Chapter 3:
Key Terms:
activation energy (Ea): the energy barrier that blocks a tendency for a chemical rx to occur
active site:region on surface of enzyme or ribosome where the substance binds, and where
catalysis occurs
adenine (A): part of a nucleotide; pairs with thymine in DNA and uracil in RNA
Allosteric regulation: regulation of an enzyme or other protein by binding an effector
molecule at the protein's allosteric site (not the active site) so the enzyme must
change shape; regulates enzymes by changing their shape!
Alpha helix: shape a protein makes when it folds into a spiral
amino acids: monomers of proteins
beta pleated sheet: shape a protein makes when it folds into a zig zag
base: a nitrogenous base is either adenine, cytosine, guanine, thymine, or uracil and it is an
essential part of the nucleutide
catalyst: making a biological rx faster and in biological conditions
competative inhibitor: a nonsubstrate that binds to the active site of an enzyme and thereby
inhibits binding of its substrate
complementary base pairing: adenine pairs with thymine in DNA or uracil in RNA; guanine
and cytosine always base pair; a purine must be paired with a pyramidine
cytosine (C): part of a nucleotide; pairs with guanine
denatured: when the proteins structure is disturbed and its function is therefore corrupted.
deoxyribose: the sugar that makes up DNA, has a hydroxyl attached to the pentose ring
disulfide bridge: connection between two sulfhydrils that underwent a denhydration rx
deoxyribonucleic acid (DNA): a nucleic acid in a double helix shape that carries genetic
information and can self replicate.
enzyme-substrate complex (ES):an intermediate in an enzyme-catalyzed rx; consists of the
enzyme bound to its substrate
feedback mechanism: ? the end-product will bind to the active site on the enzyme; wrong
step so it inactivates the enzyme
genes: DNA that codes for building proteins
genome: all of the genes in an organisms
guanine (G): part of a nucleotide; pairs with cytosine
noncompetitive inhibitor: a nonsubstrate that inhibits the activity of an enzyme by binding to
a site other than its active site
nucleic acids: DNA and RNA
nucleotide: building blocks of nucleic acids; pentose sugar, phosphate group and a
nitrogenous base.
Peptide linkage: bonding between amino acids that connect to make a long chain
(polypeptide chain), or a protein
phosphodiester linkage: how nucleic acids bond through condenstation rx to form DNA and
RNA
primary structure: initial folding for proteins; connection of amino acids
Purine: a hexagon and pentagon shaped nucleotide; adenine and guanine
Pyrimidine: only a hexagon shaped nucleotide; thymine/uracil and cytosine
Quaternary structure: folding pattern for multiple proteins; after tertiary to form complex
proteins.
R group: part of the amino acid structure that determines the identity of the aa
Ribose: sugar of RNA; doesn't have a hydroxyl group attached to the pentose
RNA: ribonucleic acid; can catalyze biological reactions, control gene expression, or sense
and communicate responses to cellular signals; unlike DNA, it is single stranded,
very short in nucleotide length, contains ribose, and is less stable because RNA is
more prone to hydrosis.
secondary structure: folding pattern for proteins; bonds form to pull the amino acids into a 3D shape
substrates: molecule on which an enzyme exerts catalytic action; the reactant
tertiary structure: folding pattern for proteins; bonds form to pull the amino acids into a 3-D
shape; after secondary folding
thymine (T): part of a nucleotide; pairs with adenine in DNA
transition state: in an enzyme-catalyzed rx, the reactive condition of the substrate after there
has been sufficient input of energy (Ea) to initiate a rx
Uracil (U): replaces thymine in RNA; part of a nucleotide that pairs with adenine in RNA
QUESTIONS:
1. (no question in packet???)
2. Four levels of protein structure:
a. Primary structure- peptide linkages link amino acids together; sequence of
aa determine structure and function of resulting protein
b. Secondary structure- the α helixes and β pleated sheets form from bonds
between aa
c. Tertiary structure- hydrogen bonds form to fold the α helixes and β pleated
sheets into the protein’s shape
d. Quaternary Structure- many tertiary structure polypeptide chains (proteins)
combine to form a complex protein
3. Denaturation can result from high temperatures or a change in pH. Denaturation
changes the shape of the protein’s higher level structuring, and therefore changes
the function. If effected by heat, the protein can often refold to its original shape
after it is cooled because the primary order of peptides has not been altered, just the
hydrogen bond folding.
4. Research feedback mechanism for insulin and gluconeogenesis:
Gluconeogenesis is the process of synthesizing glucose from non-carbohydrate
sources. It is like the revese of glycolysis, which is breaking down the glucose.
An increase in blood glucose can occur through inhibition of insulin release,
stimulation of glucose-yielding pathways (glycogenolysis and gluconeogenesis) or
the decrease of glucose uptake. Blood glucose concentration is influenced by
hormones which facilitate its entry into or removal from circulation in the blood.
Hormones regulate glucose concentration by modifying glucose uptake by the cells
for energy production. The most important hormone involved in glucose
metabolism is insulin, which inhibits glucose production by inhibiting
gluconeogenesis and glycogenolysis. Therefore insulin causes a decrease overall in
blood glucose.
When insulin resistance occurs, the body is disrupted because there is nothing in
the blood to inhibit the glyconeogenesis. Normally, there is a negative feedback
mechanism, so as blood glucose increases, the insulin is released to control the
amount blood glucose. So, if the insulin release doesn’t properly function, then
there is an uncontrolled amount of glucose in the blood, or hyperglycemia, which
could lead to type II diabetes.
Sources:
http://www.elmhurst.edu/~chm/vchembook/604glycogenesis.html
https://ahdc.vet.cornell.edu/clinpath/modules/chem/GLUCOSE.HTM
http://www.medbio.info/horn/time%203-4/homeostasis_2.htm
5. The rx in the packet is exergonic. The free energy is negative. In an endergonic rx,
the standard change in free energy is positive, and energy is absorbed. The total
energy is a negative net result.