1st Unit / Ch 1 Amino Acids and Protein Structure Flashcards
(31 cards)
What is the alpha carbon?
The central carbon closest to the carboxylic acid
What does every amino acid have?
an amino group and carboxylic acid
How are polar amino acids named by?
The character of their side chain
What is the simplist amino acid?
Glycine due to its side chain being “H”
All amino acids have D and L conformations except….
Glycine
Where do side chains attach?
the alpha carbon
Is Glycine optically active?
No
Which 8 amino acids are hydrophobic?
Hydrophobic (normally buried inside the protein core):
• Alanine - Ala - A
• Isoleucine - Ile - I
• Leucine - Leu - L
• Methionine - Met - M
• Phenylalanine - Phe - F
• Valine - Val - V
• Proline - Pro - P
• Glycine - Gly - G
Which 8 amino acids are polar?
Glutamine - Gln - Q
• Asparagine - Asn - N
• Histidine - His - H
• Serine - Ser - S
• Threonine - Thr - T
• Tyrosine - Tyr - Y
• Cysteine - Cys - C
• Tryptophan - Trp - W
Which 4 amino acids are charged and can make salt bridges?
Arginine - Arg - R
• Lysine - Lys - K
• Aspartic acid - Asp - D
• Glutamic acid - Glu - E
What does glycine help synthesize?
Collagen, the most abundant protein in the body.
Why is Proline Unique? Can proline be in hydrogen bonding?
It has a secondary amine, in that the alpha-amino group is attached directly to the side chain, making the α carbon a direct substituent of the side chain. becuz of this it cannot be involved in hydrogen binding.
Able to creat kinks in structures to form a helix and beta sheets
What type of charge does acidic amino acids have?
Negative becuz they have 2nd carboxylic group ( 2 x COO)
What type of charge does Basic amino acids have?
Posittive and becuz they have 2nd amine group at bottom of chain. ( 2 x NH2)
What makes Cysteine Unique?
It has covalent bonds becuz of S-S di sulfide bridges. These bonds stay when protein denatures and allow primary structure to stay in tact. So it can renature itself.
Purpose of Methylation?
adding methly groups to control protein synthesizing.
How are Di peptides synthasized? How are these new formed proteins broken?
Synthesized by carboynl end connecting to an amino end of another acid.
protein can only be broken by enzymes
What are some charateristics of peptide bonds?
They are planr, partial double bonds, and are rigid on main chain of amid linkage, done by covalent bond. Their is rotation about side changes.
List additional bonding charateristics of Peptide bonds?
They assume trans configuration and the carbonal “O” and amine groups “H”are polar to form hydrogen bonds.
How does the primary structure remain stable?
due to its covalent backbone (amide linkage)
What is the secondary structure?
How does it form?
What is the best example?
The primary backbone in 3 dimensional space. Like alpha helixs, where the negative end of carbonal end binds with hydrogen.
By the hydrogen bond between the 1st and the 4th in a right handed pattern (clockwise, introchain bonding)
The best example is “fibrous structure”
Do R groups participate in secondary structure?
No, they point away, but can stabilize or destabilize.
How does secondary structures arise?
What determines what kind types secondary structures can occur.
What are the 2 types?
from interactions between neighboring amino acids residues.
The rigity of the peptide backbone determines the type of secondary structures can occur.
Alpha helixs and Beta pleated sheets.
How are Beta pleated sheets made?
Can they form intra bonds?
Peptide bond planes are arranged like a folded sheet of paper with 2 or more seperate chains side by side with H—-O bonds happening.
They are more extended than alpha helixs.
Cannot form intra bonds becuz those “H” are used to bond with other chain forming the beta sheet by inter’ chain
