Ch 4 Flashcards
Enzymes
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
Structural Proteins
Provide mechanical support to cells and tissues
ex. Actin forms filaments that underlie and support plasma membrane
Transport proteins
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
Motor Proteins
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
Storage proteins
Store amino acids or ions
Signal Proteins
Carry extracellular signals from cell to cell
ex. netrin attracts growing nerve cell axons to specific locations in developing spinal cord
Receptor protein
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
Transcription regulators
bind to DNA to switch genes on or off
Describe the chemical structure of a polypeptide chain
Amino terminus (N-terminus) (H-N-H2)
Carboxyl terminun (C-terminus) (O-C=O)
R group (can be hydrophilic (polar) or phobic (non-polar)
Three types of noncovalent bonds that help proteins fold
- Electrostatic attractions
(side chains) - Hydrogen bonds
(help stabilize its folded shape)
(back - back, back - side, side - side)
(back - back –> alpha helix and beta sheets) - Van der Waals attraction
(allows for valence e- to be exchanged covalently)
The role of hydrophobic forces in protein shaping
Help fold into compact confromations
- polar side chains oriented to cytosol
- nonpolar side chains packed inside core
Role of Chaperone proteins
guide folding of newly synthesized polypeptide chain (fold along most energetically faborable pathway)
- some act as isolation chambers to (prevents aggregation in cytoplasm)
How are amyloid structures formed?
stack of beta sheets
- misfolded proteins can form amyloid structures that cause disease (abnormal prion proteins propagate and aggregate to from amyloid fibrils)
Protein structure of actin and microtubules?
Actin -> helix
microtubules –> hollow tube (stack of protein rings)
Role of covalent cross-linkages in protein formation
Stabilize extracellular proteins
(ex. interchain disulfide bonds)
How do proteins bind to ligands?
Binding sites (due to shape of proteins) allow for ligand specificity
- hydrogen bonds + electrostatic atrraction
How to increase chemical reactions involving proteins
- raise temperature to optimal operating temperature of enzymes
- increase enzyme concentration
How do enzymes encourage / speed up reactions
- position substrate molecules in an orientation that encourages reaction (sandwich)
- rearrange electrons to create partial charges –> conducive to reactions
- mechanically straining (squish / pull) subtrate into transition state for reactions
What is feedback inhibition and its importance?
- 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
What is phosphorylation and its importance?
- 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
What are GTP binding proteins?
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)
What are protein scaffolds and what is their purpose?
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)
What is affinity chromatography
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
What is mass spectrometry
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
What is CRYO- electro microspy
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
