Protein Structure and Foundations Part 2

Question 1

Forces that stabilize primary structure

Answer 1

Peptide bonds

Question 2

Forces that stabilize secondary structure

Answer 2

Local hydrogen bonds

Question 3

Forces that stabilize tertiary structure

Answer 3

Van der Waals, hydrogen bonds, ionic bonds (can be stabilizing or destabilizing depending on charges near each other) hydrophobic interactions, disulfide bonds (list goes from weakest to strongest)

Question 4

Which force’s drives the formation of tertiary structure and is an entropic process?

Answer 4

Hydrophobic interactions

Question 5

The geometric arrangement of ALL atoms in a polypeptide. The SUM of the secondary structures making it the sum of all chemical and physical properties of the primary structure.

Answer 5

Tertiary Structure

Question 6

Why are disulfide bonds important to stabilizing tertiary protein structure?

Answer 6

They are very hard to break. Ex: Proteins in thermal pools use a lot of disulfide bonds because of their strength

Question 7

Sum of 2 or more tertiary structures - more than 1 polypeptide. May or may not be covalently connected

Answer 7

Quaternary structure

Question 8

Do individual polypeptides have different conformations when they are alone vs. when they are in multimeric form?

Answer 8

They have different conformations

Question 9

Multimers or Oligomers

Answer 9

Proteins with a few repeating subunits

Question 10

What are repeated subunits called?

Answer 10

Protomers

Question 11

Proteins often have what attached that help them with their function?

Answer 11

Cofactors of Prosthetic Groups

Question 12

Interacts with proteins through non-covalent means. Binds to enable or help enhance protein’s ability

Answer 12

Cofactors

Question 13

Group that is covalently attached to enzymes or proteins. Are typically tightly bound to proteins

Answer 13

Prosthetic group

Question 14

Long, extended rope-like proteins. Mainly to give structure (shape, protection, and integrity). Usually consist of a single type of secondary structure

Answer 14

Fibrous Proteins

Question 15

Compact/ blobby proteins. Usually for “action” (enzymes, regulators, movers. Huge diversity in these proteins. Often contain several types of secondary structure.

Answer 15

Globular proteins

Question 16

Why is there a huge diversity in globular proteins?

Answer 16

They have a lot of different jobs and are involved in many different activities.

Question 17

Fibrous protein involved in hair, wool, nails, claws, quills, horns, hooves, and skin. Repeated secondary structure, strengthened by cross-linking (S-S bonds), and has a lot of hydrophobic regions to promote “packing”

Answer 17

alpha-Keratin

Question 18

Protein with a different kind of helix (left-handed with 3 strands). Cross linked by unusual covalent bonds. Found in tendons, cartilage, bone, cornea, ECMP

Answer 18

Collagen

Question 19

Collagen is a tripeptide repeat of Gly-X-Y. (X is often Proline which stabilizes the helical turn. Y is often hydroxyproline). Why does it use Glycine?

Answer 19

It uses glycine because that amino acid is flexible and packs very tightly

Question 20

Protein named “Fibroin” that has antiparallel Beta-sheets. Has many weak interactions between sheets due to Van der Waals

Answer 20

Silk

Question 21

Why are Gly and Ala situated between silk Beta-sheets

Answer 21

Fibroin is rich in Ala and Gly. This works out for the structure because of their small or no R groups, they can pack tightly and closer together

Question 22

Does silk stretch?

Answer 22

Silk does not stretch because the Beta-conformation that it is in is already highly extended.

Question 23

A globular protein that stores oxygen

Answer 23

myoglobin

Question 24

A recognizable folding pattern involving 2 or more secondary structure elements (alpha or beta) and the connection between them

Answer 24

motif

Question 25

Proteins can be organized by their motifs. What are the categories?

Answer 25

All beta, all alpha, alpha + beta (alpha and beta subunits are mostly separate), and alpha/beta (alpha and beta subunits are conjoined/intermingled)

Question 26

Independently stable and functional part of a protein that can undergo movements as a single entity. Between second and tertiary structure and are separate units of protein structure

Answer 26

Domains

Question 27

Domains can have entirely different jobs. What are some examples?

Answer 27

Binding molecules like Ca2+, enzymatic activity

Question 28

Post-translational modifications that can drastically alter a proteins shape

Answer 28

Phosphorylation (adding a phosphate group), glycosylation (attaching sugars), attaching lipids (prenylation)

Question 29

The final tertiary structure of a protein is (normally) the _ energetic of all possible conformational states that the polypeptide can assume

Answer 29

Least

Question 30

The name of the state of the fully folded, functional protein

Answer 30

Native state

Question 31

If a protein is unfolded it is typically _

Answer 31

inactive

Question 32

Disrupting a folded protein or denaturation is caused by what factors

Answer 32

Change in pH, change in temperature, exposure to different solvents, etc.

Question 33

Why does a change in pH denature a protein?

Answer 33

Change in pH changes the ionization state of R groups. This can change the electrostatic interactions between R groups which may change shape (repelling or attraction of different groups)

Question 34

“Helper” proteins that assist other proteins in folding

Answer 34

Molecular Chaperones

Question 35

Eukaryotic chaperones that use heat

Answer 35

Heat shock proteins (Hsp)

Question 36

Diseases that arise from a misfiling mechanism. The protein unfolds and becomes insoluble. The insoluble proteins act as a nucleating center for more misfolded proteins. Not infectious

Answer 36

Amyloid Diseases

Question 37

What do amyloid diseases effect and what are some examples?

Answer 37

They affect different organs like the spleen, kidney, liver, and heart. Examples include Alzheimers, Huntington’s and Parkinson’s

Question 38

“Infectious” amyloid diseases that often cause holes in brain tissue. Mad cow disease. We don’t know how it gets into the brain yet. Spreads by making other proteins unfold

Answer 38

Prion diseases

Question 39

How do the hydrophobic interactions that drive tertiary structure work?

Answer 39

They allow the protein to decrease the surface area in folding to reduce the undesirable interactions with water. Most proteins are in a hydrophilic/ water environment so the need for greater entropy makes the proteins fold.

Question 40

Do most proteins have interactions with other peptides?

Answer 40

Yes. Very few proteins are “lone wolves” and most interact with other peptides essential for their function

Question 41

Examples of proteins that interact with other peptides/ have different subunits.

Answer 41

Anthrax (2 subunits). Pertussis toxin (5 subunits). Holoenzyme

Question 42

What would phosphorylation of a protein do to it energetically?

Answer 42

It would give the protein more negative charges which would make it more energetic. This would be due to more repulsion of like charges in the protein

Question 43

Which amino acids undergo phosphorylation?

Answer 43

Amino acids with OH groups. Thr, Ser, Tyr

Question 44

How do organic solvents and detergents denature a protein?

Answer 44

They are non-polar so they turn off the hydrophobic interactions which are important for protein folding. This causes the protein to unfold.

Question 45

Do chaperonins use or create ATP?

Answer 45

They use ATP

Question 46

The GroEL system is what type of system?

Answer 46

A chaperonin system

Question 47

Why is the latency period for prion diseases long?

Answer 47

It takes a long time for the unfolded proteins to accumulate. They accumulate very slowly