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Biochemistry Test #2
biochemistry
74
Chemistry
Undergraduate 3
02/25/2009

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Term
What are the four arrangement of secondary structures of globular proteins?
Definition
1) anti-parallel alpha-helix
2) parallel or mixed beta-sheet proteins
3) anti-parallel beta-sheet
4) metal- and disulfide-rich bonds
Term
Which structure is is more likely to occur: anti-parallel or parallel
Definition
anti-parallel, due to folding back and forth to create the smallest space
Term
What forces are most important in setting up initial structure of globular protein?
Definition
Hydrophobic interactions
Term
What shape do beta-strands tend to be in in a globular protein and why?
Definition
They are curved instead of straight because there is higher stability due to increased hydrogen bonding.
Term
If the adjacent arrows of a globular protein are pointing in the same direction the structure is ___.
Definition
parallel
Term
Define protein domain (or protein module).
Definition
A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. They generally don't have the same function in different proteins, and contain between 40 to 100 amino acids.
Term
What do all beta-domains contain?
Definition
A core comprising of antiparallel β-sheets, usually two sheets packed against each other.
Term
Steps of protein folding
Definition
1) a polypeptide forms segments of secondary structure (alpha-helix and beta-sheet)
2) these unite into a globular structure, primarily through hydrophobic interactions
3) The final tertiary structure is generated by small adjustments to the folded structure
4) In the cell, protein folding may require the assistance of molecular chaperones
Term
Define quaternary structure
Definition
The arrangement of multiple folded protein molecules in a multi-subunit complex
Term
Are covalent bonds necessary to hold quaternary structures together?
Definition
No
Term
Name the forces involved in producing quaternary structures.
Definition
Hydrophobic interactions, hydrogen bonding, ionic interactions and disulfide bonds
Term
What are the structural and functional advantages to quaternary structure?
Definition
1) Stability
2) Genetic economy and efficiency
3) Bringing catalytic sites together
4) Cooperativity (e.g., with hemoglobin, the first molecule to bind makes the next molecules easier to bind)
5) The interaction between subunits allows for the subunits to influence each other's behaviors.
Term
What is the structure of DNA polymerase and hemoglobin?
Definition
quaternary structure
Term
Because hemoglobic has two alpha and two beta units, it can be considered a ______ of _____.
Definition
Dimer of dimers
Term
Give 5 examples of protein domains or modules.
Definition
a) complement control
b) immunoglobin
c) fibronectin
d) growth factor
e) kringle
Term
What are the shortest domains (i.e. zinc fingers) stabilized by?
Definition
metal or disulfide bonds
Term
How are protein domains produced?
Definition
By the duplication of DNA segments within a gene or by the movement of DNA from one gene to another
Term
What are some advantages for domains to fold individually?
Definition
a) accelerates folding process
b) reduces large combination of residue interactions
c) allows a large protein to bury its hydrophobic residues and keep hydrophilic residues at surface
Term
Define heme
Definition
the place buried in the mass of globular protein where proteins bind
Term
Define microtubule
Definition
cytoskeletal fibers built from small globular protein subunits: rigid & thick, constructed as a hollow tube
Term
Components of microtubule:
Definition
beta-tubulin + alpha-tubulin= dimer (each contains ~ 450 amino acids)
end to end dimers = protofilaments
protofilaments wrap into a hollow tube to create a microtubule
Term
Intermediate filaments are exclusively what kind of protein?
Definition
structural
Term
Basic structure of intermediate filaments:
Definition
a dimer of alpha-helices that wind into a coil of a 7-residue repeating unit wth hydrophobic residues in contact
Intermediate filament may consist of 16 to 32 polypeptides in cross section
*Crosslinked thru disulfide bonds
Term
3 main amino acids of collagen
Definition
Glycine (every 3rd), proline and hydroxyproline
Term
Conformation of collagen
Definition
three polypeptides wind around each other to form a right-handed triple helix
Term
How is collagen stabilized
Definition
hydrogen bonding (N-H group of each Gly is linked to a backbone C=O group)
Term
Collagen cross-links are ___ bonds
Definition
covalent
Term
Define tertiary structure
Definition
the folding of a single polypeptide chain in 3-D
Term
Provide examples of Type I, II and III collagen
Definition
I: bones, skin and tendons
II: cartilage
III: blood vessels
Term
Provide conformation of alpha-helices and give examples
Definition
coiled coil of two alpha-helices, which are twisted w/ additional coils into a rigid filament: examples include hair and fingernails
Term
Provide examples of fibroin and beta-keratin
Definition
fibroin: silk fibers
beta-keratin: bird feathers
Term
4 classifications of globular proteins
Definition
1) Antiparallel alpha-helix proteins
2) Parallel or Mixed Beta-Sheet Proteins
3) Antiparallel Beta-Sheet proteins
4) Metal & Disulfide-Rich Proteins
Term
Define quarternary structure
Definition
the association of monomeric protein subunits to form multi-subunit complexes
Term
Define isologous interactions
Definition
the interacting surfaces are identical and the resulting structure is dimeric (quarternary structure)
Term
Define heterologous associations
Definition
involve nonidentical interfaces with complementary surfaces (quarternary structure)
Term
Forces involved with quarternary structure
Definition
hydrophobic, hydrogen bonding & ionic interactions
Term
Advantages of Quarternary Association
Definition
1) Stability: reduces the protein's surface-to-volume ratio
2) Genetic Economy & Efficiency: less DNA is required to code monomer
3) Bringing catalytic sites together
4) Cooperativity: binding at one site increases binding at other sites
Term
Most common type of protein
Definition
globular
Term
Describe metal and disulfide-rich proteins
Definition
Have unusual amounts of methyl ions bound to disulfide bonds--highly stable structure
Term
Most important force behind initial globular protein structure
Definition
hydrophobic interactions
Term
Describe beta-strands in globular protein
Definition
Tend to curve & there are pairs of them rather than a straight line...more stability due to Hydrogen bonding
Term
Which ends of globular protein have greatest freedom of movement?
Definition
Ends projecting away
Term
How to tell anti-parallel from a parallel globular protein:
Definition
*Adjacent arrows pointing in same direction: parallel
*Adjacent arrows pointing in opposite directions: anti-parallel
Term
Define protein domain or module
Definition
Amino acid sequences used repeatedly in the same protein or found in different proteins.
Term
How many amino acids are typically found in a protein domain/module?
Definition
40 to 100
Term
How are protein domains or modules produced?
Definition
by the duplication of DNA segments w/in a gene or by the movement of DNA from one gene to another
Term
Define enzyme
Definition
Proteins that increase the rate of chemical reactions; catalysts
Term
What do enzymes do?
Definition
Create pathways that break down nutrient molecules, release energy, synthesize precursors, and link them together to form new molecules
Term
3 Distinctive features of enzymes
Definition
1) Catalytic Power--can speed reaction up to 10^6 times
2) Specificity--selectively act upon a substrate to create a particular reaction
3) Regulation--inhibitors + synthesized enzymes control levels of active enzymes in cell
Term
Define substrate
Definition
molecules at the beginning of process
Term
Substrates converted into different molecules are called ___
Definition
products
Term
Define velocity
Definition
a) the rate of disappearance of the substrate
b) the rate of appearance of the product
Term
Relationship between catalyst and reaction speed
Definition
The more catalyst present, the faster the reaction
Term
Name 6 classifications of enzymes
Definition
1) Oxioreductases (oxidation & reduction reactions)
2) Transferases (transfer of functional groups)
3) Isomerases (isomerization reactions)
4) Hydrolases (hydrolysis reactions)
5) Lysases (addition to double bonds)
6) Ligases (formation of bonds with ATP cleavage)
Term
Define cofactors
Definition
metal ions or organic molecules that bind to enzymes & are required for enzyme activity
Term
Define coenzymes
Definition
Organic molecules (particularly water-soluble vitamin derivatives) that act as enzyme cofactors
Term
Define prosthetic groups
Definition
tightly bound cofactors or coenzymes that are crucial to the enzyme's function
Term
Define holoenzyme
Definition
Catalytically active complex of protein and coenzyme
Term
Define apoenzyme
Definition
Protein without the prosthetic group
Term
Enzyme-Substrate Complex in Practice:
Definition
1) @ high substrate conc., enzyme activity levels off as it approaches max. value

2) @ low substrate conc., the enzyme quickly converts all the substate to product, but...

3) as more substrate is added, the enzyme is saturated with substrate and so not all substrate can be converted
Term
First order equation
Definition
v = k[A]
velocity = rate constant [A]
*reaction velocity is directly proportional to concentration of A
Term
Second order equation
Definition
A + B = C
v = k[A][B]
*velocity of 2nd order is proportional to the product of the two reactant concentrations
Term
Enzyme-catalyzed reaction
Definition
v = k2 [ES]
*when [S] is very high, virtually all the enzyme is in its ES form (saturated with substrate)
Term
Michaelis-Menten equation (rate equation that describes the hyperbolic curve)
Definition
vo (initial velocity) = vmax[S]/km + [S]
Term
Relationship between Michaelis-Menten equation and variables
Definition
it describes the reaction if all other variables are constant
Term
Equation for Vmax (maximum reaction velocity)
Definition
Vmax = k2[E]T
Term
How can Km and Vmax be determined graphically?
Definition
From a straight-line plot derived from the Michaelis-Menten equation
Term
Explain what happens in Michaelis-Merten equation when [S]>>Km
Definition
v = Vmax...v is no longer dependent on [S] and the reaction is zero-order
Term
What does Km represent?
Definition
the substrate concentration @ which the reaction velocity is half-maximal
Term
What does Km indicate?
Definition
how efficiently an enzyme selects its substrate and converts it to product
Term
Relationship between a low Km and effectiveness
Definition
The lower the Km, the more effective enzyme is at low substrate conc.
The higher the Km, the less effective enzyme is at high substrate conc.
Term
Why is Km useful?
Definition
It is unique for each enzyme-substrate pair:
1) comparing activities of two enzymes that act on the same substance
2) assessing the ability of different substrates to be recognized by a single enzyme
Term
Define Km
Definition
enzyme's affinity for a substrate
Term
Provide enzyme equation
Definition
Km ~ [E][S]/ [ES]
This is only true when the ES--> E + P is slower than the rate of ES --> E + S reaction
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