Proteins Flashcards
4 parts of an amino acid
*all are bonded to common carbon core
- H - hydrogen atom
- NH2 - amino functional group
- COOH - carboxyl functional group
- a distinctive “R-group”
What happens to amino acids in water?
They ionize due to the pH of 7
What acts as a base in an amino acid?
Amino group (NH2)
What acts as an acid in an amino acid?
Carboxyl group (COOH)
The two highly electronegative oxygens pull the hydrogen away
What makes the amino acids unique?
The r-group
What happens if an R-group just contains carbon and hydrogen?
They will not participate in many chemical reactions
Hydrophilic R-groups
Polar and electrically charged
Hydrophobic R-groups
Nonpolar R-groups or highly electronegative atoms capable of forming hydrogen bonds with water
Does the R-group have a negative charge?
If yes, it is acidic and will lose a proton
Does the R-group have a positive charge?
If yes, it is basic and will pick up a proton
If the R-group is uncharged, does it have an oxygen atom?
If yes, then the highly electronegative oxygen atom will form a polar covalent bond, thus making it uncharged
Dehydration reactions
also called condensation reactions
newly formed bond results in the loss of water
What type of bond is a peptide bond?
Covalent
What do peptide bonds occur between?
carboxyl group of one amino acid and the amino group of another amino acid
2 hydrogens from (NH2) react with one oxygen from (COOH) to form the peptide bond
Are peptide bonds stable?
Yes due to the degree of electron sharing
Residues
amino acids that are linked together in a chain
R-group orientation in residue
Side chains (R-group) stick out which makes it possible for them to react with eachother and to react with water
What is the directionality of the residue?
N-terminus (amino group) to C-terminus (carboxyl group)
Oligopeptide
a polymer with fewer than 50 amino acids
Polypeptide
a polymer with more than 50 amino acids
Primary structure
refers to the distinct amino acid sequence
R-groups affect chemical reactivity and solubility
Secondary structure
distinctively shaped sections that are stabilized by hydrogen bonding that occurs between the oxygen on the C=O group of one amino acid residue and the N-H groups on another
a-helix
the polypeptide’s backbone is coiled
B-pleated sheet
segments of the peptide chain fold in the same plane
Proline
rarely found in a-helixes
Tertiary structures
form using a variety of bonds and interactions between R-groups or between R-groups and the backbone
Types of interactions used for tertiary structures
- Hydrogen bonding
- Hydrophobic interactions
- van de Waals interactions
- Covalent bonding
- Ionic bonding
Hydrogen bonding
form between polar side chains and opposite partial charges either in the peptide backbone or other R-groups
Hydrophobic interactions
water molecules force the hydrophobic nonpolar side chains to merge into globular masses
van der Waals interactions
once hydrophobic side chains are close to one another, electrical attractions take place
constant motion of elections produces tiny asymmetry in charge this makes nonpolar molecules slightly attracted to eachother
Covalent bonding
can form between two cysteines
disulfide bonds create strong links
Ionic bonding
form between groups that have full and opposing charges
Quaternary structure
proteins that involve multiple polypeptides
Dimers
proteins with two polypeptide subunits
Macromolecular machines
groups of multiple proteins that assemble to carry out a particular function
ex: ribsome
Is folding spontaneous?
It tends to be
Denatured
unfolded proteins
How do we know that folding affects function?
Anfinsen studied denatured proteins and found that they could not function
Molecular chaperones
special proteins that can facilitate protein folding
Prions
proteins that can be induced to fold into infectious, disease causing agents
shapes are different
Ex: mad cow disease
What are proteins used for?
Catalysis Defense Movement Signaling Structure Transport
Active site
location where substrates bind to enzyme and react
Where can hydrogen bonding occur to form the secondary structure?
Every 4th amino acid
Between carboxyl (-) and amino (+) group
