WGU BIOCHEM C785 STUDY GUIDE ( A+ GRADED 100% VERIFIED)
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BioChem C785
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Western Governers University
WGU BIOCHEM C785 STUDY GUIDE ( A+ GRADED 100% VERIFIED)
1. Unit 2 Amino acids, peptide bonds, and protein structures
2. Amino Acids: The building blocks of proteins
3. Chemical elements, atoms and bonds—Optional Review
a. Electrons-only subatomic particle involved in chemical reactions
b. En...
wgu biochem c785 study guide a graded 100 verified
1 unit 2 amino acids
and protein structures 2 amino acids the building blocks of proteins 3 che
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BioChem C785
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bio chem study guide
1. Unit 2 Amino acids, peptide bonds, and protein structures
2. Amino Acids: The building blocks of proteins
3. Chemical elements, atoms and bonds—Optional Review
a. Electrons-only subatomic particle involved in chemical reactions
b. Energy- compacity to cause change (doing work)
c. Covalent bonds- sharing a pair of valance electrons by two atoms ex: H—H
d. Ionic bonds- chemical bond resulting from attraction of atoms of opposite charge (salt
bridge)
e. Hydrogen bonds- weak chemical bond formed when slightly + hydrogen atom and a
polar covalent bond in one molecule is attracted to the slightly negative atom of a polar
covalent bond in another molecule or in another region of the same molecule ex: H20 &
NH3 (ammonia)
4. Amino Acid Structure and Chemical Properties
a. Amino- tends to pick up a proton- giving it a positive charge ex: NH2
b. Carboxyl- group tends to have negative charge- because it tends to lose a proton ex:
COOH
c. Hydrophobic (nonpolar)- water hating
i. makes hydrophobic interactions
ii. Only has carbon and hydrogen ex: CH2, CH3
iii. Heat breaks hydrophobic interactions
d. Hydrophilic (polar)- Water loving
i. makes hydrogen bonds
ii. In addition to C & H, R group has O, N, or S
iii. Change in pH or adding salt can break hydrogen bonds, reducing agents break
the disulfide bonds.
e. Charged- positive (basic) or negative (acidic)
i. Makes ionic bonds
ii. Change in pH or adding of salt can break ionic bonds
f. Disulfide bonds
i. Strongest bond
ii. A double bond btw two Sulphur atoms in cysteine side chains
iii. What type of amino acids participate in disulfide bonds? Cysteine
iv. Disrupted by reducing agents
g. Zwitterions- a molecule or ion having separate positively and negatively charged groups.
h. What is the basic structure of amino acid?
i. Carboxyl group- tends to have a neg charge (COOH-)
ii. Amino group- tends to pick up a proton- giving it a positive charge (NH2)
iii. Carbon- alpha carbon, can form 4 covalent bonds
iv. R- where amino acids differ from one another (side chair/variable)
5. Polypeptides and Functional Proteins
a. Polypeptides- A single protein chain consisting of several amino acids bonded by peptide
bonds
b. Peptide bonds- amino acids are linked together by a specific type of bond called a peptide
bond.
6. Levels of protein structure
a. Dehydration- associated with water loss in the body
b. Hydrolysis- chemical breakdown of a compound due to reaction with water
c. Alpha helix- delicate coil held together by hydrogen bonds btw 4th amino acid ex: a-keratin,
hair (chain twists)
, d. Beta sheet- 2 or more segments of polypeptide chains lying side/side ex: spider web, silk
fibers parallel to one another
e. Denaturation-Process of ruining the functional structure of a molecule. It
will no longer be able to carry out its intended function. A process by
which the native functional structure of a molecule has been disrupted
f. What are the 4 level of protein structure? List distinguishing features of each
i. Primary
sequence of amino acids forming a protein or polypeptide chain, the most
basic element of its structure (peptide bonds)
ii. Secondary
three-dimensional structure of sheets, helices, or other forms taken on by
polypeptide chain, due to electrostatic attractions between neighboring
resides (stabilized by hydrogen bonds)
iii. Tertiary
three-dimensional structure resulting from folding and covalent cross-
linking of a protein (hydrogen bonds, ionic bonds-positive or negative
charges, and disulfide bridges)
iv. Quaternary
overall protein structure consisting of two/more polypeptide chains
aggregated into one functional macromolecule ex: hem + iron=
hemoglobin, connective tissues (hydrophobic and hydrophilic
interactions, & disulfide bridges)
7. A Protein’s Structure Depends on its Environment
a. Aggregation- clustering
b. What environmental change breaks each type of bond?
i. hydrophobic bond, weak strength, heat disrupts the interaction (fever, frying an
egg)
ii. ionic bonds, change in pH and adding salt disrupts the interaction
iii. hydrogen bonds, change in pH or adding salt can break these bonds
iv. disulfide bonds- reducing agents disrupts this process
c. What type of amino acid side chain leads to protein aggregation?
i. Hydrophobic interaction
ii. Ex: sickle-cell hemoglobin in proteins lead to their aggregation into a fiber;
capacity to carry oxygen is greatly reduced
iii. Ex: Alzheimer’s disease, accumulation of proteins inside and around neurons
leads to neuronal cell death and brain atrophy (jelly doughnut protein
aggregation)
8. Protein Function and Disease
a. How do environmental changes affect protein folding?
i. High temp, pH and salt concentration or other aspects of its environment are
altered, the weak chemical bonds and interactions within a protein may be
destroyed causing the protein to unravel and lose its native shape.
b. How do mutations affect protein structure?
i. Changes in DNA lead to changes in mRNA, and the code mRNA determines the
sequence of amino acids, which are the basis of protein structure. (changes amino
acids which changes the overall structure)
ii. Mutations cause misfolding- neurodegenerative diseases
9. Enzymology and Catalytic Mechanism
10. Enzyme Action
a. Substrates- molecule that an enzyme will specifically bind to
b. Products- released from the enzyme active site
, c. Intermediates- molecular entity that is formed from reactions and reacts further to give
the directly observed products of a chemical reaction.
d. Active Site- substrate binding site on an enzyme
e. Enzyme specificity – enzymes catalyze only one type of reaction, and most act only on a
particular substrate
f. Induced fit- when substrate and enzyme combine, the shape of the enzyme changes to
more closely bind the recognized substrate
g. Kinase- adding phosphate to a group
h. Phosphatase- removing a phosphate group
i. How do enzymes catalyze reactions?
i. Enzymes are biological catalysts; catalysts lower the activation energy for
reactions
j. How do enzymes affect reaction rate and activation energy?
i. Enzymes lower activation rate, and speed up reaction
k. What are the 4 steps of the enzymatic cycle?
i. Enzyme and substrate are in the same area. Sometimes there are more than one
substrate molecule that the enzyme will change.
ii. Enzyme grabs on to the substrate at a special area called the active site
iii. Process called catalysis happens
iv. Enzyme releases product
11. Factors that influence Enzyme Activity
12. Enzymes are affected by their environment
a. How do environmental changes affect enzymes?
i. Temp- increased temp= increased enzymatic rate, substates collide with active
sites more frequently when molecules move rapidly; however, the thermal
agitation of the enzyme molecule disrupts hydrogen bonds ionic bonds, and other
weak interactions that stabilize shape of the enzyme, leading to denaturation;
1. humans have optimal temps btw 35-40 degrees C, thermophilic bacteria
that live in hot springs contain enzymes with optimal temps of 70
degrees C or higher
ii. pH- optimal function between 6-8, but there are exceptions; pepsin digestive
enzyme in stomach, optimal at a very low pH (acidic environment); trypsin a
digestive enzyme residing in more alkaline environment in the human intestine
would denature in the in the stomach. (if pH decreases, so does enzyme activity)
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