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The Chemical Building Blocks of Life

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Title: The Chemical Building Blocks of Life


1
The Chemical Building Blocks of Life
  • Organic Chemistry

2
Comparison of Molecules
  • Inorganic Chemistry of elements other than
    carbon
  • Organic Carbon-based chemistry
  • Organic
  • Inorganic
  • Always containcarbon and hydrogen
  • Usually with - ions
  • Alwayscovalent bonding
  • Usuallyionic bonding
  • Often quite large, withmany atoms
  • Always withfew atoms
  • Usually associatedliving systems
  • Often associated with nonliving matter

3
  • All living things are mostly composed of 4
    elements H, O, N, C "honk"
  • Compounds are broken down into 2 general
    categories
  • Inorganic Compounds
  • Do not contain carbon
  • Organic compounds
  • Contain significant amounts of carbon.
  • Often found with common "functional groups"
    more on this in a minute!

4
Why Carbon?
  • Carbon is essential to life for several reasons
  • It can form strong stable (usually nonpolar)
    covalent bonds
  • It can form up to 4 chemical bonds due to 4
    valence electrons
  • It can form multiple bonds

                                               
                                                  
                                                  
 
5
More on the Carbon Atom
  • Carbon atoms
  • Contain a total of 6 electrons
  • Often bonds with other carbon atoms to make
    hydrocarbons
  • Can produce long carbon chains like octane
  • Can produce ring forms like cyclohexane

6
  • Carbon skeletons vary in many ways

Ethane
Propane
Carbon skeletons vary in length.
Isobutane
Butane
Skeletons may be unbranched or branched.
1-Butene
2-Butene
Skeletons may have double bonds, which can vary
in location.
Cyclohexane
Benzene
Figure 3.1, bottom part
Skeletons may be arranged in rings.
7
Functional groups help determine the properties
of organic compounds
  • Functional groups
  • specific groups of atoms attached to carbon
    backbones
  • retain definite chemical properties
  • Functional groups are the groups of atoms that
    participate in chemical reactions
  • Ex. Hydroxyl groups are characteristic of
    alcohols
  • Ex. The carboxyl group acts as an acid

8
Table 3.2
9
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
  • Subunit(s)
  • Example
  • Category
  • Glycerol fatty acids
  • Fat
  • Lipids
  • Monosaccharide
  • Polysaccharide
  • Carbohydrates
  • Amino acid
  • Polypeptide
  • Proteins
  • Nucleotide
  • DNA, RNA
  • Nucleic Acids

10
Cells make a huge number of large molecules
from a small set of small molecules
  • Most of the large molecules in living things are
    macromolecules called polymers
  • Polymers are long chains of smaller molecular
    units called monomers (building blocks)
  • A huge number of different polymers can be made
    from a small number of monomers

11
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

12
  • Cells link monomers to form polymers by
    dehydration synthesis, removes OH and H during
    synthesis of a new molecule.

1
2
3
Unlinked monomer
Short polymer
Removal ofwater molecule
1
2
3
4
Longer polymer
Figure 3.3A
13
  • Polymers are broken down to monomers by the
    reverse process, hydrolysis. (Breaks a covalent
    bond by adding OH and H.)

1
2
3
4
Addition ofwater molecule
1
2
3
Figure 3.3B
14
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15
The Major Organic Groups
16
What you need to know
  • The monomer of each group
  • The function of each group
  • The characteristics of each group
  • Unique properties of each group

17
Carbohydrates
  • Carbohydrates are loosely defined as molecules
    that contain carbon, hydrogen, and oxygen in a
    121 ratio.
  • monosaccharides - simple sugars
  • disaccharides - two monosaccharides joined by a
    covalent bond
  • polysaccharides
  • made of many
  • monosaccharide
  • subunits

18
Function
  • Primary Function Quick Energy!

19
Monosaccharides are the simplest carbohydrates
  • Monosaccharides are single-unit sugars
  • These molecules typically have a formula that is
    a multiple of CH2O
  • Hydrogen to oxygen ratio is 21.
  • Monosaccharides are the fuels for cellular work

Hi Honey Im home!
Youre so sweet!
Figure 3.4A
20
  • The monosaccharides glucose and fructose are
    isomers
  • They contain the same atoms but in different
    arrangements

Glucose
Fructose
Figure 3.4B
21
Isomers
  • isomers - alternative forms of the same substance
  • ex. 8 isomers of glucose

22
Cells link single sugars to form disaccharides
  • Monosaccharides can join to form disaccharides,
    such as sucrose (table sugar) and
    maltose (brewing sugar)
  • Which type of reaction forms
    a disaccharide?

Glucose
Glucose
Sucrose
Figure 3.5
Maltose
23
  • Polysaccharides are long chains of sugar units.
    These large molecules are polymers of hundreds or
    thousands of monosaccharides linked by
    dehydration synthesis.

Starch granules in potato tuber cells
Glucosemonomer
STARCH
Glycogen granules in muscle tissue
GLYCOGEN
Cellulose fibrils ina plant cell wall
CELLULOSE
Cellulosemolecules
Figure 3.7
24
Storage polysaccharides.
  • Starch - plant storage
  • Glycogen - animal storage
  • stored in the liver

Electron micrograph of a section of a liver cell
showing glycogen deposits as accumulations of
electron dense particles (arrows). Mitochondria
are also shown. x30,000.
25
Structural Carbohydrates
  • Cellulose - plants
  • alpha form or beta form of ring
  • animals can not digest cellulose - fiber
  • most abundant form of living terrestrial biomass.
  • Chitin - exoskeleton of
    arthropods and in fungi
    cell walls
  • modified form of
    cellulose

26
Lipids Basic Information
  • Lipids are loosely defined as groups of molecules
    that are insoluble in water.
  • Fats (triglycerides), oils, waxes, and steroids.
  • Phospholipids ( a special category) form the core
    of all biological membranes.

27
Lipids
  • Insoluble in water
  • Long chains of repeating CH2 units
  • Renders molecule nonpolar
  • Types of Lipids
  • Type
  • Human Uses
  • Organismal Uses
  • Butter, lard
  • Long-term energy storage thermal insulation in
    animals
  • Fats
  • Cooking oils
  • Long-term energy storage in plants and their seeds
  • Oils
  • No-stick pan spray
  • Component of plasma membrane
  • Phospholipids
  • Medicines
  • Component of plasma membrane hormones
  • Steroids
  • Candles, polishes
  • Wear resistance retain water
  • Waxes

28
Lipids are hydrophobic
  • Lipids repel water.
  • Ex. The cuticle of plants is waxy. The waxy
    covering makes the plant water proof and
    minimizes water loss.

29
Building Blocks of Lipids
  • One glycerol
  • Three fatty acids

30
Fats and Oils (triglycerides)
  • Fats and oils consist of a glycerol molecule with
    three attached fatty acids (triglyceride /
    triglycerol).
  • Saturated fats - all internal carbon atoms are
    bonded to at least two hydrogen atoms
  • usually a solid at room temperature
  • Unsaturated fats - at least one double bond
    between successive carbon atoms
  • Polyunsaturated - contains more than one double
    bond
  • usually liquid at room
    temperature

31
Fats as Energy Storage Molecules
  • Fats, on average, yield about 9 kcal per gram
    versus 4 kcal per gram for carbohydrates.
  • Animal fats are saturated while most plant fats
    are unsaturated.
  • Consumption of excess carbohydrates leads to
    conversion into starch, glycogen, or fats for
    future use.

32
Triglycerides
33
Saturated vs. unsaturated fatty acids
34
Hydrogenated Fats
  • Hydrogenation is used to add hydrogens to
    unsaturated fats and make them more solid. If a
    fat is FULLY saturated, it becomes solid, like
    candle wax. If it is PARTIALLY saturated (the
    same as partially hydrogenated) the result is a
    semi-solid, like margarine.

35
Steroids
  • Steroid hormones are crucial substances for the
    proper function of the body. They mediate a wide
    variety of vital physiological functions ranging
    from anti-inflammatory agents to regulating
    events during pregnancy.
  • They are synthesized and secreted into the
    bloodstream by endocrine glands such as the
    adrenal cortex and the gonads (ovary and testis).
  • Skeleton made of four fused carbon rings
  • Cholesterol is a steroid
    as well as the foundation
    for other steroids.

36
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37
Waxes
  • Long-chain fatty acid bonded to a long-chain
    alcohol
  • High melting point
  • Waterproof
  • Resistant to degradation
  • Why do you wax a car?

38
Waxes
39
Phospholipids
40
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

41
Phospholipid Structure
  • Phospholipid molecules have one end which is
    attracted to water while the other is repelled by
    it. The fatty acid end is not attracted to water
    and is called hydrophobic. At the other end of
    the molecule the phosphate group is attracted to
    water, it is said to be hydrophilic.

Hydrophilic Head
Hydrophobic Tail
42
Phospholipids Form Membranes
43
Proteins
  • Protein functions
  • enzyme (catalyst)
  • defense
  • transport
  • support
  • motion
  • regulation
  • storage

44
7 Classes of Proteins
  • Structural
  • Spider silk
  • Mammal hair
  • Fibers of tendons and lipids
  • Contractile
  • Muscular movement
  • Storage
  • Egg white
  • Defense
  • Antibodies
  • Transport
  • Hemoglobin
  • Signal
  • Some hormones
  • Chemical catalyst
  • Enzymes

45
Structure is related to function!
  • Structurally sophisticated.
  • Shape determines function and is crucial to the
    job of a protein.
  • Composed of amino acids joined together by
    peptide bonds.
  • 20 types of amino acids
  • Made at the ribosomes in a cell.

46
Monomer Amino Acids (AA)
  • contain an amino group (-NH2), a carboxyl group
    (-COOH) and a hydrogen atom, all bonded to a
    central carbon atom
  • twenty common AA grouped
    into five classes based on
    side groups
  • nonpolar AA
  • polar uncharged AA
  • charged AA
  • aromatic AA
  • special-function AA

47
Structural Formulas for the 20 Amino Acids
48
Amino Acids
  • Peptide bond links two amino acids.
  • A protein is composed of one or more long chains
    of amino acids linked by peptide bonds (dipetide
    and polypeptides).

49
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 AAs
  • Virtually unlimited number of proteins

50
Protein Structure
  • Protein function is determined by its shape.
  • The shape is driven by a number of noncovalent
    interactions such as hydrogen bonding.
  • Protein structure
  • primary - specific amino acid sequence
  • secondary - folding of amino acid chains

51
Protein Structure
  • tertiary - final folded shape of globular protein
  • quaternary - forms when two or more polypeptide
    chains associate to form a functional protein

52
Summary 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

53
Levels of Protein Organization
54
Examples of Fibrous Proteins
55
How enzymes workInduced Fit Model
  • The substrate (what the enzyme is going to work
    upon) comes into contact with the active site of
    the enzyme.
  • The enzyme wraps around the substrate breaking
    or forming bonds.
  • The product is released.

56
Enzyme at work
57
Unfolding Proteins
  • Denaturation refers to
    the process of changing
    a proteins shape.
  • usually rendered
    biologically inactive
  • salt-curing and pickling used to preserve food
  • temperature - high temperatures break bonds.
  • pH - designed to work at a specific pH!

58
Examples
  • You can not use fresh pineapple in jello but you
    can used canned! Why?
  • Pepsin is an enzyme that helps break down
    proteins in the stomach during digestion. It
    works at a pH of 2!
  • Trypsin is an enzyme that helps break down
    proteins as well. It works in the intestines with
    a pH of 8.
  • Many snake venoms are enzymes that work when
    directly injected into blood or tissue (pH
    7.4). If swallowed, they are denatured by the
    acidity of the stomach! (Dont try it, just take
    my word for it!)
  • Why do people without refrigeration salt their
    food for long term storage?

59
Nucleic Acids
60
Nucleic Acids
  • Deoxyribonucleic Acid (DNA)
  • Encodes information used to assemble proteins.
  • Ribonucleic Acid (RNA)
  • Reads DNA-encoded information to direct protein
    synthesis.
  • Adenosine triphosphate (ATP)
  • Provides energy

61
Nucleic Acid Structure
  • Nucleic acids are composed of long polymers of
    repeating subunits, nucleotides - the monomer.
  • five-carbon sugar
  • phosphate
  • nitrogenous base
  • purines
  • adenine and guanine
  • pyrimidines
  • cytosine, thymine, and uracil

62
Nucleic Acid Structure
  • DNA exists as double-stranded molecules.
  • Genetic info. - coded for by the order of the
    nucleotides.
  • double helix
  • complementary base pairing
  • hydrogen bonding
  • base pairing A-T, C-G
  • RNA exists as a single stand.
  • contains ribose instead of deoxyribose
  • contains uracil in place of thymine

63
Nucleotides
64
Comparison of DNA RNA
  • RNA
  • DNA
  • Feature
  • Ribose
  • Deoxyribose
  • Sugar
  • Cytosine, guanine
  • adenine, uracil
  • Cytosine, guanineadenine, thymine
  • Bases
  • Mostly single stranded
  • Double-stranded Pairing across strands
  • Strands
  • No
  • Yes
  • Helix
  • Interprets genetic info protein synthesis
  • Heredity cellular control center
  • Function
  • Cell nucleus and cytoplasm
  • Chromosomes of cell nucleus
  • Where

65
Structure of DNA
66
RNA Structure
67
DNA ? RNA? Protein
68
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

69
ATP
70
Summary
  • Biological Molecules (contain Carbon)
  • Macromolecules (polymers made of monomers)
  • Proteins (amino acids)
  • Polypeptides
  • Enzymes
  • Nucleic Acids (nucleotides)
  • DNA and RNA
  • Lipids (glycerol 3 fatty acids)
  • Fats, Oils, Waxes, Steroids, and Phospholipids
  • Carbohydrates (monosaccharides)
  • Monosaccharides, Disaccharides, and
    Polysaccharides (Starch, Glycogen, Cellulose, and
    Chitin)

71
Summary
and
Phosphate group
Enzymes
Not all inclusive!
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