Ch 4

Question 1

Enzymes

Answer 1

Catalyze (speed up by reducing activation energy) covalent bond breakage or formation
(chemically transform ligands that bind to it)
ex. DNA polymerase –> copies DNA;
ex. protein kinase –> adds phosphate group to protein molecule

Question 2

Structural Proteins

Answer 2

Provide mechanical support to cells and tissues
ex. Actin forms filaments that underlie and support plasma membrane

Question 3

Transport proteins

Answer 3

Carry small molecules or ions
ex. hemoglobin carries oxygen
ex. Ca2+ pump clears Ca2+ from muscle cell’s cytosol after ions have triggered a contraction

Question 4

Motor Proteins

Answer 4

Generate movements in cells + tissues
ex. Myosin in skeletal muscle cells provides motor force to move
ex. Kinesin interacts with microtubules to move organelles from cell
ex. Dynein enables eukaryotic cillia and flagella to beat

Question 5

Storage proteins

Answer 5

Store amino acids or ions

Question 6

Signal Proteins

Answer 6

Carry extracellular signals from cell to cell
ex. netrin attracts growing nerve cell axons to specific locations in developing spinal cord

Question 7

Receptor protein

Answer 7

detect signals and transmit them to the cell’s response machinery
ex. acetylcholine receptor in membrane of a muscle cell is asctivated by acetylcholine released from nerve ending

Question 8

Transcription regulators

Answer 8

bind to DNA to switch genes on or off

Question 9

Describe the chemical structure of a polypeptide chain

Answer 9

Amino terminus (N-terminus) (H-N-H2)
Carboxyl terminun (C-terminus) (O-C=O)
R group (can be hydrophilic (polar) or phobic (non-polar)

Question 10

Three types of noncovalent bonds that help proteins fold

Answer 10

1. Electrostatic attractions
   (side chains)
2. Hydrogen bonds
   (help stabilize its folded shape)
   (back - back, back - side, side - side)
   (back - back –> alpha helix and beta sheets)
3. Van der Waals attraction
   (allows for valence e- to be exchanged covalently)

Question 11

The role of hydrophobic forces in protein shaping

Answer 11

Help fold into compact confromations
- polar side chains oriented to cytosol
- nonpolar side chains packed inside core

Question 12

Role of Chaperone proteins

Answer 12

guide folding of newly synthesized polypeptide chain (fold along most energetically faborable pathway)
- some act as isolation chambers to (prevents aggregation in cytoplasm)

Question 13

How are amyloid structures formed?

Answer 13

stack of beta sheets
- misfolded proteins can form amyloid structures that cause disease (abnormal prion proteins propagate and aggregate to from amyloid fibrils)

Question 14

Protein structure of actin and microtubules?

Answer 14

Actin -> helix
microtubules –> hollow tube (stack of protein rings)

Question 15

Role of covalent cross-linkages in protein formation

Answer 15

Stabilize extracellular proteins
(ex. interchain disulfide bonds)

Question 16

How do proteins bind to ligands?

Answer 16

Binding sites (due to shape of proteins) allow for ligand specificity
- hydrogen bonds + electrostatic atrraction

Question 17

How to increase chemical reactions involving proteins

Answer 17

• raise temperature to optimal operating temperature of enzymes
• increase enzyme concentration

Question 18

How do enzymes encourage / speed up reactions

Answer 18

1. position substrate molecules in an orientation that encourages reaction (sandwich)
2. rearrange electrons to create partial charges –> conducive to reactions
3. mechanically straining (squish / pull) subtrate into transition state for reactions

Question 19

What is feedback inhibition and its importance?

Answer 19

• enzyme that limits its own concentration in cell (whenever it is created through reactions)
• triggers a conformational change in an allosteric (adopting two or more conformation) enzyme thereby preventing enzyme from acting

ex. enzyme binds to ADP. Increase in ADP means that enzyme activity increases. However anzyme is allosteric and can only bind to ADP in a closed conformation. So, increase in ADP also means increase in closed conformations. This allows ADP concentration to stabilize while enzyme-subtrate reactions occur

Question 20

What is phosphorylation and its importance?

Answer 20

• adding a phosphate group contently to a side chain –> results in conformation change (can either stimulate or inhibit protein activity)
  dephosphorylation is catalyzed by protein phosphatase

Question 21

What are GTP binding proteins?

Answer 21

GTP –> guanosine triphosphate
acts as a molecular switch between different conformation based on the addition / removal of phosphate group (that is part of guanine nucleotide)

Question 22

What are protein scaffolds and what is their purpose?

Answer 22

protein scaffolds –> large molecules that contain binding sites for multiple proteins

function –> act as tethers to promote reaction of proteins bounded to scaffold (creates protein complex)

Question 23

What is affinity chromatography

Answer 23

allows us to identify a protein based on what other known proteins bind to it

steps:
1. protein is attached to a matrix
2. dumped into mixture of proteins
3. some proteins attach, others do not
4. denature protein (high salt / change in pH) to get the binding proteins

Question 24

What is mass spectrometry

Answer 24

allows us to identify gene sequence of a protein by determining mass of peptides

steps:
1. proteins separated by electrophoresis
2. protein of interest digested by trpsin
3. peptide fragments loaded into mass spectrometer (exact masses measured)
4. genome sequence databases used to find protein encoded

Question 25

What is CRYO- electro microspy

Answer 25

determines protein structure

steps
1. protein molecules immobilized in thin film of ice
2. sample is examined using transmission electro microscopy
3. 2-D images obtained can be combined to form 3D models