Chemical Foundations for Cells

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Chemical Foundations for Cells

• Chapter 6

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Chemical Benefits and Costs

• Understanding of chemistry provides fertilizers,
  medicines, etc.
• Chemical pollutants damage ecosystems

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Elements

• Fundamental forms of matter
• Cant be broken apart by normal means
• 92 occur naturally on Earth

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Most Common Elements in Living Organisms

• Oxygen 65
• Hydrogen 9.5
• Carbon 18.5
• Nitrogen 3.3

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What Are Atoms?

• Smallest particles that retain properties of an
  element
• Made up of subatomic particles
• Protons ()
• Electrons (-)
• Neutrons (no charge)

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Hydrogen and Helium Atoms
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Atomic Number

• Number of protons
• All atoms of an element have the same atomic
  number
• Atomic number of hydrogen 1
• Atomic number of carbon 6

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Mass Number

• Number of protons
• Number of neutrons
• Isotopes vary in mass number

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Isotopes

• Atoms of an element with different numbers of
  neutrons (different mass numbers)
• Carbon 12 has 6 protons, 6 neutrons
• Carbon 14 has 6 protons, 8 neutrons

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What Determines Whether Atoms Will Interact?

• The number and arrangement of their electrons
• Atoms seek to be more stable complete orbitals

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Electrons

• Carry a negative charge
• Repel one another
• Are attracted to protons in the nucleus
• Move in orbitals - volumes of space that surround
  the nucleus

y
Z
X
When all p orbitals are full
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Electron Orbitals

• Orbitals can hold up to two electrons
• Atoms differ in the number of occupied orbitals
• Orbitals closest to nucleus are lower energy and
  are filled first

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Shell Model

• First shell
• Lowest energy
• Holds 1 orbital with up to 2 electrons
• Second shell
• 4 orbitals hold up to 8 electrons

CALCIUM 20p , 20e-
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Electron Vacancies

• Unfilled shells make atoms likely to react
• Hydrogen, carbon, oxygen, and nitrogen all have
  vacancies in their outer shells

CARBON 6p , 6e-
NITROGEN 7p , 7e-
HYDROGEN 1p , 1e-
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Chemical Bonds, Molecules, Compounds

• Bond is union between electron structures of
  atoms
• Atoms bond to form molecules
• Molecules may contain atoms of only one element -
  O2
• Molecules of compounds contain more than one
  element - H2O

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Chemical Bookkeeping

• Use symbols for elements when writing formulas
• Formula for glucose is C6H12O6
• 6 carbon atoms
• 12 hydrogen atoms
• 6 oxygen atoms

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Chemical Bookkeeping

• Chemical equation shows reaction
• Reactants ---gt Products
• Equation for photosynthesis
• 6CO2 6H2O ---gt C6H12O12 6H2O

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Important Bonds in Biological Molecules

• Ionic Bonds
• Covalent Bonds
• Hydrogen Bonds

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Covalent Bonding

• Atoms share a pair or pairs of electrons to fill
  outermost shell

• Single covalent bond
• Double covalent bond
• Triple covalent bond

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Nonpolar Covalent Bonds

• Atoms share electrons equally
• Nuclei of atoms have same number of protons
• Example Hydrogen gas (H-H)

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Polar Covalent Bonds

• Number of protons in nuclei of participating
  atoms is NOT equal
• Electrons spend more time near nucleus with most
  protons
• Water - Electrons more attracted to O nucleus
  than to H nuclei

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Ion Formation

• Atom has equal number of electrons and protons -
  no net charge
• Atom loses electron(s), becomes positively
  charged ion
• Atom gains electron(s), becomes negatively
  charged ion

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Ionic Bonding

• One atom loses electrons, becomes positively
  charged ion
• Another atom gains these electrons, becomes
  negatively charged ion
• Charge difference attracts the two ions to each
  other

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Formation of NaCl

• Sodium atom (Na)
• Outer shell has one electron
• Chlorine atom (Cl)
• Outer shell has seven electrons
• Na transfers electron to Cl forming Na and Cl-
• Ions remain together as NaCl

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Formation of NaCl
7mm
electron transfer
SODIUM ATOM 11 p 11 e-
CHLORINE ATOM 17 p 17 e-
CHLORINE ION 17 p 18 e-
SODIUM ION 11 p 10 e-
Fig. 2.10a, p. 26
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Hydrogen Bonding

• Molecule held together by polar covalent bonds
  has no NET charge
• However, atoms of the molecule carry different
  charges
• Atom in one polar covalent molecule can be
  attracted to oppositely charged atom in another
  such molecule

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Examples of Hydrogen Bonds
one large molecule
another large molecule
a large molecule twisted back on itself
Fig. 2.12, p. 27
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Hydrogen Ions H

• Unbound protons
• Have important biological effects
• Form when water ionizes

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The pH Scale

• Measures H concentration of fluid
• Change of 1 on scale means 10X change in H
  concentration
• Highest H Lowest H
• 0---------------------7-------------------14
• Acidic Neutral Basic

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Acids Bases

• Acids
• Donate H when dissolved in water
• Acidic solutions have pH lt 7
• Bases
• Accept H when dissolved in water
• Acidic solutions have pH gt 7

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Properties of Water

• Polarity
• Temperature-Stabilizing
• Cohesive
• Solvent

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Water Is a Polar Covalent Molecule

• Molecule has no net charge
• Oxygen end has a slight negative charge
• Hydrogen end has a slight positive charge

O
H
H
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Liquid Water

H

H

_
O
H
O

_

H

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Water Cohesion

• Hydrogen bonding holds molecules in liquid water
  together
• Creates surface tension
• Allows water to move as continuous column upward
  through stems of plants

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Temperature-Stabilizing Effects

• Liquid water can absorb much heat before its
  temperature rises
• Why?
• Much of the added energy disrupts hydrogen
  bonding rather than increasing the movement of
  molecules

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Why Ice Floats

• In ice, hydrogen bonds lock molecules in a
  lattice
• Water molecules in lattice are spaced farther
  apart then those in liquid water
• Ice is less dense than water

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Water Is a Good Solvent

• Ions and polar molecules dissolve easily in water
  
• When solute dissolves, water molecules cluster
  around its ions or molecules and keep them
  separated

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Spheres of Hydration
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Diffusion

• Brownian motion molecules are in constant
  motion
• Diffusion movement from area of high
  concentration to area of low concentration
• Affected by
• Concentration
• Temperature or agitation
• Pressure

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Dynamic Equilibrium

• Molecules are still in motion
• No net gain or loss of molecules
• Living systems seek to achieve

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Organic Compounds

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

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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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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
enzyme action at functional groups
Fig. 3.4a, p. 37
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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
enzyme action at functional groups
Fig. 3.4b, p. 37
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Carbohydrates energy source

• Monosaccharides
• (simple sugars)
• Disaccharides
• (two simple sugars)
• 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
glucose
fructose
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Disaccharides
glucose
fructose

• Two monosaccharides covalently bonded
• Formed by condensation reaction

H2O
sucrose
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Polysaccharides

• Straight or branched chains of many saccharides
• Most common are composed entirely of glucose
• Cellulose
• tough, indigestible
• structural material in plants
• Starch
• easily digested
• storage form in plants
• Glycogen
• sugar storage form in animals
• Chitin
• structural material for hard parts of
  invertebrates
• cell walls of many fungi

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Lipids

• Most include fatty acids
• Fats
• Phospholipids
• Waxes
• Tend to be insoluble in water
• Energy source, insulation protection

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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 AcidsWhat difference does the double
bond make?
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Fats

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

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Proteins

• Carbon, hydrogen, oxygen, nitrogen sulfur
• Amino acid building blocks
• AA linked by peptide bonds
• Enzymes
• Build tissue

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Enzymes

• Protein
• Act as catalyst
• Helps reaction happen faster or at lower
  temperatures
• Substrate specific shapes
• Lock key system
• Recycled not used up

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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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Nucleic Acids

• Carbon, hydrogen, oxygen, nitrogen phosphorus
• Nucleotides building blocks
• DNA, RNA
• Genetic information