Chapter 3: Biologically Important Molecules Flashcards
What roles do proteins have in the cell?
Proteins act as enzymes, hormones, receptors, channels, transporters, antibodies, and support structures inside and outside cells.
What are proteins made of?
Composed of 20 amino acids linked together in polymers
What makes each protein unique?
Composition and sequence of amino acids in the polypeptide chain is what make each protein unique/ play a special role in the cell.
All 20 amino acids have the same ___ ___ ___ backbone
nitrogen-carbon-carbon
What makes an amino acid unique?
Side chain (variable R group) which gives it hte physical and chemical properties that distinguish it from the other 19.
What are the two common types of covalent bonds between amino acids in protein?
Peptide bonds and disulfide bridges
What are peptide bonds?
Link amino acids together into polypeptide chains
What are disulfide bridges?
covalent links between the sulfur atoms of two cysteine amino acids (cysteine R groups)
What is residue?
Individual amino acids part of the polypeptide chain
The ___ terminus is the first end made during polypeptide synthesis and the ___ terminus is made last.
amino, carboxyl
In the oligopeptide The-Glu-Gly-Ser-Ala which residue has a free alpha-amino group and which residue has a free alpha-carboxyl group?
Amino terminus: Phe
Carboxyl terminus: Ala
Amino end is always written first so it begins with exposed Phe amino group and ends with exposed Ala carboxyl
What is proteolysis/proteolytic cleavage?
Hydrolysis of another protein (proteolytic cleavage is a specific method of cutting peptide bonds. Many enzymes only cleave the peptide bond adjacent to a specific amino acid.
What does the proteolytic enzyme/protease do?
Protein that does the cutting
Based on the following: H2N-Ala-Phe-Ser-Lys-Gly-Leu-COOH. If the following peptide bond is cleaved by trypsin what amino acids will be on the new N-terminus and how many fragments will result in this sequence: Ala-Gly-Lys-Phe-Phe-Lys ^2?
Trypsin will cleave on the carboxyl side of the Lys residue with Phe on the N-terminus of the new Phe-Phe-Lys fragment. There will be two fragments after trypsin cleavage: Phe-Phe-Lys and Ala-Gly-Glu-Lys.
The carboxyl group is the end of the amino acid chain terminated by COOH.
The N terminus is the one with the free amino group (H2N).
Trypsin cleaves on the ____ side of residues arginine and lysine
carboxyl
Trypsin cleaves carboxyl
Chymotrypsin cleaves adjacent to hydrophobic residues like ____
phenylalanine
Chymotrypsin is a hydrophobe who likes phenylalanine
Cysteine is an amino acid with a _____ that can react with another____ of cyestine to make a _____
reactive thiol (sulfhydryl SH group)
another thiol of cysteine
disulfide bond
What does cysteine do?
Plays a key role in stabilizing tertiary protein structure (protein folding).
Cysteine x Cysteine =
Cystine
What is denaturation?
disruption of a protein’s shape without breaking peptide bonds
What can cause proteins to denature?
urea (disrupts hydrogen bonding interactions), extreme pH and temperature, and changes in salt concentration (tonicity).
Describe the primary structure 1
The linear ordering of amino acid residues bonded by peptide bonds.
Describe the secondary structure 2
Initial folding of a polypeptide chain into shapes stabilized by hydrogen bonds between backbone NH and CO groups. Certain motifs of a secondary structure are found in most proteins: Alpha Helix and Beta pleated sheets are the two most common.
What are parallel beta pleated sheets?
Adjacent polypeptide strands running in the same direction?
What are antiparallel beta-pleated sheets?
polypeptide strands run in the opposite direction.
If a single polypeptide folds once and forms a Beta pleated sheet with itself, would this be a parallel or antiparallel Beta pleated sheet?
It would be antiparallel because one participant in the Beta pleated sheet would have a C to N direction, while the other would be running N to C.
Describe tertiary structure 3
Deals with hydrophobic/hydrophilic interactions between amino acid residues located ore distantly from one another in the polypeptide chain.
Secondary structures (like alpha helices) fold into higher order tertiary structures due to R group interactions with each other and with the solvent (water).
Hydrophobic R groups fold into the interior of the protein, away from the solvent, and hydrophilic R groups tend to be exposed to water on the surface of the protein.
Which of the following may be considered an example of a tertiary protein structure?
I. van der Waals interactions between two Phe R-groups located far apart on a polypeptide.
II. Hydrogen bonds between backbone amino and carboxyl groups.
III. Covalent disulfide bonds between cysteine residues located far apart on a polypeptide.
Item I is true this is a good example of a 3 structure. Item II is false; this describes 2 not 3. Item III describes the disulfide bridge which is tertiary.
For Item III more info: Disulfide bonds make proteins less susceptible to unfolding; typically, they will link -sheets, -helices, and loops, which means that they primarily maintain tertiary structure, not secondary, which refers to local conformations, and is maintained largely by hydrogen bonds.
Describe quaternary 4 structure
Highest level of protein structure
Describes interactions between polypeptide subunits which are part of a large complex containing many subunits (multisubunit complex).
Forces stabilizing quaternary structures are generally the same as the tertiary structures.
This includes non-covalent interactions, van der Waals forces, hydrogen bonds, disulfide bonds, and electrostatic interactions.
Exception: No peptide bond involvement in quaternary structure because it defines 1 structure.
What is the difference between a disulfide bridge involved in quaternary structure and one involved in tertiary structure?
Quaternary disulfide bonds that form chains aren’t linked by peptide bonds. Tertiary disulfides are bonds that form between residues in the same polypeptide.
