Unit 2: Protein Structure and Function

Question 1

What are the biological process that directly involve proteins (4 processes)

Answer 1

1. Breaking food polymers into smaller molecules
2. Changing the shape of a cell.
3. Defending cells against viruses.
4. Sensing light.

Question 2

What do proteins determine?

Answer 2

Proteins determine the physical traits that we see as well as much of our behavior a physiology.

Question 3

What are the three attributes that make a molecule responsible for the attributes of life?

Answer 3

For the answer to be yes, they must have the fundamental attributes of life:
1. Information
2. Replication
3. Storage

Question 4

Proteins are composed of _______.

Answer 4

amino acids

Question 5

What experiment were amino acids discovered?

Answer 5

Stanley Miller’s experiment.

Question 6

Where were amino acids originally found?

Answer 6

Found in meteorites

Question 7

Amino acids were likely abundant during ___________.

Answer 7

chemical evolution

Question 8

What is a protocell?

Answer 8

A primitive structure that is thought to be an early form of life, precursor to the first true cells.

Question 9

What types of R-groups are hydrophilic?

Answer 9

Polar and charged R-groups that interact with water are hydrophilic.

Question 10

What types of R-groups are hydrophobic?

Answer 10

Nonpolar R-groups are hydrophobic and do not form hydrogen bonds with water (don’t dissolve in water).

Question 11

Given a chemical structure of amino acids, you can determine its type by asking three questions:

Answer 11

1. Does side chain have negative charge? (Lost a proton, must be acidic)
2. Does side chain have positive charge? (has taken a proton, must be basic).
3. 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).
4. If all answers to above are NO, amino acid must be nonpolar.

Question 12

What are two facts about amino acids with nonpolar side chains?

Answer 12

1. No oxygen present in side chain.
2. No charged or polar groups to interact with water.

Question 13

What are two facts about amino acids with polar side chains?

Answer 13

1. Oxygen present in side chain.
2. Partial charges on side chains can form hydrogen bonds with water.

Question 14

What are three facts about amino acids with charged side chains?

Answer 14

1. Charged side chains can form ionic bonds, hydrogen bonds, or interact with water.
2. Acidic acids tend to have a negative charge in side chain (donate protons).
3. Basic acids tend to have a positive charge in side chain (accept protons).

Question 15

What’s a polymer?

Answer 15

A polymer is a large molecule made up of repeating subunits called monomers. Monomers that are chemically bonded together in chain-like structure.

Question 16

What type of bond is a peptide bond?

Answer 16

A peptide bond is a C- N covalent bond resulting from a condensation reaction (water is formed).

Question 17

How are peptide bonds formed in proteins? (2 ideas)

Answer 17

1. 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).
2. Amino acids are linked by peptide bonds.

Question 18

Proteins are _____ of _______.

Answer 18

Proteins are polymers of amino acids.

Question 19

_____________ when bond forms between ________ of one amino acid and an _________ of another.

Answer 19

Amino acids polymerize when bond forms between carboxyl group of one amino acid and an amino group of another.

Question 20

What is polymerize?

Answer 20

Polymerize is the process by which monomers (small molecules) chemically bond together to form a polymer (a large, chain-like molecule).

Question 21

What is a protein’s primary structure?

Answer 21

The sequence of amino acids is known as the protein’s primary structure.

Question 22

What is the first key point about peptide-bonded backbone?

Answer 22

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.

Question 23

What is the second key point about peptide-bonded backbone?

Answer 23

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.

Question 24

What is the third key point about peptide-bonded backbone?

Answer 24

Flexibility- Single bonds on either side of the peptide bond can rotate.

Question 25

What is an oligopeptide?

Answer 25

Chain of fewer than 50 amino acids.

Question 26

What is a polypeptide?

Answer 26

Chain of more than 50 amino acids.

Question 27

______ gives rise to _______ in proteins.

Answer 27

Structure gives rise to the function in proteins

Question 28

What are the three things that form the primary structure of a protein?

Answer 28

1. Made up of an amino (N-terminal) end. 2. Made up of a Carboxyl (C-terminal) end. 3. Amino acid monomers connected by peptide bonds.

Question 29

How do changes in the primary structure of a protein affect its function? Give an example.

Answer 29

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.

Question 30

How is the secondary structure of a protein formed? (2 things)

Answer 30

1. Protein secondary structure formed by hydrogen bonds between: Carbonyl group of one amino acid Amino group of another amino acid 2. Types of secondary structures: A-helix (alpha helix) B-pleated sheet (beta-pleated sheets)

Question 31

What is the tertiary structure of a protein?

Answer 31

Interactions (between R-groups) cause backbone to bend and fold to create three-dimensional shape of polypeptide.

Question 32

What are five important types of R-group interactions in the tertiary structure?

Answer 32

1. Covalent bonding- Covalent bonds between side chains of sulfhydryl groups (disulfide bonds). 2. Hydrophobic interactions- water forces hydrophobic side chains together. 3. Hydrogen bonding- form between polar side chains and opposite partial charges. 4. Ionic bonding- form between groups with full and opposing charges. 5. Van der Waals interactions- weak electrical interactions between hydrophobic side chains.

Question 33

What is the quaternary structure?

Answer 33

Bonding (between R-groups) of two or more distinct polypeptide subunits produces quaternary structure.

Question 34

What are four types of bonds in the quaternary structure? What is their purpose?

Answer 34

1. Dimers- proteins with two polypeptide subunits. 2. Homodimers- structure consists of two identical subunits. 3. Heterodimer- Subunits are not identical. 4. Tetramer- Four polypeptide chains.

Question 35

Normal protein folding is _____ and ________.

Answer 35

Normal protein folding is crucial and spontaneous.

Question 36

What is true about a folded protein's energy versus an unfolded protein?

Answer 36

Folded molecule is more energetically stable than unfolded molecule- less potential energy.

Question 37

What is a denatured protein?

Answer 37

Denatured (unfolded) protein unable to function normally.

Question 38

What bonds are broken in a denatured protein?

Answer 38

Hydrogen bonds and disulfide bonds are broken causing a protein to denature.

Question 39

What are molecular chaperones?

Answer 39

Cells contain proteins called molecular chaperones which facilitate folding. Responsible for blocking inappropriate interactions between unfolded proteins.

Question 40

What is an example of a molecular chaperone?

Answer 40

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

Question 41

What do normal proteins induce to when misfolded?

Answer 41

Normal proteins can be induced to fold into infectious, disease-causing agents.

Question 42

What are prions? What's an example?

Answer 42

Prions are altered folded forms of normal proteins. Ex. Prion protein (PrP) responsible for "mad cow disease" and "Kuru".

Question 43

How do prions change the shape of normal proteins?

Answer 43

Prions can induce normal protein molecules to change their shape to the altered form.

Question 44

What affects the solubility of a protein?

Answer 44

Polarity and charge of R-groups affect solubility.

Question 45

What is the general chemical structure of a non-ionized amino acid? (5 things)

Answer 45

1. A central carbon (alpha carbon) 2. An amino group (NH2) 3. A carboxyl group (COOH) 4. A hydrogen atom (H) 5. R-group (side chain) chemical structure varies

Question 46

What is the general chemical structure of an ionized amino acid? (5 things)

Answer 46

1. A central carbon (alpha carbon) 2. An amino group (+H3N) 3. A carboxyl group (COO-) 4. A hydrogen atom (H) 5. R-group (side chain) chemical structure varies

Question 47

In ____, amino and carboxyl groups ionize to ______ and _____ respectfully.

Answer 47

In water, amino and carboxyl groups ionize to NH3+ and COO- respectfully.

Question 48

What is Kuru?

Answer 48

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.