Transcript Notes with questions

Organic Molecules of Living
Systems (N=4)
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Principles of carbon chemistry
Principle of polymers
Hydrocarbons (book; not responsible)
Organic chemistry in living systems:
biochemistry
Carbon metabolism and energy
Minerals and vitamins (book; not
responsible)
Covalent Bonds and Carbon
C is a unique case
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C
C
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C-C
C–C–C
C
Valence electrons for C are 4 (one in each orbit of
the 2nd shell)
C – C: single covalent bond; share orbit + shared
electron
C – C – C: two covalent bonds for center carbon
atom
Covalent bond: energy stores (excited electron)
Significance:
increases
diversity of
carbon
compounds
More Principles of Carbon
Chemistry: Functional Groups
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Features of C macromolecules
• Carbon skeleton (chains, branches, rings)
• Groups of atoms attached to carbon
skeleton - functional groups
C
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Hydroxyl (OH)
Amino (NH2)
Phosphate (PO4)
phosphate (what molecule from
last week/this week also had
phosphate group?)
C – C – OH
C
C
C – C – NH2
C
Principle of Polymers
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Small molecules joined together to
form large molecules up to 1,000’s of
carbon atoms (macromolecules)
Array of combinations, each with its
own unique chemistry (e.g., polarity,
solution chemistry, three dimensional
structure, reactivity, passage
through membranes, etc.)
Simple to Complex Polymers of Carbon
Methane - 1 C atom
Ethane – 2 C atoms
Green atoms = Carbon
White atoms = Hydrogen
Red atoms = Nitrogen
Fullerene – 60+ C atoms (Buckyballs)
More Complex Carbon Polymers:
Macromolecules
nicotine
caffeine
aspirin
Principle of Polymers
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Polymers of carbon: four major
classes of macromolecules in all cells
(N=4)
• Carbohydrates
• Proteins
• Nucleic acids
• Lipids
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Diversity of carbon polymers:
effectively unbounded
Question
There are millions of organic compounds
but only a few thousand inorganic
compounds because ____?
A. Organic compounds are formed by living
critters
B. There is more C on the Earth’s surface than
most other elements
C. Atoms of elements other than C never
combine with themselves (e.g., oxygen never
combines with another oxygen atom – O2)
D. C atoms combine with up to four other atoms,
notably other C atoms
Question
The diversity of functional features
of carbon macromolecules is a
consequence of ___?
A.
B.
C.
D.
E.
nitrogen
carbon skeleton
oxygen
functional groups
B and D
Functionality of Hydrocarbons!
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Carbon skeleton
Functional groups (e.g., hydroxyl - OH,
amine group – NH2, phosphate or PO4)
Organic Chemistry and
Biochemistry
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Introduction to organic chemistry
Principles of carbon chemistry
Principle of polymers
Organic chemistry in living systems:
biochemistry
Carbon metabolism and energy
Organic Chemistry and
Biochemistry: a Template
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Keys:
• Structure of basic unit (monomer)
• Polymer structure (i.e., macromolecule)
• Functional group (e.g., OH, PO4 or NH2)
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Four types of carbon polymers macromolecules - in living systems (N=4)
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Carbohydrates
Lipids
Proteins
Nucleic acids
Biochemistry Cheat Sheet
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Carbohydrates
• Monomer: monosaccharide (e.g., glucose or C6H12O6)
• Polymer: polysaccharide
• Functional unit: hydroxyl or OH-
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Proteins
• Monomer: amino acid (peptide)
• Polymer: polypeptide and protein
• Functional unit: amine or NH2
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Nucleic Acids
• Monomer: nucleotide
• Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid)
• Functional units: organic N base, carbohydrate and phosphate
(PO4)
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Lipids
• Monomer: fatty acid + glycerol
• Polymer: fats, phospholipids and steroids
• Functional unit: glycerol (3 OH- groups)
Biochemistry: Carbohydrates
Keys
Monosaccharide (monomer); Glucose
(C6H12O6)
Functional unit: hydroxyl or OH-
Monomer Unit: Monosaccharide
Polymer: Polysaccharide
(Glycogen)
Monomer
Question
Any individual sugar molecule that is a
monomer of a carbohydrate
macromolecule is generically called
___.
A glucose
B starch
C monosaccharide
Biochemistry Cheat Sheet
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Carbohydrates
• Monomer: monosaccharide (e.g., glucose or C6H12O6)
• Polymer: polysaccharide
• Functional unit: hydroxyl or OH-
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Proteins
• Monomer: amino acid (peptide)
• Polymer: polypeptide and protein
• Functional unit: amine or NH2
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Nucleic Acids
• Monomer: nucleotide
• Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid)
• Functional units: organic N base, carbohydrate and phosphate
(PO4)
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Lipids
• Monomer: fatty acid + glycerol
• Polymer: fats, phospholipids and steroids
• Functional unit: glycerol (3 OH- groups)
Biochemistry: Proteins
Monomer = amino acid
Keys
Amino acid (monomer)
Polypeptide (polymer)
Functional unit: amine
or NH2
Polypeptide bond
serine – lysine – arginine – tryptophan – glutamic acid – etc.
Polymer called _____?
Amino Acids:
The Building Blocks of Proteins
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Side group makes each amino acid
unique
What is distinction between a polypeptide and a protein?
Amino Acids
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Bonding
• Two amino acids
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Forms peptide bond
• Polypeptide -not functional
… yet (I am getting there!)
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Chain of amino acids
Protein – functional now!
• Large molecule
• Chain of amino acids
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Only 20 different amino
acids in all living
organisms
Proteins: Linear Sequence of
Amino Acids (Monomers)
GLY
Type of bond?
LEU
VAL
LYS
LEU
ALA
Protein Conformation (1 and 2nd)
The “slinky”
structure
Protein Conformation (3rd & 4rd)
Protein Conformation
Question
Proteins are made up of strings of
monomers called ___.
A
B
C
D
amino acids
monosaccharides
nucleotides
lipids
Question
How many different amino acids
appear in the proteins of all living
organisms on Earth?
A
B
C
D
10
20
50
200
Question
The exact sequence of amino acids
that goes into a protein is called its
__.
A
B
C
D
primary structure
secondary structure
tertiary structure
quaternary structure
Organic Chemistry and
Biochemistry
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Introduction to organic chemistry
Principles of carbon chemistry
Principle of polymers
Organic chemistry in living systems:
biochemistry
Carbon metabolism and energy
Biochemistry Cheat Sheet
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Carbohydrates
• Monomer: monosaccharide (glucose or C6H12O6)
• Polymer: polysaccharide
• Functional unit: hydroxyl or OH-
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Proteins
• Monomer: amino acid (peptide)
• Polymer: polypeptide and protein
• Functional unit: amine or NH2
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Nucleic Acids
• Monomer: nucleotide
• Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid)
• Functional units: organic N base, carbohydrate, and phosphate
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Lipids
• Monomer: fatty acid + glycerol unit
• Polymer: fats, phospholipids and steroids
• Functional unit: glycerol (3 OH- groups)
Special Proteins Called Enzymes:
How They Work
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Base case for
reactions to occur
Without enzyme
• Reactants
• Products
• Activation energy
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Energy analysis
(thermodynamics)
• Energy to cause
reaction to occur
(“hill” or activation
energy)
Enzyme mediated
How Enzymes Work
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Efficacy of enzymes
• “Hill” height/activation energy
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Mechanism
• Lower the height of the “hill”
• Selectivity/specificity
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Rate of a reaction
• Absence of enzyme: minutes
to hours to days to years
• Presence of enzyme: 1,000 10,000 times per second!
• Increase in rate > 106 orders
of magnitude (1,000,000)
Biochemistry Cheat Sheet
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Carbohydrates
• Monomer: monosaccharide (glucose or C6H12O6)
• Polymer: polysaccharide
• Functional unit: hydroxyl or OH-
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Proteins
• Monomer: amino acid (peptide)
• Polymer: polypeptide and protein
• Functional unit: amine or NH2
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Nucleic Acids
• Monomer: nucleotide
• Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid)
• Functional units: organic N base, carbohydrate, and phosphate
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Lipids
• Monomer: fatty acid + glycerol unit
• Polymer: fats, phospholipids and steroids
• Functional unit: glycerol (3 OH- groups)
Biochemistry: Nucleic Acids
Keys
Monomer: Nucleotides
Functional units (N=3): organic N base, sugar, and
phosphate
Nucleic Acids as Polymers:
DNA Double Helix
Monomer:
BASES
Nucleotide
A
T
C
G
Nitrogen Base
Monomer:
Nucleotide
Biochemistry Cheat Sheet
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Carbohydrates
• Monomer: monosaccharide (glucose or C6H12O6)
• Polymer: polysaccharide
• Functional unit: hydroxyl or OH-
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Proteins
• Monomer: amino acid (peptide)
• Polymer: polypeptide and protein
• Functional unit: amine or NH2
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Nucleic Acids
• Monomer: nucleotide
• Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid)
• Functional units: organic N base, carbohydrate, and phosphate
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Lipids
• Monomer: fatty acid + glycerol unit
• Polymer: fats, phospholipids and steroids
• Functional unit: glycerol (3 OH- groups)
Biochemistry: Lipids
Keys
Monomer: Fatty acids C16-18
Functional unit: glycerol
(3 OH- groups)
Special Case: Cell Membranes
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Cell membrane
• Hydrophobic
(phosphate)
• Hydrophilic
(lipid)
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Lipid bilayer =
cell membrane
Organic Chemistry and
Biochemistry
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Introduction to organic chemistry
Principles of carbon chemistry
Principle of polymers
Organic chemistry in living systems:
biochemistry
Carbon metabolism and energy
Carbon Metabolism
Biosynthesis (photosynthesis)
CO2 + H2O + Energy
(light)
CH2O + O2
(C - C Bonds/excited electron)
Catabolism
CH2O + O2
(C - C Bonds/excited electron)
CO2 + H2O + Energy
(heat + chemical energy)
Key: C-C covalent bonding, which in turn is determined by
electrons in the valence state, which in turn is underpinned by
energy of electrons in their respective shells (remember the
granola bar!)
Question
Hearing is a process that is best categorized
as being staccato (absence of sound then
bursts of sound …)
What bonds are likely to be involved in
hearing if sound is best characterized as
being staccato?
How might those bonds operate in the inner
ear and brain, and what element is likely to
be involved?