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Outline. Organic vs Inorganic Functional Groups and Isomers Macromolecules Carbohydrates Lipids Proteins Nucleic Acids. Inorganic – Chemistry of elements other than carbon Organic – Carbon-based chemistry. Organic Molecules. Inorganic. Organic. Usually with + & - ions.

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outline
Outline
  • Organic vs Inorganic
  • Functional Groups and Isomers
  • Macromolecules
    • Carbohydrates
    • Lipids
    • Proteins
    • Nucleic Acids
organic molecules
Inorganic – Chemistry of elements other than carbon

Organic – Carbon-based chemistry

Organic Molecules
  • Inorganic
  • Organic
  • Usually with+ & - ions
  • Always containcarbon and hydrogen
  • Usuallyionic bonding
  • Alwayscovalent bonding
  • Always withfew atoms
  • Often quite large, withmany atoms
  • Often associated with nonliving matter
  • Usually associatedliving systems
carbon atom
Carbon Atom
  • Carbon atoms:
    • Contain a total of 6 electrons
    • Only four electrons in the outer shell
    • Very diverse as one atom can bond with up to four other atoms
  • Often bonds with other carbon atoms to make hydrocarbons
    • Can produce long carbon chains like octane
    • Can produce ring forms like cyclohexane
functional groups and isomers
Functional Groups and Isomers
  • Functional groups:
    • Specific combinations of bonded atoms
    • Attached as a group to other molecules
      • Always react in the same manner, regardless of where attached
      • Determine activity and polarity of large organic molecules
  • Many functional groups, but only a few are of major biological importance
biologically important functional groups
Biologically ImportantFunctional Groups

R

R

SH

OH

O

O

R

R

C

C

OH

H

O

R

R

C

H

R

N

H

O

R

R

C

OH

  • Group
  • Structure
  • Compound
  • Significance
  • Hydroxyl
  • Alcohols
  • Polar, forms H-bonds; some sugarsand amino acids Example: Ethanol
  • Polar, forms H-bonds; some sugarsand amino acids; Example: Ethanol
  • Aldehydes
  • Polar; some sugarsExample: Formaldehyde
  • Carbonyl
  • Polar; some sugarsExample: Formaldehyde
  • Ketones
  • Polar; some sugarsExample: Acetone
  • Polar; some sugarsExample: Acetone
  • CarboxylicAcids
  • Polar, acidic; fats and amino acidsExample: Acetic acid
  • Carboxyl
  • Polar, acidic; fats and amino acidsExample: Acetic acid
  • Polar, basic; amino acidsExample: Tryptophan
  • Amino
  • Amines
  • Polar, acidic; some amino acidsExample: Adenosine triphosphate
  • Polar, basic; amino acidsExample: Tryptophan
  • Sulfhydryl
  • Thiols
  • Disulfide Bonds; some amino acidsExample: Ethanethiol
  • Disulfide Bonds; some amino acidsExample: Ethanethiol
  • OrganicPhosphates
  • Polar, acidic; some amino acidsExample: Adenosine triphosphate
  • Phosphate
isomers
Isomers
  • Isomers - organic molecules that have:
    • Identical molecular formulas, but
    • Differing internal arrangement of atoms
macromolecules
Macromolecules
  • Some molecules called macromolecules because of their large size
  • Usually consist of many repeating units
    • Resulting molecule is a polymer (many parts)
    • Repeating units are called monomers
  • Some examples:
  • Category
  • Example
  • Subunit(s)
  • Lipids
  • Fat
  • Glycerol & fatty acids
  • Carbohydrates
  • Polysaccharide
  • Monosaccharide
  • Proteins
  • Polypeptide
  • Amino acid
  • Nucleic Acids
  • DNA, RNA
  • Nucleotide
dehydration and hydrolysis
Dehydration and Hydrolysis
  • Dehydration - Removal of water molecule
    • Used to connect monomers together to make polymers
    • Polymerization of glucose monomers to make starch
  • Hydrolysis - Addition of water molecule
    • Used to disassemble polymers into monomer parts
    • Digestion of starch into glucose monomers
  • Specific enzymes required for each reaction
    • Accelerate reaction
    • Are not used in the reaction
four classes of organics 1 carbohydrates
Four Classes of Organics:1 - Carbohydrates
  • Monosaccharides:
    • Single sugar molecule
    • Glucose, ribose, deoxyribose
  • Disaccharides:
    • Contain two monosaccharides joined during dehydration reaction
    • Sucrose
  • Polysaccharides:
  • Polymers of monosaccharides
    • Starch, cellulose, chitin
carbohydrates examples monosaccharides
Carbohydrates Examples:Monosaccharides
  • Single sugar molecules
  • Quite soluble and sweet to taste
  • Examples
    • Glucose (blood), fructose (fruit) and galactose
      • Hexoses - Six carbon atoms
      • Isomers of C6H12O6
    • Ribose and deoxyribose (in nucleotides)
      • Pentoses – Five carbon atoms
      • C5H10O5 & C5H10O4
carbohydrates examples disaccharides
Carbohydrates Examples:Disaccharides
  • Contain two monosaccharides joined by dehydration reaction
  • Soluble and sweet to taste
  • Examples
    • Sucrose
      • Table sugar, maple sugar
      • One glucose and one fructose joined by dehydration
    • Maltose
      • Malt sugar
      • Two glucoses joined by dehydration
carbohydrates examples polysaccharides 1
Carbohydrates Examples:Polysaccharides (1)
  • Polymers of monosaccharides
  • Low solubility; not sweet to taste
  • Examples
    • Starch
      • Polymer of glucose
      • Used for short-term energy storage
        • Plant starch
          • Often branched chain
          • Amylose, corn starch
        • Animal starch
          • Unbranched
          • Glycogen in liver and muscles
carbohydrates examples polysaccharides 2
Carbohydrates Examples:Polysaccharides (2)
  • More polysaccharide examples
    • Cellulose
      • Long, coiled polymer of glucose
      • Glucoses connected differently than in starch
      • Structural element for plants
      • Main component of wood and many natural fibers
      • Indigestible by most animals
    • Chitin
      • Polymer of glucose
      • Each glucose with an amino group
      • Very resistant to wear and digestion
      • Arthropod exoskeletons, cell walls of fungi
four classes of organics 2 lipids
Four Classes of Organics:2 - Lipids
  • Insoluble in water
    • Long chains of repeating CH2 units
    • Renders molecule nonpolar
  • Types of Lipids
  • Type
  • Organismal Uses
  • Human Uses
  • Fats
  • Long-term energy storage & thermal insulation in animals
  • Butter, lard
  • Oils
  • Long-term energy storage in plants and their seeds
  • Cooking oils
  • Phospholipids
  • Component of plasma membrane
  • No-stick pan spray
  • Steroids
  • Component of plasma membrane; hormones
  • Medicines
  • Waxes
  • Wear resistance; retain water
  • Candles, polishes
types of lipids triglycerides 1
Types of Lipids:Triglycerides (1)
  • Triglycerides (Fats)
    • Long-term energy storage
    • Backbone of one glycerol molecule
      • Three-carbon alcohol
      • Each has an OH- group
    • Three fatty acids attached to each glycerol molecule
      • Long hydrocarbon chain
        • Saturated - no double bonds between carbons
        • Unsaturated - 1 double bonds between carbons
      • Carboxylic acid at one end
      • Carboxylic acid connects to –OH on glycerol in dehydration reaction
types of lipids phospholipids 2
Types of Lipids:Phospholipids (2)
  • Phospholipids
  • Derived from triglycerides
    • Glycerol backbone
    • Two fatty acids attached instead of three
    • Third fatty acid replaced by phosphate group
      • The fatty acids are nonpolar and hydrophobic
      • The phosphate group is polar and hydrophilic
  • Molecules self arrange when placed in water
    • Polar phosphate “heads” next to water
    • Nonpolar fatty acid “tails” overlap and exclude water
    • Spontaneously form double layer & a sphere
types of lipids steroids waxes 3
Types of Lipids:Steroids & Waxes (3)
  • Steroids
    • Cholesterol, testosterone, estrogen
    • Skeletons of four fused carbon rings
  • Waxes
    • Long-chain fatty acid bonded to a long-chain alcohol
      • High melting point
      • Waterproof
      • Resistant to degradation
four classes of organics 3 proteins
Four Classes of Organics:3 -Proteins
  • Functions
    • Support – Collagen
    • Enzymes – Almost all enzymes are proteins
    • Transport – Hemoglobin; membrane proteins
    • Defense – Antibodies
    • Hormones – Many hormones; insulin
    • Motion – Muscle proteins, microtubules
protein subunits the amino acids
Protein Subunits:The Amino Acids
  • Proteins are polymers of amino acids
  • Each amino acid has a central carbon atom (the alpha carbon) to which are attached
    • a hydrogen atom,
    • an amino group –NH2,
    • A carboxylic acid group –COOH,
    • and one of 20 different types of –R (remainder) groups
  • There are 20 different amino acids that make up proteins
  • All of them have basically the same structure except for what occurs at the placeholder R
proteins the polypeptide backbone
Proteins:The Polypeptide Backbone
  • Amino acids joined together end-to-end
    • COOH of one AA covalently bonds to the NH2 of the next AA
    • Special name for this bond - Peptide Bond
      • Two AAs bonded together – Dipeptide
      • Three AAs bonded together – Tripeptide
      • Many AAs bonded together – Polypeptide
    • Characteristics of a protein determined by composition and sequence of AA’s
    • Virtually unlimited number of proteins
protein molecules levels of structure
Protein Molecules:Levels of Structure
  • Primary:
    • Literally, the sequence of amino acids
    • A string of beads (up to 20 different colors)
  • Secondary:
    • The way the amino acid chain coils or folds
    • Describing the way a knot is tied
  • Tertiary:
    • Overall three-dimensional shape of a polypeptide
    • Describing what a knot looks like from the outside
  • Quaternary:
    • Consists of more than one polypeptide
    • Like several completed knots glued together
protein folding diseases
Protein-folding Diseases
  • Assembly of AA’s into protein extremely complex
  • Process overseen by “chaperone” molecules
    • Inhibit incorrect interactions between R groups as polypeptide grows
    • Defects in these chaperones can corrupt the tertiary structure of proteins
    • Mad cow disease could be due to mis-folded proteins
four classes of organics 4 nucleic acids
Four Classes of Organics:4 -Nucleic Acids
  • Polymers of nucleotides
  • Very specific cell functions
    • DNA (deoxyribonucleic acid)
      • Double-stranded helical spiral (twisted ladder)
      • Serves as genetic information center
      • In chromosomes
    • RNA (ribonucleic acid)
      • Part single-stranded, part double-stranded
      • Serves primarily in assembly of proteins
      • In nucleus and cytoplasm of cell
the nucleotides of nucleic acids
The Nucleotides ofNucleic Acids
  • Three components:
      • A phosphate group,
      • A pentose sugar (ribose or deoxyribose), and
      • A nitrogenous base (4 kinds in DNA, 3 kinds in RNA, 3 common to both
    • Nucleotide subunits connected end-to-end to make nucleic acid
    • Sugar of one connected to the phosphate of the next
    • Sugar-phosphate backbone
comparison of dna rna
Comparison of DNA & RNA
  • Table 3.4
  • Feature
  • DNA
  • RNA
  • Sugar
  • Deoxyribose
  • Ribose
  • Bases
  • Cytosine, guanine;adenine, thymine
  • Cytosine, guanine;
  • adenine, uracil
  • Strands
  • Double-stranded; Pairing across strands
  • Mostly single stranded
  • Helix
  • Yes
  • No
  • Function
  • Heredity; cellular control center
  • Interprets genetic info; protein synthesis
  • Where
  • Chromosomes of cell nucleus
  • Cell nucleus and cytoplasm
other nucleic acids
Other Nucleic Acids
  • ATP (adenosine triphosphate) is composed of adenine, ribose, and three phosphates
  • In cells, one phosphate bond is hydrolyzed – Yields:
    • The molecule ADP (adenosine diphosphate)
    • An inorganic phosphate molecule pi
    • Energy
  • Other energy sources used to put ADP and pi back together again
review
Review
  • Organic vs Inorganic
  • Functional Groups and Isomers
  • Macromolecules
    • Carbohydrates
    • Lipids
    • Proteins
    • Nucleic Acids