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74 Cards in this Set

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Quick expl. of AA charge?
ph<pka for NH3 = +1
ph>pka for NH3 = 0

ph<pka for COOH = 0
ph>pka for COOH = -1

(requires understanding of AA structures for side groups maybe)(if no side groups you don't include em)(left AA = NH3 and side groups Right = COOH and any side groups)
What are enantiomers?
mirror image stereoisomers
What are diasteromers?
not mirror images
What are stereoisomers?
molecules with same bonds but different stereochemistry
What is the ^G eqn?
^G = ^H - T^S
What is ^G?
-gibbs free energy change
When is a rxn exergonic?
when ^G<O...spontaneous towards products
When is a rxn endergonic?
when ^G>O...nonspontaneous towards rxnts
What is ^H?
enthalpy change
When is a rxn exothermic?
when ^H<O (heat is generated, released, ie, explosion)
When is a rxn endothermic?
when ^H>O (heat energy is transformed)
List the 4 weak intxns?
1. hydrogen bds

2. ionic intxns

3. hydrophobic intxns

4. van der waals
Give 4 ex. of H-bds?
1. alcohol and H2O

2. ketone

3. between polypeptides

4. dna bases
Name the 4 colligative properties?
1. VP

2. BP

3. Mp and FP

4. Osm. P
What is osmotic pressure?
forcing H2O thru a membrane in an attempt to equalize conc.s (isotonic,etc)

-the higher the conc. of solute the higher the pressure
(if conc. dbls osm. p. dbls)
What is isotonic?
conc in sol. same as insid cell (same osm. pressure)
What is hypertonic solution?
conc greater outside cell, cause water to rush out of cell
What is hypotonic soln?
conc. greater inside cell so water rushes in
What is ionization related to?
acids and bases
What is a buffer?
bio systems are very sens to pH

-buffers help maintain pH and all cells have them

-best buffering is at pH near Pka (+or-1)

-weak acid and weak base(conj., salt)

-enzyme activity is pH sensitive
2 important buffers?
1. H2CO3

2. H3PO4
What does primary struc. of proteins involve?
sequencing and edmond degradation

1. hydrolysis (doesn't help)

2. edmond deg = good for about 50AAs...label NH3 end and remove AA, ID...can det. seq
3. mass spectrometry
Most common way of obtaining proteins?
lab synthesis
3 ways to obtain peptides?
1. isolate/purify from tissue or cell culture

2. direct chm. synthesis (merrifield, primary way)
(but expensive)

3. Genetic engineering (DNA>RNA>protein)

-ideally can make an protein about 100 AA long
What is in the plane of a protein?
6 carbons atoms in plane...(can rotate relative to eachother)
-always 6 atoms
-always planar
-2 carbon ends can twist
The general char.s of 2ndary structure?
-local 3-D strucs
-kink
-communication due to spatial arrangement
The 2 types of 2ndary structures?
1. alpha helix (kink, 5.4 or 3.6 turn)

2. beta sheet (parallel, 6.5)antiparallel
Describe tertiary structures?
1. 3-D overall

2. involves long range intxns
The 2 major tertiary structures?
1. fibrous (long, struc.)

2. globerular (enzymes, most proteins, most compact)
What level of structure do only some proteins have?
quaternary
What is quaternary struc?
3-D rel. of subunits
Domains vs. subunits of quaternary struc.?
domain = covalent bond, same polypep. with different regions

subunits - no cov. bds, different polypeps with each subunit
What are fibrous proteins?
a tertiary structure
Name 3 fibrous proteins?
1. alpha keratin (strong RH helix)(LH superhelix)(disulfide links)

2. silk fibroin (beta sheets, no cross links)

3. collagen (LH helix, not an alpha helix,RH super helix)(novel cross links)
What is a motif?
collection of 2ndary struc. in globerular protein
What is a domain?
inv. with glob. protein...two distinct polypeptides that are attached by thin region and can move rel. to eachother
Describe Oxygen binding?
1. it is important but poorly soluble because it is nonpolar
2. Transition metals (like Fe) can transport it but they can damage cells
3. so we need to sequester (hide) Fe but still have it the oxygen accessible.
4. this is accomplished by the heme group
Describe the heme binding Oxygen?
1. central Fe
2. bound to Oxygen
3. bount to two heme groups
4. prevents oxidation of Fe2 to Fe3+
5. also bound to N in histidine
6. oxygen can be bound and released
7. this heme group is hidden inside of either myoglobulin or hemoglobulin
Describe myoglobulin?
1. It is primarily a storage form for Oxygen.
2. It is alpha-helical.
3. It is relatively insensitive to [Oxygen] when binding, always the same affinity
Describe Hemoglobulin?
1. a free heme (not in Hb) binds CO 20,000X better than it binds Oxygen (so Kd for CO is 1/20,000 that of Kd for oxygen)
2. When heme is in hemoglobulin it binds CO only 200X better than oxygen
3. change is due to steric hindrance
4. Hb is very sensitive to [oxygen]
Hemoglobulin vs. Myoglobulin structure?
very similar 3-D structures but there is a lot of difference between AAs
-myoglobulin is mostly alpha-helical
What does theta represent?
fraction of sites occupied

theta = [L]/([L] + Kd)

theta = 50% when [L] = Kd = 1/Ka (this is when 1/2 the binding sites are occupied
What is cooperative binding as it relates to Hb?
As it binds oxygen at each site the binding subunits conformation changes and the affinity for oxygen increases
-the rich get richer
What is the Bohr effect?
The inversely proportional relationship between [CO2] and [H] with [O2] binding in Hb
In bohr effect if hydrogen conc increase what happens to oxygen affinity?
decreases
In high altitudes what occurs?
[BPG] goes up and affinity decreases for hemoglobin and affects affinity for O2
Keq and ^G indicate what? What do they not indicate?
they indicate equilibrium
-nothing about rate
^Gb = what mathematically?
the difference between the uncatalyzed and catalyzed ^G
Michaelis-Menten eqn?
Vo = (Vmax[S])/(Km+[S])
Where does Km = [S]
where Vo = 1/2 Vmax


rate constant for rate determining step

something to do with inhibitors
What are epimers?
sugars that differ only in their configuration at one chiral center (when compared to glucose, not when compared to eachother) They are epimers at the #C of wherever the difference may occur.
Maltose monomers and activity?
Glc-Glc (reducing)
Lactose monomers and activity?
Gal-Glc (reducing)
Sucrose monomers and activity?
Fru-Glc (non-reducing)
Trehalose monomers and acivity?
Glc-Glc (non-reducing)
Polysaccharides are also known as what?
glycans
4 types of polysaccharides?
1. storage homopolysaccharides

2. structural homopolysacch-

3. Structural heteropolysacc-

4. Glyconjugates (information carriers) (Carbohydrate and other molecule..like protein, lipid, etc)
What are storage homopolysacch.s?
food molecules stored in cell
What are structural polysacch.s?
stay in cell as framework
What is the composition of nucleosides?
base + pentose
What is the composition of nucleotides?
base + pentose + phosphate
Name the purines
Adenine and guanine
Name the pyrimidines?
cytosine, thymine, uracil
Which nucleotide base is in DNA but not RNA?
thymine
Which nucleotide is in RNA but not DNA?
uracil
Each sugar in DNA has one less what then RNA?
one less -OH group (see slides, very clear)...you will see H group in RNA where you see an OH group in DNA
How many bonds between G and C pairs?
3
How many bonds between A and T or A and U?
2
What kind of linkage do you see in RNA and DNA polymers?
phosphodiester linkage with 5' to 3' directionality...alternating sugar and phosphate groups form the backbone...in a chain there is usually a phosphate at the 5' end but not the 3'
A, B, Z in DNA?
A = RH, not seen, short and fat

B = common, RH

Z = LH, seen sometimes
A, B, Z, in RNA?
A = common

B = not seen

Z = lab only
DNA cloning steps?
1. cut DNA with restriction enzymes

2. select app. cloning vector

3. join frag.s with ligase

4. insert into host cell

5. grow and ID those with the desired recombinant DNA
What is a restriction endonuclease?
enzyme...recognizes specific palindromic DNA sequences, binds to DNA at those sites, and cuts the DNA...leaving either sticky or blunt ends
What is pbr322?
a plasma cloning vector...closed circular DNA...several restriction enzyme sites (confers resistance to ampicillin and tetracycline)