Translation & Proteins III Flashcards
As the end products of gene expression, proteins are closely aligned with biological function.
- It is the variation in biological function which provides the bases for the diversity between cells/ organisms
- The structural diversity of proteins allows for this
Polypeptide vs protein
Polypeptides:
- are the precursors of proteins
- What are assembled during translation process in ribosomes
When the polypeptide folds up and assumes its 3D structure in which it is fully functional = protein
- Often several polypeptide subunits combine to form a fully
functional protein
- The 3D confirmation is NB for a proteins function and what distinguishes it from other proteins
Folding of polypeptide
- The folding into 3D shape allows hydrophobic amino acids to huddle together within the protein core
- And the hydrophilic amino acids form the water accessible surface of the protein
- These hydrophobic and hydrophilic interactions help the protein to develop into its final folded form
Amino acids and protein structure
An NB part of protein structure and function is determined by sequence of amino acids in the polypeptide chain as well as the properties of those amino acids
- Each amino acid consists of a COOH group - NH2 group and -
R group (side chain)
R group:
- provides identity- 20 different kinds
- Provides variation in structure
Amino acid catagories
- Non-polar (hydrophobic)
- Polar (hydrophilic)
- Positively charged
- Negatively charged
Enormous number of amino acid combinations possible
To calculate how many possibilities:
20 (num of AA) to the power of X
X = num. of amino acids in the polypeptide
In a dipeptide:
400 combinations are possible
Peptide bonds
Adjacent amino acids are covalently bonded by a peptide bond between the amino group of one amino acid and the COOH group of the other
- This is formed by a condensation reaction with the release of water
> because of the type of linkage, will always have an amino group at the one end (N terminus) and a COOH group at the other end (C terminus)
- A chain of more than 10 amino acids = polypeptide
Protein structure: 4 Levels
I° ( Primary structure)
- amino acid sequence of linear polypeptide as specified by
the genetic code
- Chemical characteristics of amino acids important for higher
orders of protein structure - because of different chemical
properties of different amino acids
II° ( Secondary structure)
- Forms as a result of regular/ repeating configurations assumed
by amino acids lying close together in the polypeptide chain
Two possible configurations:
> Right-handed alpha helix
> Pleated beta-sheet
III° ( Tertiary structure)
> 3-dimensional structure (whole polypeptide)
Specific characteristics that stabilize III° structure are a result of the primary structure of the protein:
- Covalent disulfide bonds between closely aligned cysteine
residues. = very strong bonds which hold that part of the
protein together
- Nearly all hydrophilic R-groups on outer surface of molecule
> so that they can react with water
- Nearly all hydrophobic R-groups on inside of molecule
> where they can interact with each other and where they
can avoid interacting with water
These 3 stabilizing factors depend on the location of each amino acid in the chain relative to every other amino acid (primary structure)
- As folding takes place, the structure will stabilize in the most thermodynamically stable conformation
IV° ( Quatranary structure)
only relevant where proteins are composed of more than one polypeptide chain,
e.g. hemoglobin, DNA and RNA polymerases
- called oligomeric proteins
- each subunit (polypeptide) is called a protomer.
- Protomers fit together in a very specific and complementary
fashion
Secondary structure
Right-handed alpha helix:
- Consists of a spiral chain of amino acids which is held together
via H2 bonding between adjacent atoms
- The R groups of the amino acid face outwards from the helix
All alpha helixes observed in proteins are right-handed
Beta pleated sheet:
- Results when a polypeptide folds back on itself or if several different polypeptides run alongside each other in a parallel or anti-parallel fashion
- Stabilised by H2 bonds formed between adjacent atoms
Quaternary structure: Hemoglobin
2 alpha and 2 beta protomers which interact with 4 heme groups = functional haemoglobin protein
Post-translational Modification
- polypeptides are often heavily modified after they have been synthesized
- These post-translational modifications are vital for the
functional capability of the final protein - Intricate mechanisms
Examples:
> N- and C- termini removed or modified.
> Individual amino acid residues modified
(e.g. phosphorylation by kinases, acetylation and methylation).
> Attachment of carbohydrate chains – glycoproteins.
> Polypeptide chain trimmed (e.g. insulin precursor).
Protein targeting:
- Certain proteins that need to be targeted to specific areas of the cell contain signal peptides of up to 30 amino acids at their end terminals
- These signal peptides help to guide the protein to its proper destination in the cell = Protein targeting
- Once the proteins have been correctly transported, signal sequences are removed and this allows the protein to achieve functionality
The tertiary and quaternary structure of certain proteins often include and are dependent on metal atoms, such that the functional protein is a molecular complex of polypeptide chains and metal atoms
- Hemoglobin contains 4 Fe atoms along with its 4 polypeptide chains.
Several viruses generate a long mRNA that encode multiple proteins - these are translated as a single polyprotein which then autocatalytically cleave into the various proteins
Protein folding and misfolding
Posttranslational modifications are essential for proper folding and thus the functionality of proteins
- Some (not all) proteins are dependent on Chaperones (chaperonins, heat-shock proteins)
- Responsible for protein proper folding (vs spontaneous folding)
- Universal and ubiquitous (incl. mitochondria & chloroplasts)
- Misfolded proteins are tagged by ubiquitin – many copies are added together to form polyubiquitin- protein complex
- polyubiquitin-protein complex is then transported to proteasome and degraded by proteases
- ubiquitin proteins are released and recycled and the protease of the proteasome destroys the misfolded protein
slide 16 and 17 in ppt 3
Protein function
Proteins are the most abundant macromolecules in cells
Multitude of diverse roles
- Specialised proteins
e.g. haemoglobin and myoglobin transport O2 - Structural e.g. collagen and keratin (skin, hair, nails)
- Contractile proteins e.g. actin and myosin in muscles,
tubulin in mitotic and meiotic spindles - Immunoglobulins, e.g. immune systems of vertebrates
- Transport proteins are involved in translocation of molecules across membranes
- Hormones and receptors regulate chemical activities
- Histones bind to DNA in eukaryotes
- Transcription factors regulate gene expression
- Enzymes catalyse metabolic reactions
