Unit 2: Protein Structure and Function Flashcards
What are the biological process that directly involve proteins (4 processes)
- Breaking food polymers into smaller molecules
- Changing the shape of a cell.
- Defending cells against viruses.
- Sensing light.
What do proteins determine?
Proteins determine the physical traits that we see as well as much of our behavior a physiology.
What are the three attributes that make a molecule responsible for the attributes of life?
For the answer to be yes, they must have the fundamental attributes of life:
1. Information
2. Replication
3. Storage
Proteins are composed of _______.
amino acids
What experiment were amino acids discovered?
Stanley Miller’s experiment.
Where were amino acids originally found?
Found in meteorites
Amino acids were likely abundant during ___________.
chemical evolution
What is a protocell?
A primitive structure that is thought to be an early form of life, precursor to the first true cells.
What types of R-groups are hydrophilic?
Polar and charged R-groups that interact with water are hydrophilic.
What types of R-groups are hydrophobic?
Nonpolar R-groups are hydrophobic and do not form hydrogen bonds with water (don’t dissolve in water).
Given a chemical structure of amino acids, you can determine its type by asking three questions:
- Does side chain have negative charge? (Lost a proton, must be acidic)
- Does side chain have positive charge? (has taken a proton, must be basic).
- If side chain is uncharged, does it have an oxygen atom? (If oxygen is present on side chain, must be polar due to H bonding).
- If all answers to above are NO, amino acid must be nonpolar.
What are two facts about amino acids with nonpolar side chains?
- No oxygen present in side chain.
- No charged or polar groups to interact with water.
What are two facts about amino acids with polar side chains?
- Oxygen present in side chain.
- Partial charges on side chains can form hydrogen bonds with water.
What are three facts about amino acids with charged side chains?
- Charged side chains can form ionic bonds, hydrogen bonds, or interact with water.
- Acidic acids tend to have a negative charge in side chain (donate protons).
- Basic acids tend to have a positive charge in side chain (accept protons).
What’s a polymer?
A polymer is a large molecule made up of repeating subunits called monomers. Monomers that are chemically bonded together in chain-like structure.
What type of bond is a peptide bond?
A peptide bond is a C- N covalent bond resulting from a condensation reaction (water is formed).
How are peptide bonds formed in proteins? (2 ideas)
- Occurs when the carboxyl group (COO⁻) of one amino acid reacts with the amino group (-NH₃⁺) of another amino acid, releasing a water molecule (H₂O) in the process (dehydration synthesis).
- Amino acids are linked by peptide bonds.
Proteins are _____ of _______.
Proteins are polymers of amino acids.
_____________ when bond forms between ________ of one amino acid and an _________ of another.
Amino acids polymerize when bond forms between carboxyl group of one amino acid and an amino group of another.
What is polymerize?
Polymerize is the process by which monomers (small molecules) chemically bond together to form a polymer (a large, chain-like molecule).
What is a protein’s primary structure?
The sequence of amino acids is known as the protein’s primary structure.
What is the first key point about peptide-bonded backbone?
R-group orientation- Side chains extend out of backbone so they can interact with each other or water. Can create hydrophobic interactions, covalent bonding (disulfide linkage), hydrogen bonds, ionic bonds and Van der Waals interactions.
What is the second key point about peptide-bonded backbone?
Directionality- Ends with free amino group is the N-terminus. Ends with free carboxyl group is the C-terminus. The carboxyl group and amino group from two different amino acids can create peptide bonds.
What is the third key point about peptide-bonded backbone?
Flexibility- Single bonds on either side of the peptide bond can rotate.
What is an oligopeptide?
Chain of fewer than 50 amino acids.
What is a polypeptide?
Chain of more than 50 amino acids.
______ gives rise to _______ in proteins.
Structure gives rise to the function in proteins
What are the three things that form the primary structure of a protein?
- Made up of an amino (N-terminal) end.
- Made up of a Carboxyl (C-terminal) end.
- Amino acid monomers connected by peptide bonds.
How do changes in the primary structure of a protein affect its function? Give an example.
Single amino acid change and R-groups affect polypeptide’s properties and function.
Example: hemoglobin- change in R-group produces hemoglobin molecules that stick to one another.
How is the secondary structure of a protein formed? (2 things)
- Protein secondary structure formed by hydrogen bonds between:
Carbonyl group of one amino acid
Amino group of another amino acid - Types of secondary structures:
A-helix (alpha helix)
B-pleated sheet (beta-pleated sheets)
What is the tertiary structure of a protein?
Interactions (between R-groups) cause backbone to bend and fold to create three-dimensional shape of polypeptide.
What are five important types of R-group interactions in the tertiary structure?
- Covalent bonding- Covalent bonds between side chains of sulfhydryl groups (disulfide bonds).
- Hydrophobic interactions- water forces hydrophobic side chains together.
- Hydrogen bonding- form between polar side chains and opposite partial charges.
- Ionic bonding- form between groups with full and opposing charges.
- Van der Waals interactions- weak electrical interactions between hydrophobic side chains.
What is the quaternary structure?
Bonding (between R-groups) of two or more distinct polypeptide subunits produces quaternary structure.
What are four types of bonds in the quaternary structure? What is their purpose?
- Dimers- proteins with two polypeptide subunits.
- Homodimers- structure consists of two identical subunits.
- Heterodimer- Subunits are not identical.
- Tetramer- Four polypeptide chains.
Normal protein folding is _____ and ________.
Normal protein folding is crucial and spontaneous.
What is true about a folded protein’s energy versus an unfolded protein?
Folded molecule is more energetically stable than unfolded molecule- less potential energy.
What is a denatured protein?
Denatured (unfolded) protein unable to function normally.
What bonds are broken in a denatured protein?
Hydrogen bonds and disulfide bonds are broken causing a protein to denature.
What are molecular chaperones?
Cells contain proteins called molecular chaperones which facilitate folding. Responsible for blocking inappropriate interactions between unfolded proteins.
What is an example of a molecular chaperone?
Heat shock protein (Hsp70). Polypeptides can clump together and disturb the normal folding process. Hsp70 attaches to hydrophobic patches before aggregates can form. Release polypeptides to fold properly
What do normal proteins induce to when misfolded?
Normal proteins can be induced to fold into infectious, disease-causing agents.
What are prions? What’s an example?
Prions are altered folded forms of normal proteins.
Ex. Prion protein (PrP) responsible for “mad cow disease” and “Kuru”.
How do prions change the shape of normal proteins?
Prions can induce normal protein molecules to change their shape to the altered form.
What affects the solubility of a protein?
Polarity and charge of R-groups affect solubility.
What is the general chemical structure of a non-ionized amino acid? (5 things)
- A central carbon (alpha carbon)
- An amino group (NH2)
- A carboxyl group (COOH)
- A hydrogen atom (H)
- R-group (side chain) chemical structure varies
What is the general chemical structure of an ionized amino acid? (5 things)
- A central carbon (alpha carbon)
- An amino group (+H3N)
- A carboxyl group (COO-)
- A hydrogen atom (H)
- R-group (side chain) chemical structure varies
In ____, amino and carboxyl groups ionize to ______ and _____ respectfully.
In water, amino and carboxyl groups ionize to NH3+ and COO- respectfully.
What is Kuru?
Kuru is a rare neurodegenerative disorder caused by prions, which are misfolded proteins that trigger normal proteins in the brain to misfold, leading to brain damage.
