L7. Protein structure & function I

Question 1

explain the structure of a protein

Answer 1

• polypeptide backbone
• R group (side chain)
• N-terminus
• C-terminus

Question 2

protein structure - R group

Answer 2

• part of the amino acid that is not involved in forming peptide bonds
• gives each amino acid its unique properties

Question 3

protein structure: R group - what unique properties may it have

Answer 3

• Hydrophobic
• Hydrophilic
• Can have a positive or negative charge

Question 4

explain weak noncovalent bonds

Answer 4

• they allow proteins to bind to each other to produce larger structures in the cell
• 3 types:
  1. van der Waals
  2. ionic (electrostatic) attractions
  3. hydrogen bonds

Question 5

weak noncovalent bonds - van der Waals

Answer 5

• Really weak and has fluctuation in the charge of individual groups
• the individual groups will stick together bc of fluctuation in charges

Question 6

weak noncovalent bonds - ionic (electrostatic) attractions

Answer 6

• Positive or negative charges that attract and facilitate an interaction
• in absence of water: strong
• in presence of water: interactions become shielded and become weak
• the bond is also weakened by ions

Question 7

weak covalent bonds - hydrogen bonds

Answer 7

• Oxygen interacting with hydrogen
• Can interact across polypeptide chains, between different nucleotides, between interactions with water or solutions

Question 8

explain hydrophobic interactions

Answer 8

• water forces hydrophobic groups together
• this can then result in a protein being folded with hydrophilic regions being outside and interacting with the water while hydrophobic regions are pushed inside the protein

Question 9

define denaturation

Answer 9

• a protein being unfolded and losing its natural state
• can happen through treatment with solvents

Question 10

denaturation - examples of solvents

Answer 10

• urea
• high concentrations can denature a protein
• removing the urea causes the protein to renature

Question 11

define renaturation

Answer 11

a protein refolding into its original conformation

Question 12

what are the levels of protein organization

Answer 12

• primary
• secondary
• tertiary
• quaternary

Question 13

levels of protein organization - primary structure

Answer 13

• amino acid sequence
• can be resolved biochemically

Question 14

levels of protein organization - secondary structure

Answer 14

• stabilized by hydrogen bonds
• alpha helixes and beta pleated sheets form within certain segments of the polypeptide chain

Question 15

levels of organization: secondary structure - alpha helixes

Answer 15

• it is generated when a a single polypeptide chain turns around on itself
• depending on the twists, they can be either right or left handed

Question 16

levels of organization: secondary structure - where are alpha-helixes typically found

Answer 16

they are often found embedded in cell membranes as transport proteins and receptors

Question 17

levels of organization: secondary structure - coiled coil structure

Answer 17

• when two alpha helices wrap around one another to form a stable structure
• minimizes exposure to hydrophobic amino acid chains to aqueous environments

Question 18

levels of organization: secondary structure - beta pleated sheet

Answer 18

• created when hydrogen bonds form between segments of a polypeptide chain that lie side by side
• can be parallel or antiparallel

Question 19

levels of organization: secondary structure - parallel beta sheet

Answer 19

neighboring segments run in the same orientation

Question 20

levels of organization: secondary structure - antiparallel beta sheet

Answer 20

neighboring segments run in the
opposite orientation

Question 21

levels of organization: secondary structure - amyloid fibers

Answer 21

• they are created when beta sheets are stacked together
• these are insoluble protein aggregates
• causes neurodegenerative diseases and biofilms

Question 22

levels of organization: secondary structures - how can a protein turn into amyloid fibers

Answer 22

• a normal protein can adopt an abnormal, misfolded prion form
• another normal form and a prion form may bind and the normal one can turn into a prion
• abnormal prion proteins will propagate and aggregate to form amyloid fibers

Question 23

explain how prions are infectious

Answer 23

• they are an infectious protein
• they are able to withstand high temperatures, making it hard to denature
• causes numerous diseases including: MAD cow disease

Question 24

chaperon proteins - isolation chamber

Answer 24

• a partially folded polypeptide chain is put in the chamber and the cap it put on top
• the polypeptide chain will be folded correctly inside and released when the cap dissociates

Question 24

explain chaperon proteins

Answer 24

• these proteins assist with protein folding
• they bind to partly folded chains and help fold

Question 25

chaperon proteins: isolation chambers - why is this needed

Answer 25

so a single polypeptide can fold without the risk of forming aggregates in the crowded cytoplasm

Question 26

what are heat shock proteins

Answer 26

• they are chaperons that respond to elevated body heat
• function is to re-fold miss-folded proteins

Question 27

levels of organization - tertiary structure

Answer 27

• the full 3D conformation formed by an entire polypeptide chain
• consists of alpha helices and beta sheets (can have one or a combination of both)

Question 28

levels of organization: tertiary structure - what forces hold it

Answer 28

• hydrophobic forces
• hydrogen bonds
• disulfide bonds

Question 29

levels of organization - quaternary structure

Answer 29

• a complex made of more than one polypeptide chain
• subunits are connected via noncovalent bonds and disulfide bonds
• Can form a long chain or dimer to create a functional unit

Question 30

levels of organization: quaternary structure - examples

Answer 30

• hemoglobin: 2 alpha helices and 2 beta sheets
• tubulin
• actin filament
• collagen
• elastin

Question 31

levels of organization: quaternary structure - what are disulfide bonds

Answer 31

• S-S bonds
• covalent linkages between the thiol groups of two cysteine residues
• reinforces the protein’s most favored conformation
• can happen through physical interaction

Question 32

levels of organization: quaternary structure - how can you utilize disulfide bonds in a lab setting

Answer 32

• Can add reducing agent to break bonds for studying proteins
• Can done in-vito or in-vivo