Midterm 2

Question 1

What are the factors of different proteins that determine the varied functions we see in them?

Answer 1

1. Order of amino acids that creates a 3D shape (biologically functional)
2. Types and number of each type of functional group (reactivity/enzymatic activity)
3. Ability to form complex assemblies (molecular co-operation)

Question 2

Define conformation

Answer 2

Spatial arrangement of atoms that depends of specific rotation of bonds (not breaking of bonds)

Question 3

There are many types of conformations a polypeptide can take up, what’s a native conformation?

Answer 3

Native conformation is the the most stable form that a protein can assume under physiological conditions

Question 4

Can a peptide bond rotate? Why or why not?

Answer 4

A peptide bond can’t rotate because it has double bound tendencies from resonance

Question 5

What are some things that influence what the native conformation of a protein is?

Answer 5

Steric hinderance mostly decides what conformation is the most stable at physiological conditions

Question 6

Rigid proteins are usually what type of protein?

Answer 6

Structural proteins

Question 7

What are the 4 levels of protein structure and what is the type of bond(s) that holds them together?

Answer 7

1. Primary structure; linear sequence of amino acids that determines all other levels of protein structure (covalent bonds)
2. Secondary structure; repeating conformations of the peptide chain like alpha helices, beta sheets & loops (H bonds between amide H & O of peptide backbone
3. Tertiary structure; completely folded polypeptide chain interacting with other sections of the polypeptide chain (interaction of non-neighboring amino acids)
4. Quaternary structure; 2 or more polypeptide chains interacting to create a multi subunit protein

Question 8

What type of bond stabilizes the alpha helix structure? What two atoms in the alpha helix is this bond between?

Answer 8

Hydrogen bonds stabilize alpha helix structure. Hydrogen bond is formed between the carbonyl oxygen of the aa backbone and amide hydrogen of the 4th residue toward c terminus

Question 9

Different side chains have different effects on the stability of alpha helices. Name a side chain thats commonly found in the alpha helix.

Answer 9

Alanine is commonly found in alpha helices because its small and uncharged

Question 10

Name the 3 aas not found in side chains and why?

Answer 10

Tyrosine (W) and Asparagine: bulky R groups

Glycine: destabilizes bc rotation around the alpha carbon is too unconstrained (only aa that doesn’t have a chiral C)

Proline: Never found in the interior bc cyclic side chain is to rigid (steric hinderence), no amide hydrogen to bond to the carbonic oxygen

Question 11

What is usually found at the end of alpha helices? What is distinct about the interactions at this place? What amino acids are usually found in this area?

Answer 11

Helix stop signal/capping box. What’s special here is that instead of the usual backbone amide hydrogens interacting with backbone carbonyl oxygen, we see backbone amide hydrogen interacting with the N terminal side chain; thus being incompatible with formation of alpha helices. Serine, threonine, and glutamate are often found in the helix stop signal/capping box

Question 12

Which globular protein has more alpha helices content?

Answer 12

Myoglobin has more than chymotrypsin

Question 13

What is a amphipathic helices?

Answer 13

Amphipathic helices have hydrophobic amino acids on one face of the helix cylinder (inner) and hydrophilic amino acids on the other face (outer)

Question 14

How do beta sheets and beta strands differ?

Answer 14

Beta sheets are made up of many beta strands organized into a sheet through hydrogen bonding of amide hydrogen and carbonyl oxygen

Question 15

What are random coils?

Answer 15

Non-repetitive regions found in globular proteins

Question 16

What makes random coils important?

Answer 16

Random coils connect secondary structures and create directional changes needed for correct folding

Question 17

What is an important application for the non-repetitive region being less conserved?

Answer 17

Less conserved means greater mutation which is needed for greater diversity in proteins like antibodies

Question 18

What is an example of a super secondary structure?

Answer 18

Motifs; recognizable combinations of alpha helices and beta strands

Question 19

Draw the 8 different types of motifs.

Answer 19

(See page 6)

a) helix-loop-helix
b) coiled coil
c) helix bundle
d) beta-alpha-beta
e) hairpin
f) beta meander
g) greek key
h) beta sandwich

Question 20

What interactions stabilize the tertiary structure of globular proteins?

Answer 20

Non-covalent interactions (hydrophobic mostly) between the side chains of amino acid residues

Question 21

What is contranslational folding?

Answer 21

The peptide chains tendency to fold as it’s being translated

Question 22

What is cooperative folding?

Answer 22

The formation of 1 part of the protein structure leading to the formation of the remaining parts of the proteins structure

Question 23

What are the non-covalent and covalent forces that contribute to protein folding and stabilization?

Answer 23

Non-covalent: hydrophobic effect, H-bonding, charge-charge and van der waals

Covalent: disulphide bridges

Question 24

What is the most stable shape of a protein called?

Answer 24

Native conformation

Question 25

What is the benefit to having non-covalent bonds stabilize proteins rather than stronger covalent bonds?

Answer 25

All together: non-covalent bonds can create stability But because individual bonds are weak: gives proteins resilience and flexibility to undergo small conformational changes

Question 26

What is the purpose of chaperones?

Answer 26

To prevent the formation of incorrectly folded intermediates which would prevent a protein from reaching its native conformation

Question 27

Define denaturation

Answer 27

Disruption of native conformation of protein which causes loss of function

Question 28

What are the 4 methods to denature a protein?

Answer 28

- heat - pH - chaotropic agents & detergents - cleavage of disulphide bonds

Question 29

What are the 2 methods for determining primary structure of a protein?

Answer 29

1. DNA or protein sequencing | 2. X-ray crystallography & NMR

Question 30

What are the pros and cons of xray crystallography?

Answer 30

- retain native conformation | - requires extensive prep

Question 31

What is the con of NMR to study a protein?

Answer 31

Only suited for small proteins

Question 32

What are the 4 main properties of enzymes? Explain each one briefly.

Answer 32

1. Enzymes function as catalysts; decrease Ea in order to speed up a reaction. Catalysts maybe be temporarily be altered but unchanged overall 2. Enzymes catalyze highly specific reactions. Could be substrate specific but also might not be 3. Enzymes can couple reactions; energy from an exergonic reaction would drive an endergonic reaction 4. Enzyme activity can be regulated; the control point in metabolism

Question 33

What part of the reaction do Enzymes not influence?

Answer 33

Change in free energy (G) or position of the equilibrium (Keq)

Question 34

At what level of protein structure are globular proteins' domains found? What is a domain?

Answer 34

At the Tertiary structure level. A domain is an independently folded unit ~ usually each domain has a different function

Question 35

What is significant between lactate and malate dehydrogenase?

Answer 35

They're paralogs bc they had a common ancestor and arose from gene duplication

Question 36

What interactions hold together the subunits of oligomers?

Answer 36

Non-covalent factors: namely hydrophobic interactions and maybe some electrostatic

Question 37

What are the 5 reasons proteins have quaternary structure?

Answer 37

1. Quaternary structure more stable than subunits on their own 2. Multiple subunit needed to create active site 3. If it was all synthesized in one polypeptide it might increase the likelihood of error 4. Cooperative binding 5. Different protein can share the same subunits so more efficient 6. Sequential enzyme action

Question 38

What are the 7 steps of Chymotrypsin mechanism?

Answer 38

1. Enzyme-substrate complex forms, hydrophobic specificity pocket binds to R group, carbonyl side of a.a. close to the O of Ser 2. Substrate binding causes Asp to create a H-bond with His, His removes a proton from Ser, The now Nu O of Ser attacks the carbonyl c of the peptide & creates a intermediate that looks like the TS 3. The oxyanion moves to the oxyanion hole, His donates a proton, causes cleavage 4. Carbonyl group creates a covalent bond with enzyme, new amino acid leaves, water enters 5. His and Asp form a low energy H bond, His removes proton from water, creates an OH to attack 6. His donates a proton, new tetrahedral forms & is stabilized by the oxyanion hole 7. New product formed, and detached from the enzyme