Protein, enzymes and their measurements (wk3) Flashcards
Understanding of the genetic source of proteins
-Proteins are assembled from amino acids using information encoded in genes.
-Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein
Features of amino acids that make up proteins
-Amino acids are joint covalently by peptide bonds -> Peptide-shortened parts of a protein. Proteins- ‘polypeptide chains’
Protein structure and how bond and interactions determine protein folding
-Amino acids and structure of proteins
-Amino acids are the building blocks of proteins
-The variable group, or side chain determines the ID of the protein and makes it distinctive to the other proteins
-Structure of proteins -> Protein structure is complex and 3 dimensional. The structure can be broken down into primary, secondary, tertiary and quaternary. The simplest structure, primary, describes the amino acids sequence of a protein.
Protein structure and how bond and interactions determine protein folding
-Draw the protein structure
Protein structure and how bond and interactions determine protein folding
-Primary and secondary structure (and secondary structure with hydrogen bonds)
-Primary structure is the base determinant of protein shape and function ->
-Secondary structure -> Peptides fold in complex ways, referred to as secondary structure. The force responsible for this, is the hydrogen bond, created by a hydrogen atom with partial positive charge and an atom, usually O or N with partial negative charge.
-Secondary structure (hydrogen bonds) -> Though hydrogen bonds are much weaker (10-100 times) than covalent bonds, the abundance of H atoms in proteins give rise to many connectors that stabilize the secondary structure. Most widely encountered structures that are the (a) helix and (B) pleated sheet.
Protein structure and how bond and interactions determine protein folding
-Tertiary structure
-Tertiary structure -> Conformation of an entire polypeptide chain is referred to as tertiary structure. Also stabilised by hydrogen bonds, but uses other interactions: Electrostatic bonds, Van de whalls interaction, Disuldife bonds, Hydrophobic bonds
Protein structure and how bond and interactions determine protein folding
-1+2 (Electrostatic bonds and Van de Walls interaction), 3+4 (Disulifide bonds and Hydrophobic interaction)
1+2 - Electrostatic bonds and Van de Walls interaction -> Electrostatic, or ionic bonds are between positively and negatively charged groups. A Van de Walls interaction in a non-covalent attraction due to movement of ions in atomic or molecular orbitals. Momentary asymmetries in charges develop electrostatic forces that can help stabilise tertiary structure.
3+4 - Disulfide bonds and Hydrophobic interaction -> Disulfide bonds form between the sulfhydryl group of the amino acid Cysteine. Some amino acids contain hydrophobic side chains that can come together in a folded protein. The forces are a result of a mutual repulsion of the surrounding bond.
Protein structure and how bond and interactions determine protein folding
-Quaternary structure of protein and Denaturation
-Quaternary structure of protein -> Tertiary structure describes conformation of whole polypeptide chains, many proteins contain subunits, that link together via the same interactions. This is referred to as the quaternary structure.
-Denaturation -> Environmental factors, such as heat or acidity can alter or break these forces. This is known as denaturation and is exemplified when cooking an egg. The structure of the protein in the egg collapses at 62 C, causing it to lose solubility in water and solidify.
Draw the graph describing the importance of protein folding
Identify different types of protein
-Proteins (the effectors of cell biology) – DNA (the ultimate potential of a cell) -> m RNA (the current direction of a cell) -> Proteins (the functional capabilities of a cell)
-There are around 20,605 genes in humans, but are folded differently and variations which allow different functions
-Protein molecules in the cell -> Yeast, the only species with enough complete data. There are 6000 genes in yeast. Total number of protein molecules in the cell = 42 million. Least abundant around 10 molecules, most abundant, there are more than 500,000
How enzymes catalyse reactions
(essential catalysts in biology, 3 main features, the active site)
-Enzymes are essential catalysts in biology -> Enzymes accelerate metabolic reactions. Reactants are called substrates. There is almost no biological substance that is not a substrate of an enzyme. Generally named after their substrate or the type of reaction they catalyse: Ribonuclease is an enzyme of ribonucleic acid and Superoxide dismutase catalyses the dismutation of superoxide.
-Enzyme 3 main features -> They speed up reactions (by 10 5 to 10 17 times). Some facilitate reactions taking place several hundred thousand times per second. They display high specificity – each enzyme catalyses one, or a group of reactions involving substrates that have something in common, such as a chemical bond or group. Their catalytic power is regulated – the speed of a reaction is subject to a variety of factors.
-The active site -> Enzymes are very specific to one or a limited number of reactions, a feature down to the complementary structure of enzyme and substrate. Attraction is at a small area of the surface of the enzyme called the active site (the induced fit)
How coenzymes reactions
-Cofactors and enzymes
-Cofactors and coenzymes -> To catalyse reactions, many enzymes need the presence of nonprotein chemical entities, or co-factors in their active sites. Tend to me mental ions and organic compounds. Metallocoenzymes are metal ions
Draw the graph describing the regulators of enzymes (and other protein’s activity)
Factors affecting enzyme reactions
-Factors affecting enzyme reactions: substrate availability -> Increasing substrate (at the same enzyme concentration) speeds up reaction rate – to a point
-Enzyme concentration
-Temperature and pH
Basic biochemical assays used in exercise science
-Spectrophotometry, quantitation of nucleic acids, measuring total protein abundance via spectrophotometry
-Spectrophotometry -> Many compounds in a solution absorb visible light, in proportion to their concentration. While many biomolecules are colourless, combining with a reagent produces a coloured compound.
-Quantitation of nucleic acids -> Nucleic acids (DNA, RNA) absorbs UV light at a wavelength of 260nm. Commonly used to check the purity of isolated nucleic acid.
-Measuring total protein abundance via spectrophotometry -> Scientists wish to standardises the amount of protein they are analysing, which they can do through Bradford assay. Protein is mixed with a dye called Coomassie blue. In acidic conditions this results in a colour change brown-blue. Protein quality can be detected at 595nm. Bicinchoninic acid (BCA), Lowry are other examples.
