Amino acids, proteins, GAGs, and proteoglycans Flashcards
Biomolecules contain ____ and ______ amino acid groups
Polar and non-polar
What are the different parts of the structure of an amino acid in this picture?
What are the nonpolar side chains? (6)
- Glycine
- Alanine
- Valine
- Leucine
- Isoleucine
- Methionine
Of the nonpolar sidechains, these are the hydrophobic sidechains (4)
- Valine
- Leucine
- Isoleucine
- Methionine
- This AA is a nonpolar aliphatic sidechain with a unique cyclic structure, it is more conformationally restricted that other sidechains. It’s not as common due to it’s unusual properties.
- It is important for what structure?
- Proline
- Collagen helix
These are the AAs with aromatic side chains. Aromatic means it has a phenyl group. They are mostly nonpolar but some can form hydrogen bonds
- Phenylalanine (Phe, F)
- Tyrosine (Tyr, Y)
- Tryptophan (Trp, W)
This aromatic AA is important due to its OH group which makes it more reactive
Tyrosine
These are the hydrophilic AA side chains
- Serine (Ser, S)
- Threonine (Thr, T)
- Asparagine (Asn, N)
- Glutamine (Gln, Q)
- What parts of the hydrophilic sidechains make them polar?
- What types of bonds are they able to form, as donors or receptors?
- Hydroxyl or amine groups
- Hydrogen Bonds
This is a less polar but more reactive analog of serine
Cysteine
- What group of cysteine makes it very reactive?
- What types of bonds does that group often form?
- -SH (thiol group), it is more reactive than -OH
- Disulfide bridges
These are the AAs with charged hydrophilic side chains
- Lysine (Lys, K)
- Arginine (Arg, R)
- Histidine (His, H
- Aspartate (Asp, D)
- Glutamate (Glu, E)
These are the negatively charged, acidic AAs at a pH of 7.4
- Aspartate
- Glutamate
- Histidine (kinda)
These are the positively charged, basic AAs
- Lysine
- Arginine
- Tyrosine (kinda)
- Cysteine (kinda)
These are linear chains of covalently linked AAs. They have a regular main chain and variable side chains.
Proteins (polypeptides)
- Does synthesis of proteins require energy?
- Are the peptide bonds stable?
- Yes! (ribosomes translate from mRNA)
- Yes
- Polypeptide chains are directional, meaning the go from the ___–>____ end
- For a protein with N amino acids, how many different polypeptide chains are possible?
- N–>C end (amino to carbonyl end) Note that AA #1 has a free Amino group, the last AA has a free Carboxyl group
- 20N (permutation)
What types of bonds covalently crosslink different segments of a protein chain
Disulfide bonds
What kind of Bonds are involved in the Primary Structure of a Protein?
Hydrogen Bonds
Disulfide Bonds
The structure of a biologially active protein consisting of L-amino acids linked by peptide bonds in a precisely defined sequence. It can have disulfide bonds holding two chains together.
Primary Structure
What determines the 3D structure of a protein?
The sequence of amino acids
What primary structure did Fred Sanger elucidate in 1953?
Bovine Insulin
- In the secondary structure of proteins, what bond forces a planar structure?
- Why?
- Peptide Bond
- Double Bond like Character:
- The delocalized electrons on nitrogen give it double bond like characteristics (it’s flat)
- In the secondary structure of proteins, what configuration is favored among AAs to avoid steric clashes, cis or trans?
- Which AA is the exception?
- Trans
- Proline, (note that both configurations, cis and trans, can produce steric clashes for Pro)
- This right handed secondary protein structure turns counter clockwise
Alpha helix
How many AAs away is another AA when they hydrogen bond in an Alpha Helix?
4
This is the favored secondary structure for secondary protein structure
ß-Strand
Is the separation between amino acids greater in the alpha helix or ß-strand?
Greater in the beta strand by more than 2x what the alpha helix is (3.5Å vs 1.5Å)
What does the beta strand form which is even more common?
Beta sheet
What kinds of Beta Sheets are there?
Antiparallel and Parallel
In this protein secondary structure, side-chains alternate upward and downward from the plane of the sheet
ß-Sheet
Strands of the ß-sheet adopt a LEFT/RIGHT handed twist
Right
In the tightly packed tertiary structure of proteins, folding is driven by the burial of ________ residues interiorly. It is driven by charge, entropy, hydrogen bonding.
Hydrophobic. When water is condensed around a protein, the hydrophobic aspects will fold and bury away from the condensed water.
Which AAs (protein residues) are largely found on the interior of the tertiary structure of proteins?
Nonpolar (Val, Leu, Ile, Met, and Phe
Which AAs (protein residues) are largely found on the surface of the tertiary structure of proteins?
Charged residues (Arg, His, Lys, Asp, Glu)
Which AAs are usually on the surface of the tertiary structure of proteins but frequently found on th einterior as well
Polar uncharged (Ser, Thr, Asn, Gln, Tyr and Trp)
Where do hydrogen bonds form between donors and acceptors on the tertiary structure of proteins?
Interior,hydrogen bonds are buried.
This is an example of a tertiary protein structure in the body
Myoglobin