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80 Cards in this Set

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primary structure of a protein
linear sequence of amino acids
secondary structure of a protein
local, spatial arrangement of amino acids relative to one another
What are most proteins combinations of?
alpha helix, beta pleated sheet, beta turns, and random conformations
Who first proposed alpha helix and beta pleated sheet
Pauling and Corey 1951
Alpha helix
Tightly coiled rod-like structure. Side groups extend out in helical array, stabilized by H-bonding between N-H and C=O groups of separate amino acids of the main backbone
How is each residue related in the alpha helix?
Each is related to the next by 1.5 A and a rotation of 100 degrees. This yields 3.6 amino acids per complete turn of the helix.
Notes of alpha helix
alpha helices are found in proteins that are right-handed, they can range from 0-100% of a protein, and in globular domains they usually do not continue unbroken for more than 45 A, about 30 aa (exception is alpha helical coiled coil
Alpha helical coiled coil
2 or more alpha helices entwine to form
Where are coiled coils commonly found and what are some common proteins
cytoskeletal proteins where mechanical strength is required. Common proteins include myosin (thick filaments in muscle), tropomyosin (lies along actin thin filaments in muscle), and keratin (hair protein
Beta pleated sheet
polypeptide backbone is fully extended (distance between adjacent amino acids is 3.5 A rather than 1.5)
In a beta-helix where does H-bonding occur
between neighboring strands
Beta-turns
common turn where the C=O group of residue n is H-bonded to the N-H group of residue n+3
Where are Beta-turns found?
connecting adjacent Beta strands of a beta-pleated sheet
Random structure
refers to lack of repetitious secondary structure
Tertiary structure
spatial arrangement of secondary structure
Quaternary structure
structure of a protein complex, arrangement of protein domains.
ex. hemobglobin owes its structure to the association of 4 myoglobin like subunits
What are the hurdles of transporting oxygen to all tissues and cells
1.) Oxygen is poorly soluble in H20
2.) Oxygen is a strong oxidizing agent
Where are myoglobin and hemoglobin found and what do they do
Myoglobin: muscle
Hemoglobin: eurythrocytes
primary oxygen carriers
-contain heme prosthetic group responsible for binding O2 (non-polypeptide unite required for biological activity)
What does heme consist of and where is it located?
Consists of an organic protoporphyrin ring structure with an iron ion bound by 4 nitrogens.
Location: buried in a mostly hydrophobic cleft within the protein, the charged propionate groups stick out into the aqueous solvent.
How can the iron ion be b]found? Which binds Oxygen?
Ferro (Fe2+) or ferri (Fe3+)
Ferro binds oxygen
Rust comes from Fe3+ and iron
Who solved the myoglobin structure?
Who solved the hemoglobin structure
Myoglobin: (first one) John Kendrew 1957
Hemoglobin: Max Perutz
Features of myoglobin
1. extremely compact, little water inside protein
2. 75% alpha helix, no beta sheet. There are 8 major helices (A-F); 4 of these are terminated by a proline residue (structure breaker)
3. The main chain polypeptide units are planar and the side groups are trans to amide hydrogen, this geometry was predicted by Pauling and Corey
4. The interior consists almost entirely of hydrophobic amino acids, the exterior aa are almost entirely hydrophilic, the only 2 polar aa inside myoglobin are 2 His, both of which are important in binding of )2
The Fe ion is directly bound to ...
the proximal histidine and 4 nitrogens found in heme
Where is the O2 binding site
on the opposite side of the ring relative to the proximal histidine, bound to Fe2+
What does the distal Histidine do?
it is fairly close to the O2 binding site, H-bonds to O2, provides steric hindrance
Why does the iron (Fe2+) need a protein environment?
Without it O2 quickly pulls an e- off the Fe2+ to make Fe3+ (Fe2O3=rust)
Hemoglobin and myoglobin binds...
CO 200 x's stronger than O2, but isolated heme binds CO 20,000 x's stronger.
How does the protein reduce such tight binding?
The distal His physicaly prevents linear molecular arrangement between the Fe2+ and the CO. Linear is far more stable for CO than a bent geometry.
Three physiological forms of myoglobin
1.) deoxymyoglobin: Fe2+, no O2 bound
2.) oxymyoglobin: Fe2+, O2 bound
3.) ferrimyoglobin: Fe3+, no O2 bound, O2 can't bind
How is it possible for myoglobin and a subunit of hemoglobin to be virtually superimposable when only 24 of 141 aa are completely conserved in the alpha and beta chains of human hemoglobin and whale myoglobin?
Strong conservation of 3-D structure and biological function do not require similar conservation of the primary aa sequence. Different aa structures can give rise to very similar structures.
What is allostery?
When the binding of a molecule at one site in a protein affects 3-D structure or activity at a distant site.
Binding of O2 to hemoglobin...
enhances further binding of O2, Hb can bind up to 4 O2
Affinity for O2 is...
pH & CO2 dependent. Bother higher [H+] and [CO2] promote release of O2 (weaken O2 binding). Binding of O2 promotes release of H+ and CO2.
The Bohr effect
Acidity (higher [H+]; lower pH) enhances release of O2 to Hemoglobin. Rapidly metabolizing tissue produce a lot of CO2 and H+. Active tissues will contain high CO2 and H+; these 2 molecules bind to oxyhemoglobin at distinct sites, causing the release of much needed O2.
JBS Haldane showed that...
the reciprocal effect of the Bohr effect works in the lungs. Hemoglobin gets to lungs and gets rid of CO2 and H+. In the alveolar capillaries high O2 drives the release of CO2 and H+
Tense state of hemoglobin
protonation of His HC3 favors, lower affinity for oxygen, favors oxygen release
Relaxed state of hemoglobin
no protanated, favors oxygen binding
2,3 bisphosphoglycerate (2,3-BPG)
abundant in erythrocytes where it binds Hb and reduces affinity for oxygen by favoring T state
Functions of BPG
High altitude: after just a few hours at high altitude, 2,3-BPG levels go up in blood, partial pressure of Oxygen decreases and more BPG allows greater release of Oxygen into tissues

Mother-fetus oxygen exchange: fetus tetramer of alpha 2 gamma 2 has lower affinity for 2,3 BPG so has greater affinity for oxygen
Binding of oxygen favors the R state
pulls Fe 2+ into plane of the porphyrin ring; this pulls the proximal His and the rest of the F helix: which causes conformational change within the other hemoglobin subunits which favors R state which results in higher Oxygen affinity
Thalassemias
most common human single gene disorder, results from partial or comlete absence of one or more alpha or beta Hb chains, leads to aggregation and premature destruction of RBC
Anemias
reduction of red blood cells can result from defective Hb.

Sickle cell anemia: results from single aa substitution of the beta subunit
phosphoserine, phosphothreonine, phsphotyrosine
phosphorylation of these three alcohols are reversible and are used as reversible switches to regulate cullular processes
Hydroxylation: hydroxyproline and hydroxylysine
commonly found in collagen, the primary structural protein in skin, bone, tendons

the oxydation of proline requires: vitamin C
Collagen:
rich in Gly, Pro, Hyp residues, 3 polypeptide chains which coil around each other,the rise between aa is 2.9 A, h-bonding is between separate helices not w/in a single strand
Procollagen:
synthesized by fibroblasts and smooth muscle cells
1. assists in placing the three polypeptides in register with one another
2. keeps the procollagen triple helix soluble
tropocollagen
formed from procollagen (cleaved by procollagen protease), capable of self-assembly into fibers
Enzymes:
speed up chemical reactions, they do not affect equilibrium concentrations or direction of a reaction
Kcat=
the max number of reactions completed per enzyme per second

use sec -1 or 1/sec
kinetics...
predicts the rate at which a reaction proceeds
thermodynamics...
predicts the equilibrium concentration and direction of a reaction
Enzymes do not affect thermodynamics

Enzymes do affect the
do not change change in free energy

rate of the reaction, effect kinetics not thermodynamics
as activation energy becomes large...
the rate becomes smaller
enzymes and catalysts lower activation energy...
and rate increases
Active sites
take up small volume of protein

are 3-D entities composed of aa that may be very far from one another in primary aa sequence

substrates are bound to the active sit by multiple weak bonds/attractions

are clefts or crevices, water is typically excluded

specificity of binding depends on precisely defined arrangement of atoms at the active site
Lock and key model
substrate is perfect complimentary match to the enzyme binding site (not accurate)
Induced fit model
active site changes 3-d structure upon binding of substrate so that the active sit structure is then complementary to the structure of the substrate;the structure of the substarte might also change so that it is strained or closer to the transition state structure
Properties of enzyme catalysts
1. required only in trace amounts
2. unchange by net reaction
3. enchances the rate
4. facilitate both forward and reverse raection equally
5. show high specificity
oxidoreductases
catalyze oxidation reduction reactions
transferases
transfer functional group between 2 molecules
hydrolases
hydrolysis reactions, water is consumed while breaking a single bond
lyases
addition to a double bond
isomerases
move a functional group withing a single molecule
ligases
formation of bonds using energy from ATP hydrolysis
when a substrate is scarce...
enzyme activity is limited by availability of substrate
when substrate is plentiful...
the enzyzme activity reaches saturation
V =
rate of reaction
Vmax [S]/Km + [S]
Substrate is scarce...
V will be linearly dependent on [S], as long as S is significantly smaller than Km

doubling the concentration of substrate would double rate of reaction
substrate is plentiful...
the enzyme will turnover as fast as possible and the rate of the reaction is at a maximum
substrate equal Km (rate constants)
rate of reaction is half of maximum rate of reaction

you can identify Km by identifying [S] necessary to achieve 1/2 max
What do fast turnover rates of enzymes require
substrate and product be able to dissociate quickly

the tighter the binding the slower the dissociation, tight binding allows the E to work at low [S] values
inhibition
slowing down an enzyme-catalyzed reaction
Irreversible inhibition
occurs when the inhibitor dissociates very slowly from the enzyme; effectively, the inhibitor does not leave the enzyme

typically involves covalent bond with the enzyme (of I to E)
Penicillin
irreversibly inhibits the transpeptidase enzyme in bacteria which is important for cross-linking peptides in the peptidoglycan cell wall
Reversible inhibition
involves an inhibitor
Competitive inhibition
the inhibition can bind either S or I, but not both simultaneaously

Typically S & I compete for active site, this type of inhibitor works by taking a fraction of the enzyme of the game
noncompetitive inhibition
Both S and I can bind the enzyme simulataneously, works by reducing the turnover rate for each enzyme that has I bound to it
How does increasing [S] affect these two inhibitions?
Increased [S] can "swamp out" the inhibitor, I, when the two are competing for the same site; however, increasing [S] can not swamp out noncompetitive inhibition
Uncompetitive inhibitor
only binds the ES complex and alters both Vmax and Km
mixed mode inhibitor
binds either E or the ES complex and alters both Vmax and Km