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Chapter 3

BIL 160 Chapter Notes - Chapter 3: Glycosidic Bond, Chemical Formula, Thiol


Department
Biology
Course Code
BIL 160
Professor
Daniel DiResta
Chapter
3

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Exam 1 review for Macromolecule lecture
biological molecules
framework consists predominantly of carbon atoms bonded
(covalently) to other carbon atoms and/or to oxygen, nitrogen,
sulfur, or hydrogen...carbon forms maximum of 4 covalent bonds
(important basis for life) and can form both polar and nonpolar
bonds with other elements (leads to diversity of life)
carbon
Can form single, double, and triple bonds (4 valence/valence
electrons = a maximum of 4 covalent bonds) with another carbon
thereby forming long chains and/or rings. Can form polar and
nonpolar covalent bonds with various elements. Carbon bonds are
stable at the range of temperatures associated with life. These make
up the backbones of all organic molecules. All organic molecules
contain what?
hydrocarbons (C-H) are electrically neutral and nonpolar; high in
energy
C-O are polar due to oxygen being more electronegative than carbon
functional group
chemical groups that tend to act as units during chemical reactions
and confer specific chemical properties on the molecules, or portions
of the molecules, to which they are attached
hydroxyl (-OH) & carbonyl (C=O) are polar
sulfhydryl (-SH) forms covalent bonds, contributing to tertiary
structure in proteins
carboxyl (-COOH) has acidic properties, so would release hydrogen
ions in solution
isomers, sterioisomers, enantiomers
molecules with the same chemical formula but with a different form
and different name because they are an alternate form of a specific
molecule (such as fructose and galactose being alternate forms of
glucose)
enzymes can only recognize a single, specific stereoisomer
major classes of macromolecules (polymers);
monomer/building blocks; and bonds that
form between monomers
proteins (polypeptides); amino acids; peptide bonds; proteins
best represent polymer structure
nucleic acids; nucleotides; phosphodiester bonds
polysaccharides/carbohydrates; simple sugars
(monosaccharides); glycosidic bonds
lipids; glycerol & fatty acids; ester bonds

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condensation/dehydration synthesis reaction
process in which two monomers or a monomer and a polymer are
linked together by removing water when forming the covalent bond
that attaches them
*practice writing some of these
polymerization (condensation synthesis
reactions) noting the resulting bonds (what
category bond is this: ionic, covalent,
hydrogen); does this type of reaction require
an input of energy or does it release energy?
such as: amino acid + amino acid = protein + H2O (H from one
amino acid and OH from second amino acid; removal creates
peptide bond)
both hydrolysis and condensation synthesis require enzymes to have
reactions proceed in a much quicker, biologically viable time span
hydrolysis
process in which a polymer is taken apart by inserting water in the
location where the covalent bond is broken between 2 monomers
protein
function in metabolism, transport, cell recognition, and structure;
made up of a chain of amino acids linked together through covalent
peptide bonds; macromolecule with highest diversity of function
amino acid (a.a.)
consists of central carbon bonded to carboxyl group, amino group,
hydrogen atom, and a R-group (carbon containing); differences in
R-group distinguishes property differences in a.a.; monomer for
proteins; 20 naturally occurring;
peptide bond
covalent bond attaching carbon (carboxyl end) of one amino acid to
the nitrogen (amino end) of another amino acid leading to the
formation of a protein
primary structure of protein
linear sequence of amino acids; ultimately is responsible for final
functional shape (native conformation) of protein
secondary structure of protein
local structure of alpha helix or beta pleated sheets; stabilized by
peptide-linkage hydrogen bonds (no R-group interactions at this
level)
tertiary structure of protein
global structure of 3 dimensional folding; result of a.a. side chain/
R-group interactions (hydrogen, hydrophobic, hydrophilic, strongest
covalent disulfide bond); all proteins have at least tertiary level of
structure
quaternary structure of protein
protein with more than one linear sequence of a.a. (more than one
subunit)
consider: How would the occurrence of a
single amino acid mutation affect the levels of
protein structure?
Missence- point mutation that changes a codon to indicate a
different amino acid. Changes the polypeptide and the overall
function of the protein.
Nonsense mutation is a point mutation that turns one codon into a
stop codon and results in an early termination of a polypeptide
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denaturation
change in tertiary, sometimes secondary, protein form as a result of
environmental changes in pH, [ionic] , or temperature impacting
hydrogen bonds and/or R-group interactions; loss of form causes
loss of function (not always irreversible thereby indicating primary
structure's importance in establishing final functional shape)
chaperone proteins
help in folding of proteins (primarily those with quaternary level of
structure); since form determines function, loss of chaperone protein
function can have a negative impact on protein structures in the cell
and prevent them from occurring
motif
there are certain favored arrangements of multiple
secondary structure elements that recur again and again in
proteins--these are known as motifs or supersecondary
structures
a motif is usually smaller than a domain but can
encompass an entire domain. Sometimes the structures of
domains are partly named after motifs that they contain,
e.g. “greek key beta barrel”
it should be noted that the term motif, when used in
conjunction with proteins, sometimes also refers to
sequence features with an associated function, e.g. the
“copper binding motif
domain
Proteins are made up of one or more domains
proteins often have a modular organization
single polypeptide chain may be divisible into smaller
independent units of tertiary structure called domains
domains are the fundamental units of structure
classification
different domains in a protein are also often associated with
different functions carried out by the protein, though some
functions occur at the interface between domains
domain properties (polar, non-polar, etc) need to match
properties of areas in which they exist (polar domain in
polar region of membrane; non-polar domain in non-polar
region of membrane)
enzyme
protein (or RNA) that catalyzes chemical reactions
lipid
nonpolar hydrophobic organic molecule that is insoluble in water;
triglyceride (used for energy storage) made up of glycerol and three
fatty acid chains; fatty acid(s) found in monoglycerides (1),
diglycerides(3), phospholipids (2)
includes cholesterol, steroids, wax and oils, phospholipids, and
others
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