Download CHEMISTRY 112 - LECTURE NOTES

CH 112 LECTURE NOTES
PART TWO: ORGANIC AND BIOCHEMISTRY
PLEASE DO NOT PRINT LECTURE NOTES IN THE SCIENCE RESOURCE CENTER
I) Organic vs Inorganic Compounds
A) Early distinctions
1) from living organisms (organic) or not (inorganic)
2) combustible (organic) or not (inorganic)
B) Current definitions
1) containing carbon (organic) or not (inorganic)
2) food grown without petrochemicals (organic) or not
C) Working Definitions
1) an organic compound is a compound containing carbon and hydrogen, and sometimes other
elements such as oxygen, nitrogen, phosphorus, and sulfur)
2) organic chemistry is the study of properties and changes of carbon and its compounds
D) Organic Nomenclature
1) “naming system” for organic compounds
2) based on:
a) length of longest carbon chain
b) nature of carbon bonds (single, double, triple)
c) substituents (other atoms or groups)
II) Carbon Bonding Patterns (Valence of Carbon)
A) Bond info review
1) covalent bonds
a) can be polar or nonpolar
b) are formed by shared electron pairs
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* single – one shared pair (longest and weakest)
* double – two shared pairs (intermediate length and strength)
* triple – three shared pairs (shortest and strongest)
2) bond polarity influences conductivity and solubility/miscibility of substances
3) hydrogen bonds
a) intermolecular – between molecules (eg: between two water molecules)
b) intramolecular – within a molecule (eg: base pairing in nucleic acids)
B) Valence of carbon
1) four valence electrons
2) four bonds to each carbon – possible configurations
a) four single bonds (saturated if they are carbon-carbon single bonds)
b) two double bonds (unsaturated if they are carbon=carbon double bonds)
c) one triple and one single bond (unsaturated if they are carbon=carbon triple bonds)
d) one double and two singles (unsaturated if they are carbon=carbon double bonds)
C) Possible Structures for Carbon Skeleton (carbon backbone)
1) chains – carbons attached end-to-end
2) branches – intersecting carbon chains
3) rings – carbons attached in a circle (closed chain - last carbon attached to first)
D) Isomers
1) def: compounds having:
a) same molecular formula (same number and type of atoms) AND
b) different structural formula (different order of attachment of atoms)
2) examples:
a) glucose, fructose, and galactose (all C6H12O6)
b) ethanol and diethyl ether (both C2H5O)
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E) Organic functional groups
1) def: A specific atom or configuration of atoms commonly attached to the carbon skeleton of an
organic compound
2) determine structure, reactivity and function of the organic compound and makes them different
from unsubstituted hydrocarbons
3) functional groups to know this term (there are many others!)
a) hydroxyl
O-H
b) carbonyl
C=O
c) carboxyl
O-H and C=O on the same carbon (sometimes abbreviated COOH)
d) amino
NH2
e) phosphate PO4-3
F) Hydrocarbons and their derivatives
1) def: hydrocarbons are compounds composed of carbon and hydrogen
2) examples and names
a) prefix - indicates number of carbons
meth = one carbon
ex: methane CH4
eth = two carbons
ex: ethane
prop = three carbons ex: propane
C2H6
C3H8
b) middle – indicates bond type (and C:H ratio)
an = single bond (alkanes)
ex: ethane
C2H6
en = double bond (alkenes)
ex: ethene
C2H4
yn = triple bond (alkynes)
ex: ethyne
C2H2
c) ending – indicates functional groups or atoms other than carbon and hydrogen
ol = hydroxyl group present
ex: ethanol
one = carbonyl group present
ex: ethanone
oic acid = carboxyl group present
ex: ethanoic acid
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III) Intro to Biochemistry
A) def: the study organic compounds that are essential for life processes.
B) Biochemical Principles
1) diversity of biochemicals results from many small precursor molecules
2) general changes involve:
a) assembly: small precursors are assembled into larger structures
b) rearrangement: structures are rearranged
c) degradation: large structures are broken into smaller subunits
3) enzymes catalyze most reactions
C) Biomolecule Properties and Importance
1) subunits are the small building blocks (precursors) used to make macromolecules
a) subunits can be identical, similar, or very different from each other (if the subunits are
identical they are called monomers)
b) subunits can join together by covalent bonds to form larger molecules (macromolecules)
during dehydration synthesis
c) subunits can be produced by the breakdown of macromolecules during hydrolysis
examples of subunits:
subunits of carbohydrates are sugars
subunits of lipids are fatty acids, glycerol, polar head groups, and carbon rings
subunits of proteins are amino acids
subunits of nucleic acids are nucleotides
2) macromolecules are large molecules made of smaller subunits
a) macromolecules are composed of identical, similar, or very different building blocks
subunits (if the subunits are identical or very similar, they are monomers, and the
macromolecule is called a polymer)
b) macromolecules from when subunits join together by covalent bonds during dehydration
synthesis
c) macromolecueles can be broken down into monomers or subunits during hydrolysis
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examples of macromolecules
carbohydrates are macromolecules made of sugar
lipids are macromolecules made of fatty acids, glycerol, polar head groups, and/or
carbon rings
proteins are macromolecules made of amino acids
nucleic acids are macromolecules made of nucleotides
D) Dehydration Synthesis Reactions
1) reaction in which subunits join to make macromolecules
a) "dehydration” refers to the removal of water
b) "synthesis" refers to the formation of macromolecules by joining together of subunits
2) description: subunits are joined through dehydration synthesis in which a water molecule is lost
(part is contributed by each subunit) and a covalent bond is formed between the subunits
a) two subunits each provide a “piece” of a water molecule
example
one subunit contributes an “H”
the other subunit contributes an “OH”
or another example
one subunit contributes 2 “H”
the other subunit contributes an “O”
b) a water molecule is a product of each dehydration synthesis - one water molecule is
made every time two subunits join
c) a covalent bond is formed at the sites where the pieces of water are removed
3) SUMMARY OF DEHYDRATION SYNTHESIS:
SUBUNITS ARE REACTANTS
MACROMOLECULES AND WATER ARE PRODUCTS
E) Hydrolysis Reactions
1) reaction in which macromolecules break apart to make subunits
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a) “hydro” refers to addition of “water"
b) “lysis” means breaking apart of macromolecules and results in the separation of subunits
2) description: macromolecules are broken apart by hydrolysis in which water molecules are added
(a piece goes to each subunit) and the covalent bond between subunits is broken
a) two subunits each take a piece of a water molecule
one subunit gets the “H”
the other subunit gets the “OH”
b) a water molecule is a reactant (ingredient) in hydrolysis - one water molecule is used up
each time two subunits are separated
c) a covalent bond is broken at the site where the pieces of the water molecule are inserted
3) SUMMARY OF HYDROLYSIS:
MACROMOLECULES AND WATER ARE REACTANTS
SUBUNITS ARE PRODUCTS
IV) Important Families of Biomolecules: LIPIDS, CARBOHYDRATES, PROTEINS, NUCLEIC ACIDS
A) Lipids
1) description: nonpolar (hydrophobic) carbon compounds and their macromolecules
carbon:hydrogen ratio is close to 1:1, little oxygen present
2) triglycerides aka trigacylglycerols (fats and oils)
a) composed of three fatty acids joined to a glycerol
* fatty acid is a nonpolar hydrocarbon chain with a polar carboxyl group at one end
* glycerol is a polar C3 hydrocarbon with one hydroxyl group on each carbon
b) fatty acids can be the same or different
c) triglyceride with mostly unsaturated fatty acids tends to be liquid oil
d) triglyceride with mostly saturated fatty acids tends to be solid fat
e) SUMMARY OF TRIGLYCERIDE REACTIONS
* DEHYDRATION SYNTHESIS: three fatty acid subunits join to glycerol (not to
each other) to form a triglyceride and water
* HYDROLYSIS: water is used to break apart a triglyceride to form three fatty acid
subunits and one glycerol subunit
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3) phospholipids aka glycerophopsholipids
a) only two fatty acids (nonpolar, hydrophobic) are attached to a glycerol
b) the third carbon of the glycerol is bonded to a phosphate with an additional polar head
group attached (hydrophilic)
d) SUMMARY OF PHOSPHOLIPID REACTIONS
* DEHYDRATION SYNTHESIS: two fatty acid subunits and one polar head
subunit join to glycerol (not to each other) to form a phospholipid and water
* HYDROLYSIS: water is used to break apart a phospholipid to form two fatty
acid subunits, one polar head subunit, and one glycerol subunit
4) Steroids – have complex ring structures (often four rings of 5 or 6 carbons each)
examples:
a) cholesterol, testosterone
b) bile acids
NOTE: These steroids emulsify ingested fat. The hydrophobic portion of the steroid
dissolves in the fat while the negatively-charged side chain interacts with water molecules.
The mutual repulsion of these negatively-charged droplets keeps them from coalescing.
Thus large globules of fat (liquid at body temperature) are emulsified into tiny droplets
(about 1 µm in diameter) that can be more easily digested and absorbed.
B) Carbohydrates
1) description: compounds such as sugars and their polymers
ratio of carbon:hydrogen:oxygen is about 1:2:1
2) monsaccharides (simple sugars)
a) characteristics
- simplest carbohydrates
- exist mainly as closed ring structures but can convert to straight chain form
- hydroxyl attached to each carbon except one with carbonyl
b) common six-carbon (C6) monosaccharides are glucose, fructose, and galactose
c) common five-carbon (C5) monosaccharides are ribose and deoxyribose
3) disaccharides - two monosaccharides joined by a covalent bond
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common disaccharides are:
a) sucrose (a glucose joind to a fructose)
b) lactose (a galactose joined to a glucose)
4) polysaccharides – large polymers composed of several hundred to several thousand
monosaccharides
important polysaccharides to know
starch, cellulose, glycogen - these are all polymers of glucose
a) starch - coiled chains of about 1,000 glucose subunits (digestible by humans)
b) cellulose - straight chains of about 2,000 - 26,000 identical glucose subunits
(indigestible by humans)
c) glycogen - branched chains of 17,000 - 600,000 identical glucose subunits (stored in
muscle tisuue)
d) SUMMARY OF CARBOHYDRATE REACTIONS
DEHYDRATION SYNTHESIS: two sugar subunits join together to form a
disaccharide and water; OR thousands of sugar subunits join together to form a
polysaccharide and lots of water
SUMMARY OF HYDROLYSIS: water is used to break apart a disaccharide to
form two sugar subunits; OR lots of water is used to break apart a polysaccharide
to form thousands of sugar subunits
C) Proteins
DEFINITION: * A protein is a polypeptide with a known biological function
* Proteins are biologically active linear polymers of amino acids in a genetically
determined sequence, synthesized as polypeptide chains on a ribosome “workbench”.
1) description: a polypeptide is a macromolecule made of dozens to thousands of amino acids
a) twenty different amino acids are found in polypeptides and proteins
* all amino acids are alike in the following ways
- have a central (alpha) carbon with four single bonds
- what’s attached to three of the four alpha carbon bonds:
amino group on one
carboxyl group one
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hydrogen on one
* each of the 20 amino acids has a different side chain
- called the R group
- it’s what’s attached to the fourth alpha carbon bond
- can be as simple as a hydrogen atom or as complicated as a benzene ring
b) amino acids are joined together by dehydration synthesis to form covalent carbon to
nitrogen bonds called peptide bonds
c) peptide bond formation: occurs between the carbon of the carboxyl group on the first
amino acid, and the nitrogen of the amino group on the second amino acid
d) SUMMARY OF POLYPEPTIDE REACTIONS
DEHYDRATION SYNTHESIS: two amino acid subunits join together to form a
dipeptide and water; OR many amino acid subunits join together to form a
polypeptide and lots of water
SUMMARY OF HYDROLYSIS: water is used to break apart a dipeptide to form
two amino acid subunits; OR lots of water is used to break apart a polypeptide to
form many amino acid subunits
2) Four levels of protein structure
a) primary structure - unique linear sequence of amino acids in a polypeptide chain
* genetically determined
* determines all other structural levels
* directionality is from amino (N-terminus) to carboxyl (C-terminus)
b) secondary structure - develops from local interactions between amino acids
* amino acids in a peptide can interact with one another causing the peptide to fold
and twist
* due to geometry of the bond angle between amino acids
* hydrogen bonding between amino and carboxyl groups in nearby regions
* repetitive structure based on common local functional group features
* structures are alpha helix and beta sheet, as well as random coils, that are
hydrogen bond stabilized
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c) tertiary structure - develops from long-distance interactions between R groups
* hydrogen bonding between R groups in non-adjacent regions forms3-D structure
including large loops, folds, pockets...
* non-repetitive structure based on distinctive R group features; highly irregular
*stabilized by other covalent and non-covalent interactions such as disulfide
(covalent) bonds, H bonds, electrostatic interactions hydrophobic/hydrophilic
interactions
* may include one or more “domains” of ~50-350 amino acids packed tightly to
perform a specific function
ex: in aqueous environment, non-polar hydrophobic R groups fold to inside
of molecule, and polar hydrophilic R groups cluster on surface of molecule
ex: in lipid bilayer, polar R groups fold to inside to form channels for
transport of water-soluble substances
d) quaternary structure - two or more different or identical polypeptide chains joined
together
* multimeric proteins, often with high molecular weights (50,000+)
* stabilized by other covalent and non-covalent interactions (see above)
examples:
hemoglobin
(2 alpha chains, 2 beta chains)
insulin
(1 alpha chain of 21 amino acids, 1 beta chain of 30 amino acids)
ferritin
(24 identical chains)
ferritin is a protein that allows our bodies to store and release iron
because of its hollow sphere strucutre, and the channels formed by
the multiple foldings of side chains
3) Conjugated Proteins: result when proteins complex with other atoms, ions, or molecules,
including other proteins
Hemoglobin is a protein with several polypeptide chains, and each chain contains a nonprotein cluster of atoms called a heme group
other examples: glycoproteins, lipoproteins, enzyme complexes
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4) Fibrous vs Globular Proteins
5) Denaturation of Proteins – occurs when there is loss of one or more levels of protein structure
a) structure is sensitive to heat, pH changes, other chemical interactions
b) loss of function accompanies loss of structure
6) Importance Of Proteins
a) List of Some Protein Functional Capabilities (with examples)
structure (keratin, collagen); movement (actin, myosin, dynein); signaling (rhodopsin);
transport (hemoglobin, myoglobin, albumin); protection; catalysis (lactase)
b) amino acid subunits derived from dietary proteins are used to synthesize many other
biomolecules such as neurotransmitters and thyroid hormones
D) Nucleic acids
1) description: polymers consisting of nucleotide subunits
a) a nucleotide is composed of:
a five carbon sugar (ribose or deoxyribose)
a heterocyclic nitrogenous base (adenine, cytosine, guanine, & thymine or uracil)
and one or more phosphate groups
b) example:
ATP is a nucleotide that does not form polymers, but it will lose or gain phosphate
groups as part of cellular energy transformations
c) “backbone”
in both DNA & RNA, the sugar of one nucleotide subunit connects to the
phosphate group of another to form the structural “phosphate-sugar backbone” of a
polynucleotide
2) Base Sequence and Base Pairing
a) base sequence
*def: the linear order of heterocyclic nitrogenous bases along the backbone of a
nucleic acid strand
* base sequence forms the informational part or “genetic code” of a polynucleotide
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* a gene is a section of DNA base sequence that will be used as a pattern to make
one complete m-RNA molecule, which will be used as a pattern to make one
complete polypeptide chain
b) base pairing
* hydrogen bonding attracts one heterocyclic nitrogenous base to another
- double ring purines pair with single ring pyrimidines
A (adenine) forms two hydrogen bonds with T (thymine) or U (uracil)
G (guanine) forms three hydrogen bonds with C (cytosine)
* some situations where base pairing is important
- hydrogen bonding attracts one nucleic acid strand (backbone) to another
ex: in DNA
the nucleotide bases along one strand connect to their
complementary nucleotide bases on the other strand via hydrogen
bonding to form the double stranded DNA molecule
- hydrogen bonding attracts an mRNA nucleotide to a DNA nucleotide
ex: during transcription
The nucleotide bases on a DNA strand attract complementary RNA
nucleotide bases to form an MRNA strand
- hydrogen bonding attracts a tRNA nucleotide to an mRNA nucleotide
ex: during translation
The nucleotide bases on an mRNA strand attract complementary
tRNA nucleotide bases carrying amino acids during polypeptide
formation
D) Importance of Nucleic acids in Protein Synthesis
1) proteins are biologically active linear polymers of amino acids in a genetically determined
sequence, synthesized as polypeptide chains on a ribosome “workbench”
2) Flow of Information
transcription
translation
DNA---------------------------------->RNA------------------------------->protein
3) Main Steps in Protein Synthesis
a) transcription – DNA code “rewritten” as mRNA code
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* in the cell's nucleus, a section of a DNA base sequence (gene) is used to create a coded
mRNA molecule that will direct the assembly of one polypeptide chain with a specific
amino acid sequence
- DNA unwinds in nucleus; one DNA strand is preserved “as is” (coding strand)
- the other DNA strand is used as pattern (template) to make mRNA strand which is
complementary to template strand and identical to coding strand
b) translation – mRNA code “rewritten” as amino acid sequence
* in the cell's cytoplasm and ribosome, tRNA and rRNA are used to build one polypeptide
using mRNA base triplet (codon) to add each amino acid to the chain in proper sequence
(primary structure). The polypeptide gets longer as each tRNA molecule drags a specific
amino acid into its proper sequence along the mRNA attached to the ribosome.
- one tRNA molecule binds to one amino acid in the cytoplasm
- mRNA leaves nucleus and base-pairs with rRNA on ribosome
- mRNA attracts each tRNA with its amino acid
- each amino acid joins to the next by dehydration synthesis (condensation)
- amino acids are released from their tRNA
- secondary and tertiary structures develop as polypeptide chain grows; while still
attached to the ribosome, polypeptide chain begins coiling/folding
(secondary/tertiary structure) due to local hydrogen bonding between amino &
carboxyl functional groups, and R group interactions
- the polypeptide chain is released from the mRNA
d) two or more polypeptides interact (quaternary structure) to form multimeric protein
e) other processing may be required before protein assumes biological function(s):
* separation of polypeptide from assembly site (ribosome)
* glycolysation, complex formation, targeting, sorting, activation, etc
ex: proinsulin is a monomeric protein precursor (single polypeptide chain)
with 86 amino acids; it is activated into insulin by the removal of a 35
amino acid section in the middle of the chain, forming two smaller chains
(one with 21 amino acids and the other with 30 amino acids), which then
bond covalently in two places to form the insulin dimer (multimeric protein
- quaternary structure)
4) Other Important Points
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a) each amino acid is specified by a three-base mRNA sequence called a codon
b) each codon represents three m-RNA nucleotides and their bases
c) each codon is derived from a DNA triplet (a three base DNA nucleotide sequence) by
transcription via complementary base pairing in mRNA synthesis
d) example: methionine = AUG
this means that the amino acid methionine is coded by the sequence of adenine-uracilguanine in the mRNA molecule
e) most amino acids have more than one codon (the genetic code is degenerate)
example: alanine = GCU or GCC or GCA or GCB
f) a codon can specifiy an amino acid OR it can signal “stop” or “start”
ex: UAG, UAA, UGA ( = stop)
ex: AUG = start in some prokaryotes and GUG = start in some eukaryotes
g) anticodons are the three base portion of tRNA molecules that bind to mRNA on the
ribsome; at the end of the tRNA opposite the anticodon is an attached amino acid.
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