PowerLecture: Chapter 3

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PowerLectureChapter 3

• Molecules of Life

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Section 3.0 Weblinks and InfoTrac

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  this chapter online or click highlighted articles
  below (articles subject to change)
• Section 3.0 Geology of the Delphic Oracle
• Section 3.0 EPAMethane
• Section 3.0 The Delphic Oracle A
  Multidisciplinary Defense of the Gaseous Vent
  Theory. Henry Spiller et al. Journal of
  Toxicology Clinical Toxicology, Mar. 2002.

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How Would You Vote?

• The following is the question for this chapter.
  See the "Polls and ArtJoinIn" for this chapter if
  your campus uses a Personal Response System,or
  have your students vote online. See national
  results below.
• Should we work toward developing the vast
  undersea methane deposits as an energy source,
  given that the environmental costs and risks to
  life are unknown?

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Impacts, Issues Science or the Supernatural?

• Greece, 2000 BCE, the oracle of Delphi made
  cryptic prophecies
• Her temple was perched on intersecting earthquake
  faults where hydrocarbon gases seep out of the
  ground a possible scientific explanation for
  the oracles hallucinations

Fig. 3-1a, p.32
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Impacts, Issues Science or the Supernatural?

• There may be a thousand billion tons of frozen
  methane hydrate on the seafloor
• The worlds largest reservoir of natural gas (pg
  32)

Fig. 3-1b, p.32
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Impacts, Issues Video
Science or the Supernatural?
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Section 3.1 Weblinks and InfoTrac

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  this chapter online or click highlighted articles
  below (articles subject to change)
• Section 3.1 Library of 3-D Molecular Structures
• Section 3.1 World Index of Molecular
  Visualization Resources
• Section 3.1 Synthesizing Chemicals by Computer
  (from simple hydrocarbons). James Hendrickson.
  Technology Review, April 1984.

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Organic Compounds

• Hydrogen and other elements covalently bonded to
  carbon
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids

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Organic Compounds
sodium (Na)
calcium (C)
carbon (C)
chlorine (Cl)
phosphorous (P)
oxygen (O)
magnesium (Mg)
potassium (K)
hydrogen (H)
iron (Fe)
iron (S)
nitrogen (N)
p.34a
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Organic Compounds
structural formula for methane
ball-and-stick model
space-filling model
p.34b
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Carbons Bonding Behavior

• Outer shell of carbon has 4 electrons can hold 8
• Each carbon atom can form covalent bonds with up
  to four atoms

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Bonding Arrangements

• Carbon atoms can form chains or rings
• Other atoms project from the carbon backbone

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Organic Compounds
or
Simplified structural formula for a six-carbon
ring
icon for a six-carbon ring
p.34e
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Organic Compounds
Fig. 3-2, p.35
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Molecular models of the protein hemoglobin
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Organic Compound
Fig. 3-3, p.35
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Section 3.2 Weblinks and InfoTrac

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  below (articles subject to change)
• Section 3.2 Biochemistry Online
• Section 3.2 Basic Chemistry of Biomolecules
• Section 3.2 Biomolecules and Nanotechnology.
  David Goodsell. American Scientist, May 2000.

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Functional Groups

• Atoms or clusters of atoms that are covalently
  bonded to carbon backbone
• Give organic compounds their different properties

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Examples of Functional Groups

• Hydroxyl group - OH
• Amino group - NH3
• Carboxyl group - COOH
• Phosphate group - PO3-
• Sulfhydryl group - SH

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Types of Reactions

• Functional group transfer
• Electron transfer
• Rearrangement
• Condensation
• Cleavage

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Common Functional Groups in Biological Molecules
Fig. 3-4, p.36
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Functional group
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Functional Groups in Hormones

• Estrogen and testosterone are hormones
  responsible for observable differences in traits
  between male and female wood ducks
• Differences in position of functional groups
  attached to ring structure (pg 36)

An Estrogen
Testosterone
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Fig. 3-5b, p.36
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Condensation Reactions

• Form polymers from subunits
• Enzymes remove -OH from one molecule, H from
  another, form bond between two molecules
• Discarded atoms can join to form water

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Condensation
Fig. 3-6a, p.38
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Hydrolysis

• A type of cleavage reaction
• Breaks polymers into smaller units
• Enzymes split molecules into two or more parts
• An -OH group and an H atom derived from water are
  attached at exposed sites

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Hydrolysis
Fig. 3-6b, p.38
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Condensation and hydrolysis
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Consider Methane

• Methane, a lifeless hydrocarbon, is present in
  vast methane hydrate deposits beneath the ocean
  floor
• Methane hydrate disintegration can be explosive,
  causing a chain reaction that depletes oxygen
• Evidence points to such an event ending the
  Permian period 250 million years ago

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Methane
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Section 3.3 Weblinks and InfoTrac

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  below (articles subject to change)
• Section 3.3 Essentials of Glycobiology Online
• Section 3.3 Complex Carbohydrates
• Section 3.3 Carbohydrates The Next Generation
  (from various sources). Kitty Kevin. Food
  Processing, Feb. 1996.
• Section 3.3 Chitin Craze. Elizabeth Pennisi.
  Science News, July 31, 1993.

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Carbohydrates

• Monosaccharides
• (simple sugars)
• Oligosaccharides
• (short-chain carbohydrates)
• Polysaccharides
• (complex carbohydrates)

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Monosaccharides

• Simplest carbohydrates
• Most are sweet tasting, water soluble
• Most have 5- or 6-carbon backbone
• Glucose (6 C) Fructose (6 C)
• Ribose (5 C) Deoxyribose (5 C)

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Two Monosaccharides
Fig. 3-7, p.38
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Disaccharides
glucose
fructose

• Type of oligosaccharide
• Two monosaccharides covalently bonded
• Formed by condensation reaction

H2O
sucrose
Fig. 3-7b, p.38
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Polysaccharides

• Straight or branched chains of many sugar
  monomers
• Most common are composed entirely of glucose
• Cellulose
• Starch (such as amylose)
• Glycogen

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Cellulose Starch

• Differ in bonding patterns between monomers
• Cellulose - tough, indigestible, structural
  material in plants
• Starch - easily digested, storage form in plants

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Cellulose and Starch
Fig. 3-8, p.38
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Glycogen

• Sugar storage form in animals
• Large stores in muscle and liver cells
• When blood sugar decreases, liver cells degrade
  glycogen, release glucose

Fig. 3-9, p.38
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Fig. 3-9, p.39
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Structure of starch and cellulose
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Chitin

• Polysaccharide
• Nitrogen-containing groups attached to glucose
  monomers
• Structural material for hard parts of
  invertebrates, cell walls of many fungi

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Chitin

• Chitin occurs in protective body coverings of
  many animals, including ticks (pg 39)

Fig. 3-10a, p.39
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Fig. 3-10b, p.39
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Section 3.4 Weblinks and InfoTrac

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  this chapter online or click highlighted articles
  below (articles subject to change)
• Section 3.4 The Structures and Functions of
  Lipids in Biological Systems
• Section 3.4 Biochemistry of Lipids
• Section 3.4 How Fats Work
• Section 3.4 Cholesterol The Good, the Bad, and
  the Ugly. Terri D'Arrigo. Diabetes Forecast, Aug.
  1999.
• Section 3.4 Fatty Acids The Dangerous and the
  Not So Dangerous. Michael Laposata. Medical
  Laboratory Observer, Nov. 1997.
• Section 3.4 The Next Generation of Fat
  Replacers. Kitty Kevin. Food Processing, July
  1995.

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Lipids

• Most include fatty acids
• Fats
• Phospholipids
• Waxes
• Sterols and their derivatives have no fatty acids
• Tend to be insoluble in water

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Fats

• Fatty acid(s) attached to glycerol
• Triglycerides are most common

Fig. 3-12, p.40
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Fatty Acids

• Carboxyl group (-COOH) at one end
• Carbon backbone (up to 36 C atoms)
• Saturated - Single bonds between carbons
• Unsaturated - One or more double bonds

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Three Fatty Acids
Fig. 3-11, p.40
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Fatty acids
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Triglyceride formation
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Fig. 3-12a, p.40
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Phospholipids

• Main components of cell membranes

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Phospholipid structure
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Waxes

• Long-chain fatty acids linked to long chain
  alcohols or carbon rings
• Firm consistency, repel water
• Important in water-proofing

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Waxes

• Bees construct honeycombs from their own waxy
  secretions

Fig. 3-14, p.41
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Sterols and Derivatives

• No fatty acids
• Rigid backbone of four fused-together carbon
  rings
• Cholesterol - most common type in animals

Fig. 3-14, p.41
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Cholesterol
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Section 3.5 Weblinks and InfoTrac

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  below (articles subject to change)
• Section 3.5 The Amino Acid Collection
• Section 3.5 IMB Jena Image Library of Biological
  Macromolecules
• Section 3.5 Got Silk? Adam Summers. Natural
  History, July 2001.
• Section 3.5 Single-Cell Proteins (bacteria turn
  hydrocarbons into protein supplements). John
  Litchfield. Science, Feb. 11, 1983.

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Amino Acid Structure
carboxyl group
amino group
R group
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Structure of an amino acid
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Properties of Amino Acids

• Determined by the R group
• Amino acids may be
• Non-polar
• Uncharged, polar
• Positively charged, polar
• Negatively charged, polar

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Protein Synthesis

• Protein is a chain of amino acids linked by
  peptide bonds
• Peptide bond
• Type of covalent bond
• Links amino group of one amino acid with carboxyl
  group of next
• Forms through condensation reaction

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Fig. 3-15b, p.42
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Fig. 3-15c, p.42
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Fig. 3-15d, p.42
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Fig. 3-15e, p.42
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Peptide bond formation
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Primary Structure

• Sequence of amino acids
• Unique for each protein
• Two linked amino acids dipeptide
• Three or more polypeptide
• Backbone of polypeptide has N atoms
• -N-C-C-N-C-C-N-C-C-N-

one peptide group
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Protein Shapes

• Fibrous proteins
• Polypeptide chains arranged as strands or sheets
• Globular proteins
• Polypeptide chains folded into compact, rounded
  shapes

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Primary Structure Protein Shape

• Primary structure influences shape in two main
  ways
• Allows hydrogen bonds to form between different
  amino acids along length of chain
• Puts R groups in positions that allow them to
  interact

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Secondary Structure

• Hydrogen bonds form between different parts of
  polypeptide chain
• These bonds give rise to coiled or extended
  pattern
• Helix or pleated sheet

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Examples of Secondary Structure
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Secondary and tertiary structure
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Tertiary Structure
heme group

• Folding as a result of interactions between R
  groups

coiled and twisted polypeptide chain of one
globin molecule
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Quaternary Structure

• Some proteins are made up of more than one
  polypeptide chain

Hemoglobin
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alpha globin
alpha globin
heme
beta globin
beta globin
Fig. 3-17, p.44
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Globin and hemoglobin structure
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Section 3.6 Weblinks and InfoTrac

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• Section 3.6 The Principles of Protein Structure
• Section 3.6 The Protein Problem
• Section 3.6 Folding_at_Home
• Section 3.6 Misshapes and Misfits Protein
  Misfolding and Disease. Sarah Perrett. Chemistry
  and Industry, May 18, 1998.

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Polypeptides with Attached Organic Compounds

• Lipoproteins
• Proteins combined with cholesterol,
  triglycerides, phospholipids
• Glycoproteins
• Proteins combined with oligosaccharides

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Globin and hemoglobin structure
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Denaturation

• Disruption of three-dimensional shape
• Breakage of weak bonds
• Causes of denaturation
• pH
• Temperature
• Destroying protein shape disrupts function

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Fig. 3-18c, p.45
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Structure of an amino acid
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a Normal amino acid sequence at the start of a
beta change for hemoglobin
GLUTAMATE
VALINE
HISTIDINE
LEUCINE
THREONINE
PROLINE
GLUTAMATE
Fig. 3-18a, p.45
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b One amino acid substitution results in the
abnormal beta chain in HbS molecules. During
protein synthesis, valine was added instead of
glutamate at the sixth position of the growing
polypeptide chain.
VALINE
HISTIDINE
LEUCINE
THREONINE
PROLINE
VALINE
GLUTAMATE
Fig. 3-18b, p.45
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c Glutamate has an overall negative charge
valine has no net charge. The difference gives
rise to a water-repellant, sticky patch on HbS
molcules. They stick together because of that
patch, forming 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.)
sickle cell
normal cell
Fig. 3-18c, p.45
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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
Fig. 3-18d, p.45
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Section 3.7 Weblinks and InfoTrac

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• Section 3.7 Zooming into DNA
• Section 3.7 Molecular Biologists Watson and
  Crick. Robert Wright. Time, Mar. 29, 1999.

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Nucleotide Structure

• Sugar
• Ribose or deoxyribose
• At least one phosphate group
• Base
• Nitrogen-containing
• Single or double ring structure

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Nucleotide Functions

• Energy carriers
• Coenzymes
• Chemical messengers
• Building blocks for nucleic acids

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ATP - A Nucleotide
base
three phosphate groups
sugar
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Nucleic Acids
Adenine
Cytosine

• Composed of nucleotides
• Single- or double-stranded
• Sugar-phosphate backbone

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Structure of ATP
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Bonding Between Bases in Nucleic Acids
THYMINE (T) base with a single-ring structure
CYTOSINE (C) base with a single-ring structure
Fig. 3-20, p.46
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Nucleotide subunits of DNA
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DNA

• Double-stranded
• Consists of four types of nucleotides
• A bound to T
• C bound to G

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RNA

• Usually single strands
• Four types of nucleotides
• Unlike DNA, contains the base uracil in place of
  thymine
• Three types are key players in protein synthesis

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Fig. 3-22, p.49
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Fig. 3-23, p.49
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Fig. 3-23, p.49