure 3.11 Lipids with fatty acid tails.
B: The two fatty acid tails of this phospholipid are attached to a phosphate-containing head
C: A double layer of phospholipids—the lipid bilayer—is the structural foundation of all cell membranes. You will read more about the structure of cell membranes in Chapter 5.

32. Waxes
Complex mixtures with long fatty-acid tails bonded to long-chain alcohols or carbon rings
Protective, water-repellant covering

33. Steroids
Lipids with a rigid backbone of four carbon rings and no fatty-acid tails
Cholesterol
Most important steroid in animal tissue
Component of eukaryotic cell membranes
Remodeled into bile salts, vitamin D, and steroid hormones
The female sex hormone estrogen
The male sex hormone testosterone

34. Steroid Hormones an estrogen testosterone female male O OH HO O
Figure 3.12 Steroids. Estrogen and testosterone are steroid hormones that govern reproduction and secondary sexual traits. The two hormones are the source of gender-specific traits in many
species, including these wood ducks.

36. 3.6 Proteins (this is really important!)
The most diverse biological molecules
Vary in structure and function but participate in all processes that sustain life
Composed of 20 kinds of amino acids
Small organic molecules with a central carbon bonded with an amine group (—NH3+), a carboxyl group (—COO-, the acid), and one or more variable groups (R group)
Figure 3.13 Generalized structure of an amino acid. See Appendix I for the complete structures of the twenty most common amino acids found in eukaryotic proteins.
amine group
carboxyl group H OH
R group

37. Polypeptides Amino acid chains formed from protein synthesis
A chain of amino acids
Bonded together by peptide bonds
Condensation reaction between the amine group of one amino acid and the carboxyl group of another amino acid

38. Where does this occur in the cell???

39. Primary and Secondary 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

40. Polypeptide Formation
methionine
serine
methionine
serine
glutamine
methionine
serine
arginine
Figure 3.14 Animated Polypeptide formation. Chapter 9 offers a closer look at protein synthesis.
Two amino acids (here, methionine and serine) are joined by condensation. A peptide bond forms between the carboxyl group of the methionine and the amine group of the serine.
Stepped Art

41. A protein’s primary structure consists of a linear sequence of amino acids (a polypeptide chain). Each type of protein has a unique primary structure. 1
glycine
lysine
arginine 3
Tertiary structure occurs when a chain’s coils and sheets fold up into a functional domain such as a barrel or pocket. In this example, the coils of a globin chain form a pocket. 4
Some proteins have quaternary structure, in which two or more polypeptide chains associate as one molecule. Hemoglobin, shown here, consists of four globin chains (green and blue). Each globin pocket now holds a heme group (red). 2
Secondary structure arises as a polypeptide chain twists into a coil (helix) or sheet held in place by hydrogen bonds between different parts of the molecule. The same patterns of secondary structure occur in many different proteins. 5
Many proteins aggregate by the thousands into much larger structures, such as the keratin filaments that make up hair.
Figure 3.14 Animated Protein structure.
Stepped Art

42. Protein Structure – A Peptide Bond
serine
methionine
methionine
serine
1) A condensation reaction joins the carboxyl group of one amino acid and the amine group of another to form
a peptide bond. In this example, a peptide bond forms between the amino acids methionine and valine.
methionine
proline
glutamic acid
valine
histidine
leucine
threonine
Figure 3.14 Protein Structure
2) A protein’s primary structure consists of a linear sequence of amino acids (a polypeptide chain). Each type of protein has a unique primary structure

43. Protein Structure – Primary Structure
3) Secondary structure arises as a polypeptide chain twists into a helix (coil), loop, or sheet held in place by hydrogen bonds.
4) Tertiary structure arises when loops, helices, and sheets fold up into a domain. In this example, the helices of a globin chain form a pocket.
5) Many proteins have two or more polypeptide chains (quaternary structure). Hemoglobin, shown here, consists of four globin chains ( green and blue). Each globin pocket now holds a heme group (red ).
Figure 3.14 Protein Structure
6) Some types of proteins aggre-gate into much larger structures. As an example, organized arrays of keratin, a fibrous protein, compose filaments that make up your hair.

44. Tertiary and Quaternary 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
Some proteins aggregate by thousands into larger structures, with polypeptide chains organized into strands or sheets (e.g., hair)

46. 3.7 Why is Protein Structure So Important?
Proteins function requires a correct 3D shape
Denatured proteins no longer have correct shapes
Heat, changes in pH, salts, and detergents can disrupt the hydrogen bonds that maintain a protein’s shape
Once a protein’s shape unravels, so does its function

47. Prions Prion diseases are caused by misfolded proteins
Mad cow disease (bovine spongiform encephalitis)
Creutzfeldt–Jakob disease in humans
Scrapie in sheep
Infectious diseases
Characterized by deterioration of mental and physical abilities
Eventually cause death

48. Variant Creutzfeldt–Jakob Disease
Figure 3.17 Variant Creutzfeldt–Jakob disease (vCJd). A Charlene Singh was one of the three people who developed symptoms of vCJD disease while living in the United States. Like the
others, Singh most likely contracted the disease elsewhere; she spent her childhood in Britain. Diagnosed in 2001, she died in B Slice of brain tissue from a person with vCJD. Fibers of prion
proteins (amyloid fibrils) radiating from several deposits are visible.

49. 3.8 Nucleic Acids Nucleotides are small organic molecules
Function as energy carriers, enzyme helpers, chemical messengers, and subunits of DNA and RNA
Composed of monosaccharide ring bonded to a nitrogen-containing base and one, two, or three phosphate groups
Figure 3.18 Example of a nucleotide: ATP. ATP is a monomer of RNA, and also a participant in many metabolic reactions
base (adenine)
phosphate
groups
ribose
sugar

50. 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
Figure 3.19A Nucleic Acid structure
A chain of nucleotides is a nucleic acid. The sugar of one nucleotide is covalently bonded to the phosphate group of the next, forming a sugar-phosphate backbone.

51. RNA and DNA RNA (ribonucleic acid) DNA (deoxyribonucleic acid)
Contains four kinds of nucleotide monomers, including ATP
Important in protein synthesis
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

52. The DNA Molecule
Cells use the order of nucleotide bases in DNA (the DNA sequence) to guide the production of RNA and proteins
Figure 3.19B Nucleic Acid Structure
DNA consists of two chains of nucleotides, twisted into a double helix. Hydrogen bonding maintains the three-dimensional structure of this nucleic acid.

54. Directionality In DNA--Replication

55. Points to Ponder
Consider trans fat foods such as red meats and dairy products. Are there dangers in limiting these foods in different age groups, such as in children? Benefits?
Why do athletes eat high carbohydrate meals before they perform?
Consider the effects of nutritional deficiencies on the body. Why is a balanced diet so critically important?