ucr BCH100 Fall 2009 – Flashcards
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Unlock answersElectonegativity Most electronegative? |
Up and to the right Flourine is most at 4.0 |
| NonCovalent Bond Energies |
Hydrogen Bonds 20KJ*mol Ion dipole bonds 20 KJ*mol Hydrophobic Interactions 4-12 Van der Waals 4 |
| Micelle |
•a spherical arrangement of organic molecules in water solution clustered so that: •their hydrophobic parts are buried inside the sphere and •their hydrophilic parts are on the surface of the sphere and in contact with the water environment |
Hydrogen bond Strength |
•the attractive interaction between dipoles when the: •positive end of one dipole is a hydrogen atom bonded to an atom of high electronegativity, most commonly O or N, and •the negative end of the other dipole is an atom with a lone pair of electrons, most commonly O or N •The strength of hydrogen bonding is about 2-5 kcal•mol -1 •for water, it is 5 kcal•mol-1 |
| Strong base |
| LiOH, NaOH, KOH, Ca(OH)2, and Ba(OH)2 |
| Ka |
Ka = [H+][A-] / [HA]
|
| pH= |
| -log[H+] |
Calculate pH when 1L of water is added to 10ml of 5M HCl b) then same for 10ml 5M Naoh |
(.01L)(5M)/ 1.01L = .05M = [H+] => -log[.05]
b) [OH-] =.05M => [H+]= 10-14/[OH-] =>-log[H+] |
| Calculate the oH of a 1L solution to which has been added 6mL of 1.5M acetic acid (pka4.76) and 5ml .4 Sodium acetate |
[H+] = (.06L)(1.5)/1.011L = .009M
[OH-]= (.005L)(.4M)/1.011L = .002M
pH = 4.76 + log(.002/.009) |
| Hydrophobic Amino Acids Trend? |
| Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Methionine, Tryptophan, Proline Side Chains terminate in with Carbon |
| alpha-Amino acid |
| a structure in which the amino group is on the carbon adjacent to the carboxyl group |
| Polar Amino Acids Trend |
| Serine, Threonine, Tyrosine, cysteine, asparagine, glutamine, histidine Side chains terminate with xH |
| Cysteine Special Property |
| Can form disulfide bonds with other cysteines |
| Acidic AA and Basic AA |
| Acidic: side chain end in COOH which wants to become COO- Basic: Sidechain ends with NHx that wants to become Nx+1 |
| Amino Acid Ionized form at Ka |
| 50% is ionized and 50% is protonated |
| Finding Ionization ratio at a specific pH |
| Ka/[H+] = [OH-]/[H+] =# 1:# is ratio For basic Ka/[H+] = [NH2]/[NH3+] = # => 1/# 1:1/# is ratio |
| Calculating Charge at pH |
| When acids give up a H add a -1 when base gains an H add a +1 NH2 pka = 9.69 and pH below that it will be NH3+ = +1 COOH pka 2.34 and pH above it will give off its H COO- add -1 |
| Bohr Effect |
The pH of blood to promote/discourage oxygen holding ability of hemoglobin.
Muscles produce CO2 which increases acidity. The Increased Acidity caused the release of O2 |
| Chirality of Amino Acids |
COOH H2N+H R
N and H switch sides |
Polypeptide Bonding
How to write |
O- of COOH and the NH3+ bind to form
C-OH part and NH2-C part disapear to make
H C-N-C
Write
NH3->COOH |
| Aldose & Ketose |
Aldose: Monosaccharides with an aldehyde group
Ketose: Monosaccharides with a Ketone group |
| D+L Saccharides Fischer Projection |
| The Bottom most (closest to CH2OH) switches places |
| Alpha and Beta Glycosidic Bonds |
Alpha = opposite side C1 Beta = Same Side C4 |
| Alpha Helix |
- One ploypeptide per turn - Peptide bond is planar and rigid - C=O is hydrogen Bonded to N-H for AA away - The bonds are PARALLEL to the axis -ProLine prevents Alpha helix becuase N isnt free for H bond |
| Beta Pleated Sheet |
-Polypeptide chains run next to each other parallel or anti parallel C-N or C-N C-N N-C
-Can be diff parts of 1 chain or 2 chains
-R group alternate above and below the plane
-C=O and N-H hydrogen bonds and perpendicular to sheet |
| Collagen Triple Helix |
-Called Tropocollagen
- 3 polypeptide chaines wrapped around each other
-every 3rd AA is GLY
-Alternate X-Pro-Gly and X-Hyp-Gly |
Fibrous Proteins Vs Globular Proteins |
Fib: Long Rod, very strong, no folding
Glob: Sphereical, lots of folding |
| Myoglobin |
-takes O2 from Hb
- two polar histidines that coordinate the Heme group
-Fe(II) of heme has 6 coordination sites, 4 interact with N atoms, 1 N of His, and 1 O2
-1 hist is a covalent tether for heme group
- 1 hist acts as a lid to prevent CO2 from bind straight on, weak angle allows removal, straight would be permanent
-CO2 binds to Heme better that O2 |
| Hemoglobin |
-2 alpha and 2 beta chains
-each chain has 1 heme group so it can carry 4 O2
-O2 Binds cooperatively, 1st is hardest but it makes it easier for the next O2 to bind and so on
-goes through conformational change to bind O2
-Uses BPG to bind and transport Oxygen -BPG lowers affinity so it can get rid of it |
| Fetal Hemoglobin |
Higher affinity for O2 the adult Hemoglobin
-Binds less strongly to BPG which means tighter O2 binding
-Sereine replaces Histadine |
Allosteric Change
Denaturization |
Allo: Temporary Protein shape change
Denature: Permanent shape change |
| endergonic vs exergonic |
ender: gives of less energy than it consumes
Exer: gives of more energy than it consumes |
| Enzyme rate equation |
A+B-> C+D
Rate=k[A]1 * [B]1 |
| Chymotrypsin |
Cut polypeptides into smaller pieces Active form of chymotrypsinogen seperate pepetides with Cysteine S-S bonds
|
Km
equation |
how tightly an enzyme binds to a substrate Lower number = tighter bond 0 = permanent
Km = k-1 + K2 / K1 |
Lineweaver-Burk Plot eq y intercept x intercept x and y axis |
1/v = Km/Vmax * 1/[S] + 1/Vmax
y intercept = 1/Vmax x intercept = -1/Kmax
x axis = 1/[S] y = 1/V |
Competitive Inhibition Burk graph |
- inhibitor binds to active site preventing substrate and enzyme from binding
LOWERS Km but Vmax stays the same so slope gets steeper X intercept moves closer to 0
slope = Km/Vmax * (1 + [I]/Ki)
new Km = -1/Km * (1 + [I]/Ki)
|
| Noncompetitive inhibition |
inhibitors bind elsewhere on the enzyme
Vmax decreases (y intercept gets higher) Km stays the same
New Vmax = 1/Vmax * (1 + [I]/Ki)
Slope = slope = Km/Vmax * (1 + [I]/Ki) |
Allosteric inhibitor 2 types |
Changes shape to the protein
does not change Km or Vmax
Homotropic: Allosteric interaction occur when several identical molecules bind to a protein (O2 and Hb)
Heterotropic: Allosteric interaction occur when several different molecules bind to a protein |
R and T Concerted Model Sequential Model |
R= active T= deactive
Concerted: Allosteric activation binds to R and stabilizes it, more R or Allosteric Inhibitor binds to T and Stabilizes it, less R.
Sequential: Inhibitor or activator induces a conformational change make the active site more active or less |
ΔG>0 ΔG<0 |
ΔG<0 exergonic, spontaneous, warm ΔG>0 endergonic, nonspontaneous, cold |
