Finals: Proteins Flashcards
naturally occuring, unbranched polymer in which the monomeric units are amino acids
proteins
all proteins contain elements ?
carbon, hydrogen, oxygen and nitrogen most also contain sulfur.
the presence of ______ sets them apart from carbohydrates and lipids, which most often do not contain ____
nitrogen
the main of protein of milk - which contains ____
Casein , phosphorus
amino acids found in proteins
a-amino acid
R group
- amino acid side chain
- distinguishes a-amino acids from each other
an organic compound that contains both amino
NH2 group and carboxyl (-COOH) Group
has non polar side chain
non polar amino acid
hydrophobic (water fearing)
non-polar amino acid
found in the interior of proteins, where their is limited contact with water
non-polar amino acid
R group - hydrocarbons (aliphatic or aromatic )
non polar amino acid
has polar side chain
polar amino acid
hydrophilic (water loving)
polar amino acid
found on the surfaces of proteins
polar amino acid
Polar amino acids are subcategorized to:
- polar neutral
- polar acidic
- polar basic
why are standard amino acids named that way
commonly encountered in proteins
R group consists of aliphatic:
alkanes, alkenes, alkynes
Polar neutral: At physiological pH, R group is neither?a
acidic nor basic
polar amino acids:
contains polar but NEUTRAL SIDE CHAIN
Polar neutral
side chain of polar neutral has groups that contain?
heteroatom
Polar neutral: R group can
hydrogen bond with water
for polar neutral, can it exhibit hydrogen bonding
yes
contains a carboxylc group as part of the side chains
polar acidic
side chain of polar acidic:
carboxylic acid
Polar acidic: physiological pH, R group bears a
negative charge, the side chain carboxyl group has lost its acidic hydrogen atom
contains an amino group as a part of the side chain
polar basic
side chain of polar basic
amine, imine
polar basic: at physiological pH, R group bears
negative charge, the side chain carboxyl group has accepted a proton
amino acids are linked together by an ?
amide (peptide) bond via a condensation reaction
Structure of proteins: Primary (1)
amino acid sequence (how many? which ones?, arrangement)
structure of proteins: secondary (2 degrees)
H-bonds on proteins backbone (how structures are stabilized)
Structure of proteins: Tertiary (3 degrees)
overall 3D shape of folded protein (overall 3d shape of a folded)
Structure of protein: Quarternary (4 degrees)
subunit organization (how polypeptides are assembled in a complex structure)
every protein has its own unique amino acid sequence
primary structure
It is the order sequence in which amino acids are linked together in a protein
primary structure
amino acids are linked to each other by peptide bonds
primary structure
arrangement in space adopted by the hydrogen-bonded arrangement of the backbone portion of a protein
secondary structure (2 degrees)
folding is stablizied by noncovalent interactions (specifically H bonds)
secondary structure
Beta sheets
- 2 or mroe polypeptide chains
- H-bonds are between adjacent strands
- R-groups are on opposite faces of the sheet
Alpha Helix
- has 1 polypeptide chain
- H bonds are within a single polypeptide chain
- R-groups are outside
- right handed or clockwise, spiral
secondary structure: A single protein chain adopts a shape that resembles a coiled spring
alpha-helix structure
secondary structure: Hydrogen bonds between C=0 and N- H entities are orientated parallel to the axis of the helix
* All of the amino acid R groups extend outward from the spiral
alpha helix structure
secondary structure: Coil configuration maintained by hydrogen bonds
alpha -helix structure
secondary: Two fully extended protein chain segments in the same or different molecules
- Held together by hydrogen bonds.
H-bonding between chains - Inter and/or intramolecular.
beta-pleated sheet structure
Overall three-dimensional shape of a protein.
- Results from the interactions between amino acid side chains (R groups) that are widely separated
trom each other. - hydrophobic residues cluster in the core
- polar residues in helices and sheets
Tertiary structure
Tertiary structure: 2 main factors for folding of a protein
1, hydrophobic residues cluster in the core
2. polar residues in helices and sheets
Amino acids are linked together by an?
amide (peptide) bond via a condensation reaction
The carboxyl group of one amino acid
interacts with?
with the amino group of the other amino acid.
What are the products when a carboxyl group of one amino acid interacts with the amino group of the other amino acid?
molecule of water and a molecule containing the 2 amino acids linked by an amine bond
It is when all peptide bonds are broken, and the only products are amino acids
complete hydrolysis
It is when some but not all peptide bonds are broken, and the product is a mixture of amino acids and small peptides
partial hydrolysis
Partial or complete disorganization of a protein’s characteristic three- dimensional shape
Protein Denaturation
what are the common proteins in the body?
fibrous and globular
type of protein:
Filamentous or elongated shape
FIBROUS PROTEIN
type of protein:
Function is mostly structural
(strength/support)
fibrous protein
type of protein:
Repetitive AA sequence
o Have a single type of secondary structures
o Simple, regular, linear structures
fibrous protein
type of protein:
Usually water-insoluble
· Examples; alpha-keratin and collagen
what type of protein are these ·alpha-keratin and collagen
fibrous protein
fibrous protein:
α-Keratin
provides protective coating for organisms
Mainly made of hydrophobic amino acid residues
a-Keratin
type of fibrous protein:
Most abundant protein in humans (30% of total body protein)
* Major structural material in tendons, ligaments, blood vessels, and skin
collagen
predominant structure of collagen
Triple-helix Glycine and proline help maintain the structure of the triple-helix
Organic component of bones and teeth
collagen
Protein classification:
- Spherical or globular shape
- Function is mostly as catalyst, transport, etc.
Protein classification:
irregular AA sequence
globular
Protein classification:
Usually, water-soluble
*Hydrophobic aa residues are in the protein
core
globular
Protein classification:
Function is mostly as catalyst, transport, etc.
globular
type of globular protein:
Oxygen-storage molecule in muscles
myoglobin
examples of globular protein
hemoglobin and myoglobin
type of globular protein:
Monomer
– Consists of a single peptide chain and one heme unit
– One molecule carries one O2 molecule
myglobin
Has a higher affinity for oxygen than hemoglobin
myglobin
Oxygen stored in myoglobin molecules serves as a ?
reserve source for working muscles when oxygen demand exceeds its supply
An oxygen-carrier molecule in blood
–Transports oxygen from lungs to tissues
hemoglobin
Hemoglobin: Iron atom in ??? interacts with ???
heme with oxygen
a compound, usually a PROTEIN, that acts as a CATALYST for a biochemical reaction.
enzyme
Most enzymes are
globular proteins
Enzymes are neither
consumed nor permanently altered after the reaction
enzymes undergo all the reactions of proteins including ?
denaturation.
enzymes are highly?
efficient, specific and can be regulated
enzyme composed only of protein (amino acid chains)
- Simple enzyme
enzyme that has a nonprotein and protein parts
conjugated enzyme
Classes of enzymes:
Redox reactions
Oxidoreductase
Classes of enzymes:
Transfer of functional groups
Transferase
Classes of enzymes:
Hydrolysis reactions
Hydrolase
Classes of enzymes:
Isomerization
Isomerase
Classes of enzymes:
Addition of groups to double bonds or Removal of groups to form double bonds
Lyase
Classes of enzymes:
Joining of two molecules (hydrolysis of ATP as energy source)
Ligase
an enzyme that catalyzes an oxidation- reduction reaction.
OXIDOREDUCTASE
an enzyme that catalyzes the transfer of a functional group from one molecule to another.
Transferase
It oxidases, Reductases, Dehydrogenases
Oxidoreductase
help disposal of nitrogen during the metabolism of amino acids for energy production or for synthesis of bioactive compounds from
Aminotransferases
an enzyme that catalyzes a hydrolysis reaction in which the addition of a water molecule to a bond causes the bond to break.
. HYDROLASE:
effect the breaking of glycosidic bonds in oligo- and polysaccharides,
Carbohydrases
effect the breaking of peptide linkages in proteins,
Proteases
effect the breaking of ester linkages in
triacylglycerols.
Lipases
an enzyme that catalyzes addition or removal of atoms across a double bond
LYASE
adds water across the double bond in
trans-Enoyl CoA during the oxidation of fatty acids for biochemical energy production
Enoyl CoA hydratase
small part of an enzyme’s structure that is involved in catalysis; it is where the substrate binds to the enzyme.
Active Site
formed due to folding and bending of the protein.
Active Site
location in the enzyme
“CREVICE-LIKE”
contains catalytic amino acid residues or groups.
active site
Increasing temperature will
increase reaction rate
is the temperature where maximum activity is observed
Optimum temperature
Enzymes are sensitive to the?
acidity and basicity of their chemical environment
Going beyond the optimum temperature will
destroy the enzyme structure
is the pH where maximum activity is observed
Optimum pH
Putting enzymes anywhere lower or higher the optimum pH will ?
destroy the enzymes structure
in the body is usually physiological pH, but exceptions are proteolytic enzymes in the stomach (pH ~2)
optimun pH
are the reactants for enzyme- catalyzed reactions
Substrates
is the maximum amount of substrate molecules that an enzyme can convert to products
Turnover number
When an enzyme is saturated, its activity reaches a
plateau
Changes in enzyme concentration are directly proportional to enzyme activity
Enzyme Concentration
