learning objectives 3.1 Flashcards
List and describe the 9 functional categories of proteins
- transport proteins - transport ions and molecules
- enzymes - catalyze cellular reactions
- scaffold proteins - hold proteins together that interact in catalytic or signaling pathways
- signaling proteins - cellular communication
- structural proteins - provide mechanical support and structural organization
- motor proteins - move along other molecules for transport or synthesis
- storage proteins - repositories for ions and molecules
- receptor proteins - signal detection and involved in transmission
- regulatory proteins - regulate cellular processes
Nonpolar amino acids (9)
Valine
Alanine
Methionine
Tryptophan
Proline (contains imino group)
Glycine
Leucine
Isoleucine
phenylalanine
Polar Acid amino acids (2)
Aspartate/Aspartic Acid
Glutamate/Glutamic Acid
*Have a net charge of (-1) at ph 7
Polar Basic amino acids (3)
Histidine (contains imidozal group)
lysine
Arginine (contains guanidium group)
*have a net charge of (+1) at ph 7
Polar neutral amino acids (6)
Serine
Threonine
Asparagine
Glutamine
Cysteine (slightly polar)
Tyrosine (slightly polar)
Aromatic amino acids
Tryptophan
Phenylalanine
Tyrosine
Sulfur-containing amino acids
Methionine
Cysteine
Carboxyl-containing amino acids (secondary carboxyl)
Aspartic Acid
Glutamic acid
Hydroxyl-containing amino acids
Serine
Tyrosine
Threonine
special amino acids
cysteine (forms disulfide bonds)
Glycine (R-group is just Hydrogen)
Proline (forms a bond to itself)
Hydrophobic amino acids (8)
Alanine
Valine
Leucine
Isoleucine
Methionine
Phenylalanine
Tryptophan
Tyrosine
Aliphatic
Valine
Leucine
Isoleucine
Methionine
what are the groups that modify amino acids
acetyl
phosphate
hydroxyl
methyl
carboxyl
o-GlcNAc
functional groups and linkages
Hydroxyl
Acyl
Carbonyl
Carboxyl
Sulfhydryl
Amino
Phosphate
Pyrophosphate
ester
ether
amide
Describe alpha helices
- Right-handed (clockwise)
- H-bonds b/w peptide backbone
- H-bonding occurs b/w all peptides. Oxygen in Carbonyl bonds with w/ hydrogen in amino 4 peptides away
- turns every 3.6 residues
- h bonds run parallel to axis
- r-groups determine hydrophobic/hydrophilic character and formation
- stiff structure
- often found in membrane proteins
- contain amphipathic helices (hydrophobic and hydrophilic)
What amino acid do you not see in alpha helices?
Proline, because they cannot fit and the steric hindrance
What bonds stabilize alpha helices?
Hydrogen bonds within the backbone
Where do the r-groups point in alpha helices and Beta sheets
Alpha helices: point outward
Beta sheets: point out top and bottom
What makes up secondary structure?
alpha helices and beta sheets, turns
Describe beta sheets
- can be parallel or anit-parallel
- are made of short segments of peptides
- Hydrogen bonding occurs between adjacent Beta sheets. they can be close by, a little distant, or in a different polypeptide
- flat but can be bent or twisted
Describe beta turns
- 4 residues in a turn
- often found on the surface of globular proteins. This helps facilitate compact folding
- Glycine and Proline are commonly found
- stabilized by H bonds b/w residues 1 and 4
describe beta loops
- loops are longer and more complex than turns
- do not have a regular structure. instead they are unique to each protein
- usually found on protein surface
- often involved in specific binding interactions
Motifs
- 2 or more repeating structures
- can be small or large. (small: Helix-loop-helix)
(large: Beta barrel) - associated w/ specific function. Ex.) Helix-turn-helix motif of DNA binding proteins
Helix-turn-helix motif
- 2 helices seperated by a turn
- found in DNA binding proteins
- found in Ca2+ binding proteins (EFhand)
Coiled-coil motif
- 2 alpha helices wrapped around each other
- stabilized by weak interactions b/w aliphatic side chains
- amphipatic
- protein family: fibrous proteins, some transcription factors
Zinc finger motif
- a-helix + 2 antiparallel beta strands
- stabilized by a central Zn2+ bound by 2 cys, and 2 HIs or 4 cys
- zinc finger = C2H2
- found in DNA or RNA binding proteins
list Protein structure
Primary
secondary
tertiary
quaternary
describe primary structure
- amino acid sequence
- stabilized by peptide bonds
- determines shape and function
describe peptide bonds
- usually found in trans configuration
- formed b/w Amino acids.
- is a condensation rxn. yields H20
- two amino acids= 1 peptide bond
- formed b/w the oxygen of the carboxyl group and the nitrogen of the amino group of the other A.A
- uncharged. so it can pack tightly
- NCC-NCC-NCC Backbone
- formed N-terminus to C-terminus. (from left to right)
- hydrogen bonding
- small peptides still have biological activity
- no rotation around peptide bond b/c of the double bond.
rotation is possible around the alpha carbon - steric hinderance of R-groups affect protein folding
describe secondary structure
- made of alpha helices and beta sheets
- stabilized by H-bonding within the backbone
- most common is a-helices and Beta sheets +turns
describe tertiary structure
- folded protein structure.
- stabilized by many interactions within the peptide r-groups/residues. (hydrophobic interactions, h-bonds, van der waals, salt bridges, disulfide bridges)
- can be flexible or stiff
describe quaternary structure
multiple subunits
- stabilized by non-convalent bonds/interactions
- often required for protein function
- can be identical (homo-) or different (hetero)
- dimer (2 subunits)
- trimer (3 subunits)
- tetramer (4 subunits)
