PROTIENS Flashcards
protiens and binding
-binfing is chatarcterised by two properties affinity and specificity
-eg. enzymes
-eg. antibodies
other functions of proteins
-cell structure
-organisation
-biomechanics
-carriers
proteins plus other macromolecules
-protein+ carb = glycoprotein
- protein + lipid = lipoprotein
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amino acids
-there are 20 standard amino acids common to all species
-amino acids have a C with 4 variable groups attached
-all amino acids except glycine are enantiomers, C is chiral centre
R side chains
vary in size, shape, charge, H-bonding capacity, hydrophobicity and chemical reactivity all this combined contributes to the varied functions of proteins
diff types of amino acids
-basic (positive amino groups)
-acidic (negative, carboxyl groups)
-polar (uncharged at neutral pH as pos and neg charges cancel out)
-amino acids normally exist as zwitterion
-As the pH decreases a H+ ion will be added to the carboxylate; as the pH increases the H+ will be removed from the NH3+ and this also applies to the R groups
hydrophobic amino acids examples:
Non-polar, aliphatic amino acids have hydrophobic interactions in protein structures. The small size of glycine offers high flexibility whereas proline confers enhanced rigidity to a protein structure
-The aromatic side-chains are hydrophobic, but the hydroxyl of tyrosine can form H-bonds and is important in enzyme activity/signalling
hydrophilic amino acids examples:
-Polar, uncharged amino acids undergo hydrophilic interactions in protein structures and H-bond with water and other polar compounds. Cysteine can be readily oxidized, resulting in intra- or intermolecular interactions by disulphide bonds
-Positive or negative side chains tend to be hydrophilic and are often important in enzyme activity and influence protein structure
peptide
-is a covalent that connects amino acids
-peptide bonds cannot rotate
4 levels of protein structure
-primary structure: the linear sequence of amino acids
-secondary: the localised organisation of the polypeptide chain (forming an alpha helix or beta pleated sheet) stabilized by hydrogen bonds between the backbone atoms (not the R groups).
-tertiary: over all 3D arrangement interactions between R groups and binding of prosthetic groups
-quaternary: the association of two or more polypeptide chains
diff bonds in the 3d structure
-3-D structure and stability also maintained by a combination of non-covalent interactions; electrostatic forces, van der Waals forces, H- bonds; hydrophobic forces; and covalent interactions; di-sulfide bonds
Alpha (a) helix
-Repetitive local hydrogen bonding between carboxyl and amino groups with distinct spacing
-Cylindrical, rod-like structure with R groups all positioned on outside of helix
whats the exception to the alpha helix structure
proline , has a distinct hydrogen bonding pattern It’s often found at the ends of alpha helices, where it causes a directional change in the polypeptide chain, essentially creating a “kink” or “bend” in the helix.
Beta (b) ‘pleated’ sheet
Repetitive hydrogen bonding between adjacent sections of the polypeptide
Parallel b-sheet; polypeptide sections running in same direction
Anti-parallel b-sheet; polypeptide sections running in opposite direction
R groups protrude above and below the plane of the sheet
Connecting loops (coils)
Not repetitive, containing fewer backbone hydrogen bonds. Sections that connect the regular
structures of helices and sheets
how does hydrogen bonding stabilise
the alpha helix is stabilized by hydrogen bonds between the carbonyl group of one amino acid and the amino group of another amino acid that is four residues away in the chain. This pattern of bonding keeps the polypeptide chain coiled in a regular, stable helical shape.
how is beta stabilised by H bonds
The individual strands are stabilized by hydrogen bonds between the carbonyl oxygen of one strand and the amino hydrogen of a neighboring strand. These hydrogen bonds occur between alternating residues on adjacent strands, providing stability to the sheet-like structure.
more detail on quaternary structure
Homomeric (identical polypeptide chains) heteromeric (different chains)
Stabilized by hydrogen bonds and van der Waals forces`
May also include prosthetic groups – see lecture of protein function
protein folding and thermodynamics
This process follows the principles of thermodynamics: the protein will fold in a way that minimizes its free energy, meaning it adopts the most stable conformation.
chaperones
While some secondary structures (like alpha helices and beta sheets) can form relatively spontaneously due to the inherent properties of the amino acids, the tertiary structure (the full 3D shape of the protein) often requires assistance. Chaperones, which are specialized proteins, help by guiding the folding process and preventing misfolding or aggregation. These accessory proteins ensure that the protein reaches its correct 3D structure efficiently.
role of Golgi
As proteins are synthesized in the endoplasmic reticulum (ER), they often need to be folded correctly before being transported to other parts of the cell, like the Golgi apparatus. During this trafficking process, proteins may undergo unfolding and refolding to ensure they are properly modified and folded for their specific functions. This dynamic process is crucial for the protein’s stability and function.
-miss folded proteins lead to diseases
Formation of a disulphide bond
This is a covalent bond that forms between cysteine residues, which are closely located with each other in the final conformation, but can be separated by many amino acids in the primary sequence
Facilitates intra and inter-molecule bonding
Function to stabilize the overall 3D structure
Formed under oxidizing conditions in the ER and are mainly found in secreted proteins and proteins of the extra-cellular matrix
Domains
are distinct regions of proteins, that often function and fold independently and have structurally and functionally conserved features.
A protein is often made up of multiple domains, which are specific sections of the polypeptide chain that are responsible for particular functions or structural features. These domains are distinct from one another and contribute to the overall function and stability of the protein.
functional domains
are parts of the protein that are involved in carrying out specific biological activities. For example, a DNA-binding domain allows the protein to interact with DNA, or an enzymatic domain enables the protein to catalyze chemical reactions. These domains are essential for the protein’s biological function.
