Chemical Level of Organization Chapter 2

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Chemical Level of OrganizationChapter 2

• Atoms, Molecules and Bonds

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What Are Atoms?

• Smallest particles that retain properties of an
  element, smallest particle of a substance
• Made up of subatomic particles
• Protons ()
• Electrons (-)
• Neutrons (0) no charge)

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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
• Hydrogen
• Carbon
• Nitrogen
• P and S

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Representing the Hydrogen Atom
Shell model
Ball model
Electron density cloud
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Atomic Number and Mass

• Number of protons
• All atoms of an element have the same atomic
  number
• Mass of P on N
• 1.0079 ----- Atomic Mass
• H element symbol
• 1 --- Atomic number

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Mass Number

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

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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

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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

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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

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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
• Compound /- atoms

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Important Bonds in Biological Molecules

• Ionic Bonds
• Covalent Bonds
• Hydrogen Bonds

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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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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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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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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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hydrogen bond
Examples of Hydrogen Bonds
water molecule
ammonia molecule
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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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Organic CompoundsHydrogen and other elements
covalently bonded to carbon

• The Biomolecules
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids

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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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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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Glycogen

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

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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
• 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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Sterols and Derivatives

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

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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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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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Tertiary Structure

• Folding as a result of interactions between R
  groups

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Quaternary Structure Some proteins are made up
of more than one polypeptide chain
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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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Nucleotide Structure

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

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

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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