Chapter 4: Protein Structure and Function Flashcards
Protein Conformation
Precise, three-dimensional shape of a protein or other macromolecule, based on the spatial location of its atoms in relation to one another.
Residue
an individual amino acid, a single molecular unit (monomer) within a polymer
Protein Side Chain
Portion of an amino acid not involved in forming peptide bonds; its chemical identity gives each amino acid unique properties.
Protein Backbone
Repeating sequence of the atoms (–N–C–C–) that form the core of a protein molecule and to which the amino acid side chains are attached.
N-Terminus and C-Terminus
C-Terminus: The end of a polypeptide chain that carries a free carboxyl group (–COOH)
N-Terminus: The end of a polypeptide chain that carries a free α-amino group.
Peptide
Covalent chemical bond between the carbonyl group of one amino acid and the amino group of a second amino acid containing two or more amino acids.
Transmembrane Protein
Membrane protein that extends through the lipid bilayer, with part of its mass on either side of the membrane. Protein that cross the lipid bilayer usually form an α helix, composed largely of amino acids with nonpolar side chains
What is primary structure? What determines primary structure?
The primary structure of a polypeptide is determined by it’s sequence of amino acids. The unique sequence of amino acids in a protein is called the primary structure of that protein, and only cosists of peptide bonds and amino acids.
On the DIPEPTIDE, label the following: Two central carbons, N-term, C-term, two R groups
What is secondary structure?
- What are the two major types of secondary structure?
- What type of bond is found in secondary structure?
- Are R groups involved with secondary structure?
-A secondary structure is a local conformations induced by hydrogen bonding along the peptide backbone. Regular local folding pattern of a polymeric molecule. In proteins, it refers to α helices and β sheets.
-One type is alpha helix is a folding pattern, common in many proteins,
in which a single polypeptide chain twists around itself to form a rigid cylinder stabilized by
hydrogen bonds between every fourth amino acid. Another type is Folding pattern found in many proteins in which neighboring regions of the polypeptide chain associate side-by-side with each other through hydrogen bonds to give a rigid and, flattened structure.
-hydrogen bonds that form between the N–H and C=O groups in the polypeptide backbone
-R groups are involved with secondary structure as side chains.
What is tertiary structure?
What types of bonds are found in tertiary structure?
Are R groups involved with tertiary structure?
-Complete three-dimensional structure of a fully folded protein, and is formed due to the interactions between the R-groups.
-Bonds found in a tertiary structure are a covalent bond such as that of a disulfide bond of covalent linkages containg chains of cysteines
-R-groups are what give rise to the structure of the teritary structure due to the side chains, keeping the shape unique from side interactions.
What is quaternary structure?
Complete structure formed by multiple, interacting polypeptide chains that form a larger protein molecule that contain two or more amino acids in a linked bond.
Define the following:
Dimer:
Trimer:
Tetramer:
Subunit:
Homotrimer:
Heterotetramer:
Protein Domain:
Protein Family:
Ligand:
Allosteric:
Dimer: A chemical compound composed of two identical or similar (not necessarily identical) subunits or monomers.
Trimer: A chemical compound that is composed of a polymer comprising three monomer units.
Tetramer: A chemical compound that is composed of a polymer comprising four monomer units
Subunit: A monomer that forms part of a larger molecule, such as an amino acid residue in a protein or a nucleotide residue in a nucleic acid. Can also refer to a complete molecule that forms part of a larger molecule. Many proteins, for example, are composed of multiple polypeptide chains, each of which is called a protein subunit.
Homotrimer: A trimer , especially a biologically active one, derived from three identical monomers.
Heterotetramer: is protein containing four non-covalently bound subunits, wherein the subunits are not all identical. A homotetramer contains four identical subunits.
Protein Domain: Segment of a polypeptide chain that can fold into a compact, stable structure and that often carries out a specific function.
Protein Family: A group of polypeptides that share a similar amino acid sequence or three-dimensional structure, reflecting a common evolutionary origin. Individual members often have related but distinct functions, such as kinases that phosphorylate different target proteins.
Ligand: General term for a small molecule that binds to a specific site on a macromolecule.
Allosteric: Describes a protein that can exist in multiple conformations depending on the binding of a molecule (ligand) at a site other than the catalytic site; such changes from one conformation to another often alter the protein’s activity or ligand affinity.
How do proteins interact with ligands? (What holds them together?)
The ability of a protein to bind selectively and with high affinity to a ligand is due to the formation of a set of weak, noncovalent interactions—hydrogen bonds, electrostatic attractions, and van der Waals attractions—plus favorable hydrophobic forces. Each individual noncovalent interaction is weak, so that effective binding requires many such bonds to be formed simultaneously. This is possible only if the surface contours of the ligand molecule fit very closely to the protein, matching it like a hand in a glove
What are the FOUR ways that protein function is regulated (function turned ON/OFF). Explain each.
- Some proteins are regulated by the non-covalent binding of small molecules, such as amino acids or nucleotides, that cause a change in the conformation and thus, the activity of the protein.
- Some proteins are regulated by phosphorylation (the addition of phosphate groups) of specific amino acids on the protein. Since phosphorylation is reversible, this process serves as a handy on-off switch.
- Some proteins are regulated by interactions among the polypeptides making up the protein, or between the protein and other proteins in the cell.
- Some proteins are regulated by enzymes that is controlled through digestion of a particular ion or macromolecule to break it down.
How many different amino acids are commonly used in making proteins?
*Proteins are made from a set of 20 common amino acids. Therefore, a protein that is n amino acids long has 20n different possible sequences.*
20
Which parts of amino acids are involved in a peptide bond?
*The peptide bond is formed between the nitrogen atom of the amino group of one amino acid and the carbon atom of the carboxyl group of another amino acid.*
amino group of one amino acid and carboxyl group of the other
What is the best type of model for visualizing the surface of a protein?
*The space-filling model is the best type of model for visualizing the surface of a protein. This model provides a contour map of a protein’s surface, which reveals which amino acids are exposed on the surface and shows how the protein might look compared to a small molecule such as water or to another macromolecule in the cell.*
Space-filling model
What are the two types of β sheets?
*The two types of β sheets are parallel and antiparallel. In a β sheet, several segments (strands) of an individual polypeptide chain are held together by hydrogen bonding between peptide bonds in adjacent strands. The amino acid side chains in each strand project alternately above and below the plane of the sheet.*
parallel and antiparallel
What does the primary structure of a protein refer to?
*The primary structure of a protein refers to the linear amino acid sequence of the protein.
The chain of linear polymers of amino acids that compose proteins is termed a polypeptide. The primary structure determines the secondary and tertiary structures.*
the linear amino acid sequence of the protein