Please enable JavaScript.
Coggle requires JavaScript to display documents.
Week 4, What type of bond is - Coggle Diagram
Week 4
Proteins
Primary Structure
The primary structure of a protein is formed through peptide bonds linking amino acids.
Each bond forms between the carboxyl group (–COOH) of one amino acid and the amine group (–NH₂) of another through a condensation (dehydration) reaction, which releases a molecule of water (H₂O).
This is the same type of reaction used in the synthesis of all biological polymers, such as proteins, nucleic acids, and polysaccharides.
Secondary Structure
Characterized by hydrogen bonds between the backbone of the amino acids, specifically between the C--O and N--H
-
Tertiary Structure
Bonds that form during this structure is between the side chain (r-group) and other side chains or the backbone previously mentioned. This forms the 3D shape of the protein, usually giving its function
-
-
Hydrophobic Interactions
The interaction that moves hydrophobic regions away from water, towards the inside of the protein.
-
Ionic bonds (really, these are electrostatic bonds)
Attraction forces, between two opposite forces. Not quite as strong as ionic bonds.
An amino acid residue is what each amino acid is called once it’s incorporated into a polypeptide—i.e., after losing H and OH to form the peptide bond. It contributes the backbone (N–Cα–C) plus its unique R-group (side chain) that gives proteins their properties.
Quarternary Structure
A structure characterized by the same bonds found in tertiary structure except these bonds form between the backbone and r groups, or r groups and r groups of different proteins
-
-
-
Hierarchal
-
- The amino-acid sequence (primary) dictates which hydrogen bonds form (secondary).
- Those folding patterns then determine tertiary shape, and multiple folded units can assemble into quaternary complexes.
Functions of Proteins
Motor Proteins
Move parts of the cell, like myosin and actin filaments in the cleavage furrow of the cell!
Transport Proteins
Transport materials within the cell like kinesin or dynein, or transport materials into the cell (like transmembrane proteins: channels and carriers)
-
Defense
Proteins make up antibodies, which search for cellular labels and determine targets for the immune system
Catalysts
Enzymes! They speed up chemical reactions by lowering the energy required to reach transition state (stabilizing the transition state), they do not partake in the reaction (are not used up!). Like Hexokinase, or Lipase!
Active Site
Properties
Amino acid groups in the active site can have polar, nonpolar or charged properties, depending on the type of substrate binding to the active site.
Where the substrate (reactants) bind to the enzyme, so that the enzyme can catalyze reactions in the human body
-
Induced Fit, not Lock and Key
Hypothesizes that active sites undergo a conformational shape change when the substrate binds, to better bind to it. This also shows that the active site is highly specific to its substrates
The lock and Key model suggests that the enzyme (key) is already the perfect shape to unlock the substrates (lock) into products.
-
Inhibitors
Competetive
These inhibitors bind at the active site, competing directly with the substrates. they have similar shape as the substrates, and get in the way to slow down catalysis.
Non competitive
These bind at the allosteric site of the protein, and cause a change in shape. This change in shape makes it harder or impossible for the substrates to bind, inhibiting the enzyme
Allosteric regulation occurs when a molecule binds to a site other than the active site (the allosteric site) and changes the enzyme’s shape.
If this change enhances activity, it’s an allosteric activator; if it reduces activity, it’s an allosteric inhibitor.
Phosphorylation is a covalent form of allosteric regulation—it adds a phosphate group that can stabilize either the active or inactive form of the enzyme, depending on the enzyme.
Importance
Many reactions in the body, which are spontaneous, would still take way too long to occur, which is not sustainable for life. It is important that we have enzymes to speed up this process
Structural Proteins
The structure of the inside of the cell is largely protein! Like cytoskeleton (microtubules), which provide structural support and highways to move material on.
Gibbs Free energy
-
-
-
Positive delta G indicates an endergonic reaction (not spontaneous, energy input required)
-
What type of bond is
Glycosidic bond: Covalent bond between two monosaccharides (carbohydrates) formed through dehydration synthesis between hydroxyl (–OH) groups.
Peptide bond: Covalent bond between the amino group (–NH₂) of one amino acid and the carboxyl group (–COOH) of another, also formed by dehydration synthesis.
Phosphodiester bond: Covalent bond linking nucleotides in DNA/RNA between a phosphate group and hydroxyl groups on adjacent sugars (3′–5′ linkage).
Ester bond: Covalent bond between a hydroxyl (–OH) and carboxyl (–COOH) group, common in lipids (e.g., glycerol and fatty acids).