Mod 4 Flashcards
What is the primary structure of a protein?
The primary structure is the sequence of amino acids in a polypeptide chain.
What drives the folding of a protein’s secondary structure?
Folding in secondary structure is primarily driven by peptide backbone interactions.
What drives the folding of a protein’s tertiary structure?
Folding in tertiary structure is primarily driven by side-chain interactions.
How does side chain polarity effect tertiary structure?
-side chain location varies with polarity
-np residues -> INTERIOR of protein (hydrophobic) extend outward
-charged residues->surface of protein in contact with water (inward)
-uncharged residues-> surface and interior, always H-bonded -> neutralizes polarity
How do secondary structures and motifs contribute to tertiary structure?
Determine underlying structure of protein that confers how it may be fold to best ensure a low energy state
Motifs form domains, which are globular clusters of protein
What drives quaternary structure in proteins?
Quaternary structure results from interactions between more than one polypeptide chain.
Are peptide bonds rigid? Why?
Peptide bonds form between two amino acids, are rigid due to resonance, and have partial double-bond character, restricting rotation
What is psi? Phi?
Psi refers to the bond between the alpha C and C of the carbonyl group in the peptide backbone. Phi refers to bond between alpha C and N.
What is the significance of a Ramachandran plot?
A Ramachandran plot is a plot of ψ vs. φ, and it shows the sterically reasonable values of those angles (allowed conformations of polypeptides in secondary structure).
What defines the alpha helix?
The alpha helix is a helical structure stabilized by hydrogen bonds, with R groups protruding outward. It has 3.6 residues per turn.
What stabilizes the alpha helix structure?
Hydrogen bonds between the carbonyl oxygen of residue i and the amide nitrogen of residue i+4 stabilize the alpha helix.
What primary sequences more likely to lead to natural alpha helices?
Alanine the most
Leucine also
Proline helix breaker because the rotation around the N-Calpha (phi) bond is IMPOSSIBLE since it forms a ring with itself
Glycine breaker bc small r group means lots of conformational flexibility
= supports other conformations
What are beta sheets in protein structure?
Beta sheets consist of beta strands that extend in a zigzag pattern and are held together by hydrogen bonds, either in parallel or antiparallel alignment.
antiparallel more common in proteins
T/F: Alpha helices and B sheets are the only secondary structures.
FALSE. Irregular loops!
What is the role of hydrophobic interactions in protein folding?
Hydrophobic residues cluster in the protein core, excluding water, increasing entropy, and driving protein folding through the hydrophobic effect.
Contrast fibrous and globular proteins.
FIBROUS: single polypep. structure, simple tertiary structure, function in the shape and structural conservation in verts. Stiff, elongated conformation, tend to form fibres. Insoluble in water
GLOBULAR: water-soluble, compact, highly folded structure. enzymes and reg. proteins
What are protein motifs?
a recognizable folding pattern involving two or more elements of secondary structure and the connections between them
aka super secondary structure
What are protein domains?
a part of a polypeptide chain that is independently stable or could undergo movements as a single entity with respect to the entire protein
Can still perform their function when separated from the protein
What are the three types of proteins?
Fibrous, globular, and membrane proteins
Membrane proteins
- high proportion of hydrophobic amino acids present
- use those to interact with lipid bilayer hydrophobic acyl chains
integral or peripheral
ex. ATP synthase, insulin receptors
Fibrous proteins
- play structural roles
- elongated/filamentous shape
- can be permanent (collagen and keratin) or regulated
- regulated aren’t themselves fibrous but form regulated fibres (actin and tubulin)
Globular proteins
- do chemical synthesis, transport, and metabolism
- folded into compact structures
- philic surfaces and phobic cores
- tertiary structure determines function
ex. myoglobin and hemoglobin
What forces govern protein folding?
Electrostatic forces, hydrogen bonds, van der Waals forces, and the hydrophobic effect all play roles in protein folding.
Electrostatic forces
- Strong interactions (in vacuum)
- Typically charge-charge
- Long distance interactions 1/r^2
Strength of these interactions severely weakened on surface of proteins due to water and its large dielectric constant which acts to screen the charges from one another
Hydrogen bonds
Usually occur between peptide groups and water on the surface of a protein
In the core of the protein (where water is not as prevalent) these bonds are generated between peptide groups
H-bonds are highly directional
Van der waals forces
- Very short interaction range (1/r^6) - only significant when molecules are almost in contact
- Also have corresponding repulsive forces
Cooperativity in protein folding
Proteins are highly cooperative with respect to folding - due to their regular secondary structural elements
What is the role of enzymes in biochemical reactions?
Enzymes catalyze reactions, speeding them up without being consumed, by lowering activation energy.
Do enzymes affect the equilibrium of a reaction?
No
How does Gibbs Free Energy relate to reaction rates?
The Gibbs Free Energy of activation (ΔG‡) determines the reaction rate
While the Gibbs Free Energy change (ΔG) indicates if a reaction is favorable
Gibbs free energy of activation vs. free energy change
Gibbs Free energy of activation → the difference in free energy between the transition state and the substrate (S)
Gibbs free energy change → the free energy difference between the substrate (S) and the product (P)
Enthalpy vs entropy
Enthalpy (H) → the heat energy in the system / some form of bond energy
- More and/or stronger bonds
Entropy (S) → measure of disorder
- More molecules
What is enzyme catalysis?
Enzyme catalysis speeds up reactions by stabilizing the transition state and lowering activation energy.
What is the Lock and Key model in enzyme catalysis?
The Lock and Key model describes enzyme-substrate complementarity, where the enzyme’s active site is perfectly shaped for the substrate.
What is the Induced Fit model in enzyme catalysis?
In the Induced Fit model, the enzyme undergoes a conformational change upon binding the substrate, improving the fit for catalysis.
What is the role of antibodies in the immune system?
Antibodies are proteins that bind to specific antigens on pathogens, marking them for destruction.
Two types of immune system barriers in the innate response
Anatomical barriers
- Barriers before pathogens get into the bloodstream
Ex. skin, mucous membrane, stomach acid
Humoral barriers
- Barriers mediated by substances found in our humours or body fluids
Ex WBCs in the inflammatory response doing phagocytosis
Two types of immune responses
- Innate, non-specific
- Adaptive
Adaptive immune response
- Much more complicated and takes longer to kick in
- Has the ability to remember specific pathogens (unlike innate)
- Mediated by lymphocytes - 2 classes of these called B-cells (humoral immunity) and T-cells (cell-mediated immunity)
What is the structure of antibodies aka immunoglobulins (Ig)?
Immunoglobulins have a Y-shape with a constant domain (C) and variable domain (V). The variable region binds antigens, constant region same for all of same class.
they are produced by b-cells
What are Fab and Fc fragments of antibodies?
Fab fragments
- Contain the antigen-binding sites
- Only one binding site/fragment
Fc fragments
- Contain the constant domains that mediate immune response
- Two heavy chains
How does Western Blotting work?
Western Blotting uses antibodies to detect specific proteins separated by gel electrophoresis, often with enzyme-linked secondary antibodies for visualization.
How do enzymes speed up reactions?
Enzymes lower activation energy by stabilizing the transition state and holding substrates in an optimal position.
What is the importance of enzyme active sites?
Active sites recognize substrates, often involving amino acids that directly participate in catalysis (e.g., proton donation).
usually flexible
Enzymatic rate acceleration
Enzymatic rate acceleration = catalyzed rate / uncatalyzed rate
Without enzymes, would need heat energy to speed it up
Where is collagen found
¼ of all protein in your body
provides structure through…
- Cables strengthening tendons
- Sheets that support skin and organs
- Bones and teeth = mineral crystals + collagen
- Connects tissues to skeleton
Collagen appearance
- Triple helix (three chains woven together) with different types of ends
- 1400 aas long each
- Every third amino is glycine (prevents crowding)
- Lots of proline (forms a king in the chain) and hydroxyproline
Ropes and sheets formed
Two types of collagen
Type 1 collagen molecules
- Associate side by side
- Blunt ends
- Form tough fibrils
- In the space between cells
Type 4 collagen
- Structural basis of the “basement membrane” that supports the skin and other organs
- Globular head / extra tail
- Heads bind together, 4 c molecules associate through their tails
- Form an X shaped complex
Collagen in vit C
Hydroxyproline made by modifying proline after collagen chain is built
Reaction required vit c
scurvy = vit c deficiency = less collagen formed
Collagen in gelatine
- Collagen loses structure once heated
- Denatured mass of tangled chains soak up water as they cool = gelatine
Myoglobin structure
- Has a heme group to hold iron that bonds with oxygen
- Carbon-rich aas inside, charged aminos on surface and sometimes form salt bridges
Myoglobin in whales and dolphins
- 30x more myoglobin than land animals
- Due to mutations that add extra positively charged aas to the surface
Repel neighbouring molecules and prevent aggregation when myoglobin is at high concentrations
Myoglobin different conformations
- Oxygen binds deep inside
- Allowed entry bc myoglobin has different forms (open vs closed) and is constantly in motion
Blood colours
- Oxygenated blood is bright red, deoxygenated blood is deep purple
- Looks blue bc dark blood absorbs red light but blue is reflected in the surface layers of the skin so we see it
- Use copper to transport oxygen so they really have blue blood
Hemoglobin structure
- Four protein chains
- Two alpha and two beta chains, each with a ring-like heme group containing an iron atom
- Oxygen binds to iron (reversibly) and is transported through blood
Nitric oxide and carbon monoxide in hemoglobin
Also transported by hemoglobin
Nitric oxide
- Causes blood vessel walls to relax = reduces blood pressure
- Binds to specific cysteine residues and to iron
- Helps regulate blood pressure
Carbon monoxide
- Toxic gas
- Replaces oxygen at the heme groups and is hard to remove
- Blocks oxygen binding = suffocates surrounding cells
Artificial blood
- Maybe use pure hemoglobin to replace lost blood (instead of transfusions), but difficult to keep the four proteins together without the protective casing of the RBC
- So, design hemoglobin molecules where 2/4 chains are physically linked together using two added glycine residues to form a link between chains
Hemoglobin cousins
- Human adult vs fetal hemoglobins
- Leghemoglobin in legumes - protects the oxygen sensitive bacteria that fix nitrogen in leguminous plant roots
- Truncated hemoglobins which are missing several parts - but must keep the histidine amino acid that binds to heme iron
Cooperation in hemoglobin
- Non-simultaneous oxygen binding at four sites in hemoglobin
- Once first heme binds oxygen, changes protein chain structure that influences neighbouring chains
Histidine reaches to bind to the iron atom, oxygen binds to the iron and pulls it upward
- Difficult to add first oxygen, gets easier and easier to add subsequent ones
- Also chain reaction when oxygen removed
- Oxy added in lungs, removed when in high carbon dioxide environments
Sickle cell hemoglobin
- Glutamate 6 to valine mutation in the beta chain
- Makes deoxygenated hemoglobins stick together = stiff fibers = deform RBCs into a C or sickle shape
- Distorted cells are fragile and sometimes burst = loss of hemoglobin
Usually bad, beneficial in malaria
* Malaria can’t live in fiber-filled sickle cells = malaria resistance
Thalassemia
Happens when unequal amounts of alpha and beta proteins
ATP synthase
- Is an enzyme, 2x molecular motor, ion pump all put together
- Builds most of the ATP that powers our cellular processes
Two rotary motors - connected through a stator = when F0 turns on so does F1
F0 vs F1 motors in ATP synthase
Top one = F0
- Electric motor
- Embedded in the membrane
- Powered by the flow of hydrogen ions across the membrane
Lower one = F1
- Chemical motor
- Powered by ATP
One motor turns the other into a generator
Vacuolar ATPase
Like ATP synthase but in reverse; use ATP-driven motor to pump protons across a membrane
Insulin, glucose, and cell energy
Insulin and glucagon hormones (small proteins recognized by cell-surface receptors) are part of the signalling system to deliver glucose to cells or store it
When blood glucose levels drop, alpha cells in the pancreas release glucagon, which then stimulates liver cells to release glucose into the circulation
When blood glucose levels rise, on the other hand, beta cells in the pancreas release insulin, which promotes uptake of glucose for metabolism and storage
Signal transduction to insulin receptors
- 2 copies of a protein come together to form receptor site
- Connected through the membrane to 2 tyrosine kinases
- Constrained when no insulin
- Released when insulin binds
- First phosphorylate + activate each other, then phos other proteins inside the cell
Insulin binds where?
Binds to outer edge of receptor, and only one side of the symmetrical receptor
2 types of diabetes mellitus
Type 1
* Caused by problems with insulin
* Either pancreatic cells that produce insulin are destroyed by autoimmunity
* Or insulin is mutated and inactive
* Requires treatment with insulin, usually occurs early in life
Type 2
* Usually occurs later in life
* Caused by acquired resistance to the action of insulin on its receptor
* Involves phosphorylation of the receptor and its substrates, modifying their action in insulin signaling
* Treated with attention to diet, lifestyle, and medication
