Lecture 14 Flashcards
What are E coli
E coli are prokaryotic cells and are full of proteins
Describe proteins and give examples
Proteins are the work force of the cell - come in different shapes, forms, and sizes and with different functions
Examples:
Haemoglobin - transport oxygen in our blood
Alpha amylase breaks down carbohydrates/starch into monomeric glucose, they are present in saliva
Collagen in our muscle tissue and skin build structures
Atp synthase and pilus machinery are membrane bound proteins.
DNa helicase rna polymerase help in transcriptions
aspartyl-tRNA-synthetase - basically just the tRNA that bring the amino acid
What are proteins made form
20 diff amino acids, with different side chains or R groups
R groups determine the amino acid properties, also dictate the final shape of the protein
Some groups are hydrophobic - not charged and nonpolar (groups with only alkyl groups and maybe with a S atom or amine (NH) group), some hydrophilic - charged and/or polar (have an OH, SH, or amide (NO) group)
Amino acids have a carbonyl group and amino group
When two amino acids join, two H lost and one O lost, therefore called dehydration due to loss of one H2O molecule. This is when the peptide bond is formed between the carboxyl group and amino group of diff amino acids
Bond between one amino and carboxyl group (peptide bond) is catalysed by ribosomes
After translation, folding
What are the levels of Protein folding/structure
Primary
Secondary
Tertiary
Quatenary
Describe primary structure
Primary structure - refers to the linear sequence of amino acids (what the ribosome spits out)
Each monomeric unit (amino acids) of chain is called residue
Have two sides of polypeptide chain - N-terminus (amino group, the part of the protein that is made first/read starting from this), and C-terminus (end of protein)
Describe secondary structure
Secondary structure - most commonly fold into alpha helix or beta sheets (localised folding of polypeptides)
Alpha helix - when the backbone of amino acids for a spiral shape with usually ~3/4 amino acids per turn. Normally all of the R groups point on the outside of the helix/spiral
Bet sheets - backbone extends one way and then turns to go in opposite directions - to form a sheet.
Sequence of primary structure dictates whether helix or sheets
Both of secondary structures are held together by H bonds (weak bonds, therefore need multiple), mostly formed from the peptide backbones - the H-bonds form between the N and C=O groups of amino acids that are not directly next to each other
Describe tertiary structure
Tertiary structures: (complete folding pattern of the individual polypeptide chain)
Fold even further - depends on the amino acids in chain
Tertiary folding brings together residues that are far apart
Typically in tertiary structure the hydrophobic residues will hide inside of the protein
Hydrophilic residues will be on outside so can interact with water
This process/phenomena is also known as the hydrophobic effect - interaction of non-polar hydrophobic side w/ the aqueous environment and their subsequent burial in the interior of the protein. Hydrophobic effect is like the key driver for protein folding, without it proteins don’t tend to fold well
What are the different shapes of proteins
Globular protein - tight, compact, blob like shape
Fibrous protein - long and spindly proteins: e.g. a lot of structural proteins
An example: Artemis - a globular protein that plays a super important role in making antibodies, without it anything would give us infection
In our hair there is a fibrous protein called keratin. Keratin is full of cysteine. In hair dressers, they can use chemical that can break di-sulfide bonds in your hair and reform them to cause your hair to go from straight to curly or curly to straight. Therefore this process is a chemical process (bonds being broken and reformed)
Describe Quaternary structure
Quaternary structure: (multiple polypeptide chains come together and interact)
Two or more polypeptide chains coming together to form an even larger structure- a protein with a certain function
The separate polypeptide chains are called a subunit
Not all proteins need to form quaternary structure to function properly
What keeps protein structure intact
Proteins/protein folding held by multiple weak bonds:
H-bonds (secondary structure)
Electrostatic interactions/ionic interactions/salt bridges - two oppositely charged R-groups from different amino acids interact when close (e.g. negative glutamic acid r-group and positively charged lysine r-group interact) (tertiary folding)
Hydrophobic interactions - where hydrophobic side chains bond together, they are the weakest but have strength in numbers (tertiary folding)
Disulfide bridge/covalent bond- strongest bond other than peptide bond, occur spontaneously under mild oxidising conditions (also a covalent bond) (e.g. cysteine is an amino acid with sulphate atom therefore can form disulfide bond) (tertiary)
What can cause structure to break
When the shape of protein is broken - the protein is denatured (the process of denaturation) - function is lost. Often this process is irreversible
Shape can be affected by
pH (e.g. milk goes off because of pH is reduced due to bacteria and casein proteins in milk curdles - likely due to interaction with charged groups)
Salt concentrations (as salts can bind to charged side changes and therefore electrostatic interactions can be broken)
Temperature (albumin proteins in egg change shape due increase in temperature which causes it to unravel and lose shape, cysteine will start forming random disulphide bonds and cause it to become out of solution/solidified)
Summarise protein structure
Proteins are marginally stable due to the fact that they are held together by the aforementioned weak interactions/bonds
However, protein structure can be impacted by pH, salt conc, and temp
Summarise protein structure
Proteins are marginally stable due to the fact that they are held together by the aforementioned weak interactions/bonds
However, protein structure can be impacted by pH, salt conc, and temp
