What are proteins?
Proteins are ubiquitous, diverse, and versatile
Many of the cellular activities and reactions that are involved in cellular function are mediated by proteins
Recall that proteins are linear polymers of a combination of 20 amino acids → Like letters in an alphabet
What are amino acids?
Recall that amino acids are the building blocks of protein → ts is key as protein function is related to structure
What are the four components of an amino acid?
Each component is bound to the alpha carbon
3 components are identical for all amino acids
Carboxyl Group
Amino Group
Hydrogen
At physiological pH the amino & carboxyl groups are charged
4th component is the side chain → R Group
R Groups make each amino acid unique
Are responsible for the chemical and physical properties of each amino acid monomer
How are amino acids classified?
R Groups of amino acids are grouped according to their properties
Amino acids are classified based on
1. How they interact w/ water → Hydrophilic or Hydrophobic
2. Basic or acidic
3. Polar or non-polar
Hydrophobic Amino Acids
Tend to be buried in the interior of folded proteins
Hydrophobic R groups aggregate together away from the water
Weak van der Waals forces help w/ stability → by causing the hydrophobic R groups to be attracted to each other
Hydrophilic Amino Acids
Recall that polar molecules contain electronegative elements → N and/or O
Results in an unequal charge → allows the R groups to interact w/ each other or w/ H2O via H-bonding
Basic amino acids tend to be → Positively Charged
Has amine group
Acidic amino acids tend to be → Negatively Charged
Has carboxylic acid in the side chain (R group)
Charged groups can form ionic bonds → w/ one another & with other charged molecules
Hydrophilic amino acids are typically found on the “outer” surface of proteins
Special Amino Acids
3 stand out b/c of how they affect the structure of proteins
Glycine → R group is Hydrogen
The alpha carbon is bonded to 2 H atoms → glycine is not asymmetric
It is small and nonpolar → allows free rotation around the C-N bond
Ts increases the flexibility of the polypeptide backbone
Proline → R group links back to the amino group
Linkage restricts rotation of the C-N bond → this limits the amount of protein folding around proline
Cysteine → R group contains a -SH Group
This allows 2 cysteines to form a S-S disulphide bond → forms a cross-bridge
The cross-bridges can connect different parts of the same protein or different proteins together
Linking amino acids
Adjacent amino acids are joined together in a peptide bond
This is a dehydration reaction where the carboxyl group of one amino acid reacts with the amino group of another amino acid
Releases a molecule of H2O
The free amino group is at the amino end of the peptide → forms the N-Terminus
The carboxyl group is at the carboxyl end → forms the C-Terminus
A polymer of amino acids connected by peptide bonds is a polypeptide → used synonymously w/ protein
*r groups are not involved in the peptide bond
Protein Structure
Each amino acid in a protein gives the structure and thus the function of the protein
The proteins will fold in a particular way based on the sequence of amino acids and thus the order of the R groups
Protein structure has 4 levels of organization → primary (1°), secondary (2°), tertiary (3°), and quaternary (4°)
3D structure of a protein is the protein conformation → described by 2°, 3°, and 4°
Primary Protein Structure
Specific linear sequence of amino acids that make up the polypeptide chain → from amino end to carboxyl end
Most polypeptides contain many amino acids → these are coded for by the genome
Primary structure determines 2°, 3°, 4° structure of the protein
Sequence of the primary structure can be written as a sequence of the 3 letter or 1-letter abbreviations
Eg. Val-Gly-Ala-His or V-G-A-H
R groups alternate position on either side of the chain of amino acids
This affects protein folding and the interaction of R groups
Secondary Protein Structure
Describes conformation of portions of the polypeptide chain
2 types → Alpha Helix & Beta Sheet
Results from H-bonding between neighbouring amino acids of the polypeptide backbone → occurs between functional groups
R groups are not involved
It is a fixed configuration of the polypeptide backbone
Secondary Protein Structure: Alpha Helix vs Beta Sheet
Alpha Helix
Very stable structure
Right handed helices → let molecules that are not nearby in the main structure to interact w/ one another
Form due to H-bonds to the 4th amino acid neighbour above & below in the spiral → the carbonyl group of one amino acid and the amide group of the 4th amino acid
Beta Sheet
Segments of the polypeptide lying side by side → assumes a pleated (folding) conformation
Can be parallel or antiparallel
Structure is stabilized by H-bonds formed between carbonyl groups in one chain & amide groups in the other chain within the same polypeptide
Tertiary Protein Structure
Describes conformation of entire protein → single polypeptide folded into 3° structure
Ultimately this is how regions of 2° conformations are oriented
Results in its functional form → unless it is part of a protein that has multiple subunits
Tertiary structure is determined by the following:
Spatial distribution of the hydrophilic and hydrophobic R groups
Chemical bonds and interactions that form between the R groups
Includes
H-bonds, hydrophobic bonds, & ionic bonds
Disulfide bonds → covalent bond between 2 cysteine residues
Sequence of the primary structure governs the secondary and tertiary structure of a protein
Overall shape (3° structure) of a functional protein may result in
Areas of the protein that form active sites for enzymes
Exterior R groups that may impact how a protein interacts w/ other molecules or proteins
Quaternary Protein Structure
Many proteins are made up of more than one polypeptide chain → Subunit
Spatial arrangement of these subunits is the 4° structure
These arise due to the same bonds as found in 3° structure
Polypeptide chains in each subunit may be
Identical → eg. protein containing 2 identical subunits is known as a homodimer
Non-identical → eg. protein containing 2 non-identical subunits is known as a heterodimer
Protein Synthesis
Recall, the Central Dogma
Transcription - sequence of DNA is used as a template
Makes the mRNA
Translation - sequence of bases in mRNA is used to specify the order of amino acids to be added in the growing polypeptide
Final stage of the Central Dogma
Translation
Requires several components
Ribosome
Transfer RNAs → tRNAs
Aminoacyl tRNA synthetases
Initiation factors, elongation factors & release factors
Ribosomes
Ribosomes → Protein Factories
This is where translation takes place
Are a complex structure of RNA and protein
Consist of a small subunit and a large subunit
Eukaryotic ribosomes are larger than prokaryotic ribosomes
The mRNA is bound by the large and small ribosomal subunits → it then moves through the centre of the ribosome
Ribosome moves down the mRNA → from 5’ to 3’ and reads individual codons to incorporate the appropriate amino acids
Codon
nucleotide combination that specifies the placement of an amino acid → codes for the amino acid placement
Each group of 3 adjacent nucleotides → arranged as a nonoverlapping series of nucleotide triplets
Reading frame is where the ribosome begins reading the sequence of nucleotides
Where does Translation Begin
Does not begin w/ 1st 5’ RNA base on mRNA
Begins w/ start codon → AUG
Codes for methionine
Ribosome Sites
3 functional sites within the ribosome
Aminoacyl tRNA is accepted in → A Site
Peptide bond formation happens in the → P Site
tRNA exits the ribosome in the → E Site
Transfer RNAs
Translation needs the transfer RNA molecules → tRNA
Small molecules containing 70-90 nucleotides
Each tRNA bonds w/ itself → forms base pairs
Results in structure that looks like a cloverleaf
2 important sites on each tRNA
3’ hydroxyl site on the 5’-CCA-3’ end of the tRNA → where the specific amino acid attaches
3 bases in the anticodon loop make up the → Anticodon
How are amino acids attached to the tRNA
Specific amino acids area connected to specific tRNA molecules by enzymes called → aminoacyl tRNA synthetases
tRNA w/o amino acid attached → Uncharged
tRNA w/ amino acid attached → Charged
tRNA synthetases are very accurate
Translation Process: Genetic Code
During translation, anticodon of tRNA base pairs w/ the codon on the mRNA
Recall base pairing is the specificity of DNA-RNA or codon-anticodon interactions
Like all nucleotide sequences, the anticodon of tRNAs base pair in an antiparallel fashion
So, the 1st base of the codon pairs w/ the last base of the anti codon
Genetic code has 20 amino acids → specified by 64 codons
Many of the amino acids are specified by more than one codon → makes the genetic code redundant or degenerate
Bases are read 5’ - 3’ on the mRNA using the standard genetic code
Translation Process: Translation Stages
3 stages in translation
1. Initiation → AUG Codon is recognized & MET is the 1st amino acid
2. Elongation → each successive amino acid is added to the growing polypeptide chain
3. Termination → adding amino acids stops & the polypeptide chain is released from the ribosome
