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Chapter 4 Lecture Outline Chemical Building Blocks Atoms and Molecules Big fleas have little fleas Upon their backs to bite ‘em Little fleas have littler fleas And so ad infinitum Atoms and Elements Physical world composed of 92 elements Simplest building blocks

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chapter 4 lecture outline

Chapter 4Lecture Outline

Chemical Building Blocks

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

atoms and molecules
Atoms and Molecules

Big fleas have little fleas

Upon their backs to bite ‘em

Little fleas have littler fleas

And so ad infinitum

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

atoms and elements
Atoms and Elements
  • Physical world composed of 92 elements
  • Simplest building blocks
  • Atom - smallest unit of an element

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

periodic table of the elements
Periodic Table of the Elements

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

atomic components
Atomic Components
  • Atoms are composed of 3 subatomic particles
  • Electrons – negatively charged
  • Protons – positively charged
  • Neutrons – no charge (neutral)
  • Protons & neutrons are contained in the nucleus
  • Electrons orbit the nucleus
  • Gain or loss of an electron: ion

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

atomic and mass numbers
Atomic and Mass Numbers
  • Atomic Number: Number of Protons
  • Determines the element’s properties
  • Mass Number: Number of Protons +

Number of Neutrons

  • Isotopes: different numbers of neutrons
  • Unstable isotopes: Radioisotopes

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

covalent bonds
Covalent Bonds
  • Electrons are held in shells
  • Atoms are stable when

its shells are filled

  • Atoms share electrons

to fill these shells

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

covalent bonds examples of molecules
Covalent Bonds – Examples of Molecules

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

noncovalent bonds
Noncovalent Bonds
  • Link molecules together (intermolecular)
    • Much weaker than covalent
    • Much more prevalent
  • Hydrogen bonds: very common in biology
    • Attraction between partial charges
    • Hold biological molecules together
  • Ionic bonds: form between charged particles (Ions)

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

hydrogen and ionic bonds
Hydrogen and Ionic Bonds

Ionic bonds form

between Na+ and Cl-

Hydrogen bonds

form between

water molecules

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

hydrogen bonds water
Hydrogen bonds: Water

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

hydrogen bonds are like velcro
Hydrogen bonds are like Velcro

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

velcro and h bonds form weak temporary bonds
Velcro and H Bonds form weak, temporary bonds
  • Each Velcro link is weak
  • Each H bond is weak
  • Many Velcros are strong
  • Many H bonds are strong

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

ionic bonds salt crystals
Ionic Bonds: Salt crystals
  • Form between atoms of opposite charge
  • Weak in aqueous conditions
  • Strong in dry conditions
  • Ions are bound by polar water molecules

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

water molecules break up salt
Water molecules break up salt

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

rearranging atoms in molecules
Rearranging Atoms in Molecules
  • Chemical reactions:
    • Breaking covalent bonds
    • Forming new bonds
  • Require energy

3 H2 + N2 2 NH3

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

acids and bases
Acids and Bases
  • Acid: releases H+ in water

HCl + H2O  Cl- + H30+

  • Base: accepts H+ from water

NH3 + H20 NH4+ + OH-

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

slide18
pH
  • A measure of H+ concentration
  • The scale pH is from 0 to 14
  • Scale is 10X
    • More than 7 is basic
    • Less than 7 is acidic

Coke

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

buffers control ph
Buffers Control pH
  • Buffer - weak acid or base
  • Maintains pH within very narrow limits
    • Accepts H+ when pH is low
    • Releases H+ when pH is high

AH + H2O  A- + H3O

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

stop here
STOP HERE
  • To be Continued………..

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

carbon based molecules
Carbon-based Molecules
  • Biomolecules are mainly C and H
    • Carbon chains can be very long
  • O, S, P, and N are also present
    • These comprise functional groups
    • Functional groups allow molecules to interact
  • Biomolecules are combined to form polymers

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

what are biological molecules
Carbohydrates

Sugar

Starch

Cellulose

Fats

Lipids

Fatty acids

Cell membranes

Proteins

Amino acids

Collagen

Fibrin

Nucleic Acids

DNA

RNA

What are Biological Molecules?

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

carbohydrates simple sugars
Carbohydrates: Simple Sugars
  • Sugars are carbohydrate monomers
  • Used to store and release energy
    • Glucose plays a key role
  • Dehydration synthesis: combining sugars
  • What other kinds of sugars to you know?

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

other kinds of sugars
Other kinds of sugars:

Glucose

Fructose

Lactose

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

carbohydrates complex sugars
Carbohydrates – Complex Sugars
  • Monosaccharides – one sugar molecule
  • Disaccharides – two sugar molecules
  • Oligosaccharides – a few sugar molecules
  • Polysaccharides – many sugar molecules

Don’t ask me to define “few” or “many”

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

branched chain polysaccharide
Branched Chain Polysaccharide

Very complex

Indeed!

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

carbohydrates polymers
Carbohydrates: Polymers

Cellulose: Structure

Starch: Energy storage

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

nucleic acids nucleotides
Nucleic Acids: Nucleotides
  • Made of three parts
    • Sugar (ribose), phosphate, and nitrogen base
  • Monomers can be used as “energy currency”

ATP

Energy

Energy

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

slide29

Nucleic Acids: DNA and RNA

  • Information storage molecules

Phosphate Group

Bases

Nucleotide

Adenine (A)

Thymine (T)

Sugars

Ribose

Guanine (G)

Cytosine (C)

Uracil (C)

Deoxyribose

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

proteins amino acids
Proteins: Amino Acids
  • There are 20 amino acids
  • They all have:
    • Central C
    • Amino group (nitrogen)
    • Carboxyl Group
    • R group
  • Each amino acid differs in its R group
  • Amino acids link together to form proteins

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

kinds of r groups
Kinds of R Groups

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

proteins polypeptides
Proteins: Polypeptides
  • Amino acids are covalently linked
    • Peptide bonds C to N
  • Primary structure: sequence of amino acids
  • This determines folding of

the protein

NOT!!

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

proteins 3d structure
Proteins: 3D Structure

Telephone

cord

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

lipids fatty acids
Lipids: Fatty Acids

Charged polar end

  • Long hydrocarbon chains
    • Very hydrophobic
    • Oil and water don’t mix
  • Used for energy storage
    • Very high energy
    • Long-term storage

Lipid tail end

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

lipids structure
Lipids: Structure
  • Fats are bonded to glycerol with phosphate
  • Produces hydrophobic and hydrophilic parts
    • Forms a bilayer in water
    • Structure of cell membrane

Lipid bilayer:

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

concept quiz
Concept Quiz

What types of intermolecular bonds are formed between biological molecules and hold them together?

  • Hydrogen bonds
  • Covalent bonds
  • Ionic bonds
  • All of the above
  • A & C

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

concept quiz37
Concept Quiz

What determines the folding pattern of a peptide into a completed protein?

  • The amino acid sequence (primary structure)
  • The source of the amino acids
  • The absorption of light
  • The size of the ribosomes used

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

concept quiz38
Concept Quiz

_________ bonds are the strongest bonds formed between molecules.

  • Hydrogen
  • Covalent
  • Ionic
  • Non-polar

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

concept quiz39
Concept Quiz

The main difference between the 20 amino acids is the

  • central carbon.
  • amine group.
  • acid group.
  • side chain.

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e

slide40

Process Animation 4.1Formation of Covalent Bonds

Macintosh

Windows

© 2006 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 3/e