Term
| What is considered the alpha carbon on an AA |
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Definition
| Carbon which is attached to the amino and carboxy end |
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Term
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Definition
aa with one positive and one negative charge. which means it is neutral
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Term
| when is an amino acid alpha carbon considered " asymmetric" |
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Definition
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Term
| AA are able to polymerize into peptides how? what characteristics allow this? |
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Definition
2 idenifying groups
NH3+ amino
&
COO- carboxyl end |
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Term
| the amino and carboxyl groups can react in a ____ to ____ fashion. Eliminating a ___ molecule and forming a ____ ____ linkage or _____ bond**. |
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Definition
The amino and carboxyl groups can react in a
head-to-tail fashion, eliminating a water molecule
and forming a covalent amide linkage, which
is called a peptide bond, in the case of peptides
and proteins.
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Term
| all AA except ____ have a free alpha amino and a free alpha carboxyl |
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Definition
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Term
| Why are nonpolar AA important in protein? |
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Definition
| drive protein chains to FOLD, forming their natural structures |
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Term
| what important characteristic does proline have? |
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Definition
| because of its lack of rotational ability, proline can provide STRUCTURAL RIGIDITY TO PROTEINS |
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Term
| Polar uncharged amino acids EXCEPT FOR GLYCINE contain R groups that can form _____ bonds with ____ and play a variety of _____ roles in enzyme reactions |
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Definition
polar, uncharged amino acids except for glycine, contain R groups that can form hydrogen bonds with
water and play a variety of nucleophilic roles in enzyme reactions
exception: Glycine, has only one single hydrogen for an R group and this hydrogen is not sufficient for
hydrogen bond formation.
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Term
| AA are weak polyprotic acids meaning.. |
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Definition
an acid which has the capability of donating not just one, but 2 protons to a base during acid-base rxn
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Term
|
Definition
Remember - pKa Rule of Thumb
• 1 pH unit below
pKa ~ fully protonated
• 1 pH unit above
pKa ~ fully deprotonated
C comes before N
N=9
C=2
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Term
| peptide bond formation results in the release of what? molecule |
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Definition
H20!
loss of O from carboxyl and lost of 2 H's from amino of other AA |
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Term
Arginine, Arg, R: pKa(guanidino group) = 12.5
Aspartic Acid, Asp, D: pKa = 3.9
Cysteine, Cys, C: pKa = 8.3
Glutamic Acid, Glu, E: pKa = 4.3
Histidine, His, H: pKa = 6.0
Lysine, Lys, K: pKa = 10.5
Serine, Ser, S: pKa = 13
Threonine, Thr, T: pKa = 13
Tyrosine, Tyr, Y: pKa = 10.1
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Definition
R- really old 125 years
D dylan looks old at 39
C loks like pt of an 8 in 83
E you are ugly at 43
H his his his 6 year olds only think of them selves
K in lysine similar to leuk which has 105 cells GREAT
S in serine looks like 13
T in three- onin 3 in 13
Y in tyrosine like 10.1 |
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Term
•At what wavelength does one typically check the concentration of a protein?
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Definition
280 nm- is a good absorbance for AA
NMR- help to figure out 3D structure of protein |
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Term
| which 3 AA only absorb UV |
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Definition
Phenylalanine
Tryosine
Tryptophan
all the cyclo type groups can absorb at UC- they are very special =) |
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Term
| Except for what AA all amino acids have four different groups attached to the alpha carbon making itasymmetric or chiral |
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Definition
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Term
| because DL are is baed on glyceraldehyde with only ONE chiral center, which nomenclature system is used instead? ( bc they have more chiral centers) |
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Definition
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Term
| again. Peptide bond formation results in a release of what? |
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Definition
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Term
| what configuration is AA carbonyl and amino in from each other and why? |
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Definition
| they are TRANS from eachother. more stable energetically- less steric hindrance |
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Term
| only what kind of acid is found in Proteins? |
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Definition
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Term
| why is rotation around the nitrogen and carbonyl bond restricted by not the alpha carbond (Carbon with R group) |
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Definition
carbonyl and nitrogen have partial double bond (double bonded and resonance), making the peptide bond
PLANAR, RIGID, and RESTRICTED rotation of peptide backbone restricted to alpha carbon.
Good thing too could you imagine our bodies if it was a huge blob! |
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Term
peptide bond resonance has several important consequence:
1. 2 degrees of free motino at where?
2. amide plane
3.shorter bond length at what location>
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Definition
1. restricts free motion around N alpha and alpha carbonyl
2. six atoms composing peptide bond - coplanar
3.carbonyl and Nitrogen bond length= .133 nm |
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Term
| peptide bond is estimated to have ___% double bond character |
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Definition
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Term
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Definition
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Term
| what is a residue of peptide |
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Definition
| unit of AA making up a peptide is called a residue- what is left over after release of water to form a peptide bond |
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Term
dipeptide
tripeptide
oligopeptide
poly |
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Definition
di- 2
tri- 3
oligo- 12-20
poly- 20<X |
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Term
| oligo makes up how many residue |
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Definition
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Term
monomeric protein
multimeric protein
homomultimer
heteromiltier
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Definition
monomeric- ONE polypeptide chain
Multi- more than one
Homomulti- One kind of chain
Heteromultimer- 2 or more different chains
ie heterotetramer (2 alpha chains and 2 beta chain)
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Term
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Definition
| broadly defines molecules composed of one or more polypeptide chains |
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Term
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Definition
| proteins with ONE amount of polypeptide chain |
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Term
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Definition
general definition to describe more than one monomer. but does not specify if they are same or different.
can be same or different.
for generalized |
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Term
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Definition
several different TYPES of polypeptide chains
- alpha or beta type |
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Term
difference between multimeric and hetermultimer
****EXAM question
1. insulin: alpha/betal subunit
2. cytochrom c : alpha
3. chymotrypsin: alpha/beta/gamma
4. y-globin: alpha2/beta2
5. glutamine synthetase: alpha12
which is hertomultmeric, monomeric, multimeric, homomultimeric |
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Definition
1. heteromultimeric
2. monomeric
3. heteromultimeric
4. multimer heteromultimer
5.homo multimeric |
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