3D Protein Structure (Exam 2)

What is the primary structure of a protein?

Sequence of amino acids in a polypeptide chain

What is the secondary structure of a protein?

Shaped formed by hydrogen bonds

What is the tertiary structure of a protein?

Structure stabilized by non-covalent interactions and disulfide bonds

What is the quaternary structure of a protein?

Structure made up of subunits

What is a peptide bond?

Covalent bond between the amino and carboxyl group of amino acids

What is an alpha helix?

Coiling secondary structure formed by hydrogen bonds

What is a protein motif?

Super secondary structure (tertiary) in proteins

What happens to hydrophobic regions of a protein structure?

Move to the core of the protein increasing entropy

What are 6 interactions that are favorable in proteins?

- Peptide bonds

- Disulfide bonds

- Hydrophobic effect

- Hydrogen bonds

- London dispersion

- Electrostatic interactions

What is phenyl isothiocyanate?

- Binds to N-terminal amino acid breaking it off to be identified

- Short amino acids only

What is trypsin?

Breaks peptide bonds of lysine-arginine

What are the structures of preproinsulin?

- N-signal sequence

- A chain

- B chain

- C-peptide

What are the structures of proinsulin?

- A chain

- B chain

- C-peptide

- Disulfide bonds

What are the structures of insulin?

- A chain

- B chain

- Disulfide bonds

What are examples of helix breakers?

- Proline

- Glycine

- Charged AA

What are examples of strong helix formers?

- Alanine

- Leucine

What are examples of B-sheets formers?

- Valine

- Isoleucine

- Tyrosine

- Cysteine

- Tryptophan

What are examples of B-turn formers?

- Glycine

- Proline

Do parallel b-sheets have stronger or weaker bonds?

Weaker, angled hydrogens bonds

Are parallel or antiparallel beta sheets stronger?

Antiparallel

What shape and levels of structure do globular proteins use?

- Compact / rounded

- Secondary and quaternary structures

What shape and levels of structure do fibrous proteins use?

- Long / narrow

- Primary and secondary structures

What is the solubility of globular proteins?

Soluble and can bind to membranes

What is the solubility of fibrous proteins?

Insoluble

What is the function of globular proteins?

Dynamic roles

- Catalyze reactions

- Transportation

What is the function of fibrous proteins?

Structural roles

What are examples of globular proteins?

- Hemoglobin

- Myoglobin

- Enzymes

What are examples of fibrous proteins?

- Collagen

- Keratin

- Elastin

Where is keratin found?

hair, skin, nails

Describe the structure of keratin.

- 2 a-helices forming a supercoil

- Disulfide bonds for strength

What is the most abundant protein in the body?

Collagen

What is the structure of collagen?

Three peptide alpha chains forming a triple helix

What is each collagen chain?

Aeft handed helix

How are the collagen alpha chains assembled?

Right handed superhelical triple helix

What is the sequence of amino acids in collagen?

Glycine-X-Y

***X-Y is either proline or lysine

***Y may be hydroxyproline

What does the triple helix do for collagen?

Gives it strength

What are the 3 types of collagen?

- Fibril forming

- Network forming

- Fibril-associated

What is collagen cross linkage?

Holds different collagen molecules together

What enzymes add a hydroxyl group?

- Lysl hydroxylase

- Prolyl hyroxylase

What enzyme creates collagen cross linkage?

Lysyl oxidase

What does lysyl oxidase require?

Iron and vitamin C

What are examples of type 1 fibril forming collagen?

- Skin

- Bone

- Tendon

- Blood vessels

- Cornea

What are examples of type 2 fibril forming collagen?

- Cartilage

- Intervertebral disk

- Vitreous body

What are examples of type 3 fibril forming collagen?

- Blood vessels

- Skin

- Muscle

What are examples of type 4 network forming collagen?

Basement membrane

What are examples of type 8 network forming collagen?

- Cornea

- Vascular endothelium

What are examples of type 9 fibril associated collagen?

Cartilage

What are examples of type 7 fibril associated collagen?

- Tendons

- Ligaments

How are collagen proteins initially made?

Translation synthesizes pro a-chain in rough ER

What happens to collagen after a-chain is made?

- Hydroxylation of Pro and Lys

- Glycosylation of OH and Lys

What happens to collagen after hydroxylation and glycosylation?

Triple helix formation

What happens after the triple helix formation?

Pro-collagen secreted by Golgi apparatus

Where does cleavage of extension peptides from procollagen occur?

- Outside the cell

- N and C - terminal are cleaved in ECM using peptidases

Where does microfibrils and crosslink formation occur?

Outside of cell

How are microfibrils assembled?

Spontaneously

How are separate microfibrils attached?

Lysyl oxidase

-What is osteogenesis imperfecta?

- Mutation of type 1 collagen

- Weak bones that fracture easily

What is chrondiodysplasias?

- Mutation of type 2 collagen

- Abnormal cartilage, bone or joints

What is ehlers-danlos syndrome?

- Mutation of types 3 and 5 collagen

- Type 3: fragile skin / blood vessels

- Type 5: hypermobile joints

Where is elastin found?

Lungs and tendons

What type of structure does elastin have?

Desmosine

Describe the desmosine structure.

4 crosslinked lysine residues in random conformation

What is the potential benefit of intrinsically disordered protein?

- Potential to bind well to many different partner proteins

- Overly ordered proteins would be limited to specialization

What does the PONDR score tell you about any given section of a polypeptide?

Likelihood that an amino acid within a protein region is disordered

What PONDR score would indicate a disordered protein?

Above 0.5

What are the 3 proteins without a fold?

- Intrinsic disorder protein

- Denatured protein

- Misfolded protein

What 3 things affect proteostasis?

- Protein synthesis

- Chaperones

- Proteasomal degradation

What is proteostasis?

Maintenance of cellular protein activity

How does protein synthesis affect proteostasis?

Ribosomes make proteins that spontaneously fold

How do chaperones affect proteostasis?

- When proteins misfold, chaperones help to refold it

- May use ATP or additional enzymes to ensure correct folding

How does proteasomal degradation affect proteostasis?

- Misfolded proteins get tagged by ubiquitin for destruction

- Transported to proteosome to be recycled

What is protein denaturation?

When a loses its native fold due to loss of forces that stabilized its 3D structure

What are 5 things that denature proteins?

1. Temperature

2. pH

3. Detergents

4. Reducing agents

5. Chaotropic agents

How does temperature denature proteins?

Hot or cold temperature breaks hydrogen bonds

How does pH denature proteins?

Acids and bases disrupt electrostatic interactions

How does detergent denature proteins?

Sodium laurel sulfate disrupts the hydrophobic effect

How does reducing agents denature proteins?

DTT or mercaptoethanol breaks disulfide bonds

How do chaotropic agents denature proteins?

Urea of guanidinium hydrochloride disrupts hydrogen bonds

What is a chaotropic agent?

Substance that disrupts protein structures by minimizing order of 3D structure by disrupting hydrogen bonds

What is 4 examples of protein-misfolding diseases?

1. Alzheimer's

2. Parkinson's

3. Huntingtons

4. Prion

What is a common feature of amyloidosis?

- Plaque deposits

- B-sheet structures

- Neuro-degeneration

How do prions spread?

The infectious misfolded protein acts as a nucleus triggering

misfolding of healthy proteins as well - this results in more

misfolded/denatured proteins - development of plaques and progression of disease

What is the term for a Parkinson's disease plaque of beta-aggregates

of alpha-synuclein?

Lewy bodies

What hormones stimulate Pancreas to produce zymogens

Secretin and CCK

What are zymogens?

Inactive enzyme precursors

What are 7 zymogens?

- Pepsinogen

- Trypsinogen

- Chymotrypsinogen

- Proelastase

- Procarboxypeptidase A/B

- Aminopeptidase

- Enteropeptidase

What is the 1) source 2) mode of activation and 3) target of pepsinogen?

1) Stomach

2) [H+] -> pepsin

3) Mostly phenylalanine

What is the 1) source 2) mode of activation and 3) target of trypsinogen?

1) Pancreas

2) Enteropeptidase -> Trypsin

3) Lys and Arg

What is the 1) source 2) mode of activation and 3) target of chymotrypsinogen?

1) Pancreas

2) Trypsin -> Chymotrypsin

3) Aromatic & bulky AA

What is the 1) source 2) mode of activation and 3) target of proelastase?

1) Pancreas

2) Trypsin -> elastase

3) Small AA Ala/Gly/Ser

What is the 1) source 2) mode of activation and 3) target of procarboxypeptidase A/B?

1) Pancreas

2) Trypsin -> carboxypeptidase

3) Carboxy-end AA

What is the 1) source 2) mode of activation and 3) target of aminopeptidases?

1) Small intestine

2) Non needed

3) Amino-end AA

What is the 1) source 2) mode of activation and 3) target of enteropeptidase?

1) Small intestine

2) Non needed

3) Trypsin (C-side of Lys6)

What are beta conformers?

Misfolded proteins that form b-sheets where there shouldn't be

T/F: Amino acids can be broken down to generate ATP.

True

What is a prefix or suffix for zymogens?

Pre: pro-

Suf: -ogen