Amino Acids Flashcards by Christian Kassicieh

The essential amino acids are

Phen Alan, Val, and Lucy took Three Trips to Isolate from His Meth Arguments and his Lyce
Phe, val, thr, trp, ile, met, his, arg, leu, lys

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Glycine

Nonpolar
-H good ol easy glycine

Position 3 of hairpin turn, prevents hindrance with H as R group

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Alanine

non

-CH3 alan is boring, 1 carbon

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Valine

non, BCAA

-CH2-CH3-CH3 upside down V for Val

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Leucine

non, BCAA

-CH2-CH-CH3-CH3 Lucy is like Val, but taller with extra carbon

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Isoleucine

non, BCAA

Lucy isolates her 4 carbons w single bonds

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Proline

Non
The pro feline has 3squared lives in a cyclic ring, makes agile turns
Involved position 2 in sharp turn in hairpin loop

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Phenylalanine

Aromatic, nonpolar

Alan tries to have phen with his new ring

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Tyrosine

Aromatic, Polar

OH when Alan has phen he gets TYRed

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Tryptophan

Aromatic, non polar

Don’t trip fam, just a ring on an amine dbl bond

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Asparagine

Polar, Uncharged

Asparagus Doubles Oxygen, and adds Nitrogen

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Glutamine

Polar, Uncharged

Lucy is taller than Val, Glutamine is taller than Asparagine

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Serine

Polar, Uncharged

Alan puts down the ring, and becomes OH so serene

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Threonine

Polar, Uncharged

Three groups, H, OH, and CH3

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Aspartate

Neg charge (acidic)
Part that I hate is that he thinks he COO- or somethin

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Glutamate

Neg charge (acidic) 
Mate is taller than Aspartate, still thinks he COO-

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Histidine

Positive (basic)

“His positivity is great”

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Arginine

Positive (basic)

Arg, +pirate has a sword of 4 Cs and 3 Ns,

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Lysine

Positive (basic)

Positive for lice ( 4 C chain with NH3 on end)

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Methionine

Nonpolar
Sulfur Containing
Susie did meth, now shes surrounded by 3 Crooks

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Cysteine

Polar
Sulfur Containing
SH, you’re in the cysteine chapel

Primary Structure of AAs are held together by what forces

Linear sequence with covalent bonds between carbonyl carbons and amide nitrogens (Peptide bond) w R groups in trans position from each other

Secondary Structure of AAs and Forces involved

Alpha Helix stabilized by H bonds, with hydrophilic out and hydrophobic inside
Beta pleated Sheet stabilized by H bonds, R groups alternate between above&below plane w bulk hydrophobic core for density

Three types of Beta Sheets

Parallel-same direction
Anti-Parallel-opposite direction
Mixed- Combo of both

What connects different stretches of anti-parallel Beta sheets?

Reverse or Hairpin turn, 4 AAs, Stabilized by single H bond between 1st and 4th residue Proline at 2, Glycine at 3

Super-Secondary AA Structures, and Forces Involved

Alpha-Alpha Corner, All Beta, and most commonly Beta-Alpha-Beta (BAB) motif -Stabilized by R group interaction from above the sheet and the outer helix

When Beta Alpha Beta motif repeats 7-8 times, It folds into a donut (Alpha-Beta-Barrel) called what, and in what process is this commonly found?

Rossmann fold (Ross loves donuts) Common among glycolysis enzymes

Tertiary Structure of AAs and Forces

Final folded state of complete polypeptide, stabilized by hydrophobic interactions, H bonds, Ionic interactions, Disulfide bonds

Quaternary Structure of AAs and Forces

Multiple polypeptides form supra-molecular complex (di-, tri- meric) May be identical or different subunits (homo- or hetero-polymeric)

Forces Controlling tert and quat AA structures (four)

H-bonds, Hydrophobic Forces, Electrostatic forces (charges, dipoles, salt-bridges), Van der Waals Forces(proximity of uncharged non-bonded atoms)

Do not contain RNA or DNA, cause neurodegenerative diseases that are from infection (Mad Cow) or Inherited (Creutzfeld-Jakob disease (CJD)

Prions (proteinaceous infectious particles)

The most abundant protein in body, that provides tensile strength, is formed by what AAs

Collagen (Kola=glue)(Pro-Gly) Formed in triple helix by glycine (fits into small spaces), proline, (kinks polypeptide), and hydroproline&hydroxylysine (stabilize triple helix)

What characterizes Scurvy, and why does it occur?

Lack of Vit C, which is required to hydroxylate proline and lysine, so triple helix is not stable, and collagen has low tensile strength

What characterizes Ehlers-Danlos Sydrome and why does it occur?

E-D makes you stretchy, mutation in collagen

Osteogenesis Imperfecta (Brittle Bone Disease)

Type I collagen formation disruption, mutation may interfere with proper cleaving of end, so stacks of triple helix are misaligned and loose

Induced by tobacco smoke elements, which AA has an R-group subject to oxidation?

Methionine, which impairs protein function

Which AA has R-group subject to spontaneous oxidation that creates disulfide link within protein

Cysteine: thiol group | relatively uncommon w intracellular proteins, but common in extracellular proteins (****Insulin has this bond**)

Isoleucine, Leucine and Valine are increased in what condition?

Maple Syrup Urine Disease (MSUD)

Phenylketonuria (PKU) is characterized by what?

Lack of Phenylalanine hydroxylase, which leads to accumulation of phenylalanine

Modified AAs such has 4-hydroxyproline and 5-hydroxylysine are found in what compound?

Collagen

Blood clotting factors, which involve Ca2+ binding, have which important AAs?

Carboxyglutamate, which requires cofactor Vit K which activates the clotting factors

How does Vit K deficiency lead to prolonged bleeding and hemorrhage potential?

Vit K serves as cofactor in conversion of inactive to active clotting by carboxylation of glutamate

Definition of pK and pI

pK- prot and unprot exists in approximately equal proportions across all like groups in solution pI- pH at which molecules possess net charge of 0

Which type of AAs form Elastin?

Mostly small, nonpolar (gly, alan, val) Also rich in Proline and Lysine -Synth from tropoelastin precursor into EC space

Amyloidosis is caused by what, and which diseases is it associated with?

Accumulation of Amyloid (beta sheet folded into long fiber) protein -Beta amyloid accum in Alzheimer's

Henderson-Hasselbalch Equation

pH=pKa + log (A-)/(HA)

Lower the pKa for an acid, the ____ the acid will be

stronger (more readily release H+)

What can denature proteins?

- Inc or Dec pH - Ionic strength changes (salting out) - Heating - Urea, mercaptoethanol, or guanidine salts that disrupt H-bonds - Detergents like sodium dodecyl sulfate (SDS) that disrupts hydrophobic interactions

What helps to fold protein into native/functional state?

Some spontaneous, some w help of chaperonins. | Chaperones AKA heat shock proteins (HSPs) which increase at high temps

Three major properties of proteins that you can separate them with

Ion- differences in sign and magnitude of net charge at given pH Size- w gel filtration Affinity- Binding specificity to ligand