Unit 2 – Amino Acids, Peptide Bonds, Protein Structure
Amino Acid: building blocks of proteins
Monomer: single amino acid
Polymer: amino acid chain of linked monomers called
polypeptides
Amino Group: N with at least 1 H, can be NH2 or NH3
Hydrogen Hat: between amino grou...
WGU Biochemistry C 785 Study Guide
Page 10 Video Notes for Units 2-7
Unit 2 – Amino Acids, Peptide Bonds, Protein Structure
Amino Acid: building blocks of proteins
Monomer: single amino acid
Polymer: amino acid chain of linked monomers called
polypeptides
Amino Group: N with at least 1 H, can be NH2 or NH3
Hydrogen Hat: between amino group and carboxyl group,
attached to alpha carbon
Variable Group “side chain” “R”: unique portion of amino acid
Carboxyl Group: C with 2 attached O’s, can be COOH, or COO
Hydrophobic Amino Acid: consists only of carbons and hydrogens
end in H, CH, CH2, CH3 – they are nonpolar –Hydrophobic
interactions occurs between two nonpolar amino acids H, CH,
CH2, CH4, are the weakest type of bond – but the most important
type for protein structure – are broken with heat (increased
temperature)
Polar Amino Acid: end in OH, NH, SH, create hydrogen bonds, can
be broken by changes in pH or changes in salt concentration.
SH: Disulfide bond/bridge made by SH side chains, is strongest,
fewest in number, and only broken with reducing agents
Peptide Bonds: form at amino group and carboxyl group, “loss of
H2O”
Ionic Bonds: occurs between two amino acids with opposite
charges (charged amino acids, -/+, negative is acidic positive is
basic), are broken with pH changes or changes in salt
concentration
, Dehydration Synthesis: when two molecules are covalently
bonded with loss of a water molecule (H20) one provides
hydroxyl group OH and the other provides hydrogen H. Amino
group and carboxyl group both give up something and then they
bind and form a new bond polymer chain
Hydrolysis: addition of a water molecule H2O to break a bond,
breaks polymers
4 Levels of Protein Structure: Primary linear chain of amino
acids, Secondary alpha helix and beta sheet shapes, create by
Hydrogen bonds of polypeptide backbones Tertiary 3D,
stabilized by side chains Quaternary consists of two or more
polypeptide chains, more than one subunit – tertiary and
quaternary are mature structures that are properly folded.
Denaturation: high temperatures and various chemical treatments
will denature a protein, causing it to lose its shape and ability to
function “form=function” it may renature when chemical and
physical aspects of environment are restored to normal.
Unit 3 – Enzymology and Catalytic Mechanism
Enzymes: are proteins, they catalyze reactions when properly
folded, can be disrupted just like amino acids by heat, pH, etc.,
“enzymes are proteins that act as biological catalysts, Lactose is
a substrate that can be converted to glucose and galactose which
are products by lactase which is an enzyme (enzymes usually end
in “ase”). Enzymes lower the activation energy of a reaction
“makes it easier and quicker”. People who are lactose intolerant
do not have lactase that breaks it down into usable products.
Excessive internal heat can denature hydrophobic interactions
thus causing important enzymes to lose their function.
, Enzymes bind a specific substrate and catalyze a specific reaction,
speed up reactions, and decrease activation energy “faster and
easier”
Substrates bind to an enzyme’s active site. When an enzyme is
fully folded it creates an active site for the substrate to bind to.
Tertiary/Quaternary enzymes have active sites only, fully mature
enzymes, enzymes recognize specific substrates (lock and key)
“enzyme specificity”
Enzyme 4-step Cycle: Step 1= substrate recognition, the substrate
recognized a specific enzyme and binds to its active site. Step 2=
enzyme-substrate complex formation. Step 3= enzyme-product
complex formation (the substrate converts to products) Step 4=
products release and the enzyme is recycled.
Induced fit: takes place in second step “Enzyme-Substrate
Complex: Induced Fit” when the enzyme and substrate bind
together the shape of the enzyme may change slightly to facilitate
the chemical reaction in the product formation step.
Kinases: an enzyme, kindly gives a phosphate to a molecule
Phosphatases: an enzyme, remove phosphate groups from
molecules
Temperature and pH affect enzymes, even slight changes can
significantly decrease effects “human enzymes thrive at 37 C/98”
Enzyme regulation by inhibition if an enzyme in the pathway is
inhibited the final product will be inhibited and the prior enzyme
can build up. Build up of a final product will inhibit the first
enzyme of the pathway thus decreasing the production of a final
product. This is feedback inhibition. “Supply vs. demand” the
end=-product of a pathway can feedback and inhibit one of the
first enzymes in the pathway by binding to an allosteric site
causing prevention of the necessary steps of the pathway to be
, carried out, once demand increases this will reverse and allows
the cycle to continue, this is a type of noncompetitive inhibition,
binds to allosteric site not active site.
Uninhibited Reaction: the substrate binds to the active site on the
enzyme and gets turned into products.
Competitive Inhibition: an inhibitor binds to the enzyme in the
place of a substrate, they will have similar shapes “lock and key”
to the substrate. You can overcome competitive inhibition by
increasing the amount of substrate present.
Noncompetitive Inhibition: The noncompetitive inhibitor does not
bind to the active site in the place of a substrate like competitive
inhibitors, instead they bind to allosteric sites, which is a site other
than the active site. When this occurs, this causes a change in the
shape in the active site thus preventing binding of the substrate.
Thus, preventing an enzyme from converting a substrate into
product. Because they are noncompetitive, they cannot be
outcompeted by adding more substrate. “Noncompetitive can
always inhibit the enzyme”
Key Points: enzymes are specific to one substrate or family of substrates
and catalyze one type of reaction – enzymes lower the activation
energy of a reaction – enzymes increase the rate of a reaction – kinases
kindly add a phosphate group – phosphatases remove a phosphate
group – enzymes usually end in “ase” - enzymes function at an optimal
temperature and pH, deviation from these optimal values will decrease
enzyme function – competitive inhibitors bind to the active site when
the substrate is suppose to bind, they have a similar shape as the
substrate “lock and key”, and can be outcompeted by increasing the
amount of substrate – non-competitive inhibitors bind to the allosteric
site (any site other than the active site) – the end product of a pathway
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