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BCHM 270 Module 2 Test With
Correct Answers
Amino acids - ANSWER building blocks of proteins noncovalant interactions - ANSWER - essential for life because they are relatively weak and can be broken and reformed
- they are normally weak, but when many are combined in a macromolecule or between molecules, they can be a strong force 4 main types of non-covalent interactions - ANSWER - electrostatic
- molecular dipoles
- polar molecules
- hydrogen bond electrostatic (charge-charge) - ANSWER - interactions between positive and negative charged molecules
- ex. DNA has a negative charge, and proteins that bind to DNA are positively charged molecular dipoles - ANSWER - uncharged molecules can have a distribution of charge
- dipole moment is when there is slightly negative side of the molecule and a slightly negative side of the molecule, which allows molecules to naturally align opposite to each other to maximize interactions
polar molecules - ANSWER - molecules with large dipole-dipole moments hydrogen bond - ANSWER - aren't a true bond
- most important
- are the strongest
- made up of a hydrogen donor and a hydrogen acceptor (the donor is a bound to an electronegative atom ex. O, S, N which makes it slightly positive, the acceptor is an atom with a lone pair of electrons ex. N or O, so the positive H binds to the negative electron) Hydrophobic - ANSWER Water fearing
- modules will clump up together to avoid water
- the driving force for this is that entropy (disorder)is always increasing for a system, hydrophobic molecules coming together leaves more room for water molecules around it, creating entropy hydrophilic - ANSWER water loving amphipathic - ANSWER A molecule that has both a hydrophilic region and a hydrophobic region.
- ex. phospholipid has a hydrophilic head and a hydrophobic tail amino acid structure - ANSWER - amino group
- A-carboxyl group (the hydroxyl is lost when participanting in a peptide bond)
- called the alpha-carboxyl group because its attached directed to the alpha carbon
- non polar amino acids are normally clumped together in the middle of the protein to avoid water
- 9 amino acids where the side chain is non polar (some are aliphatic branches, and some are aromatic rings) glycine - ANSWER nonpolar amino acids
- smallest side chain (H) Alanine (Ala, A) Valine (Val, V) Leucine (Leu, L) Isoleucine (Ile, I) - ANSWER nonpolar amino acids
- all have side chains containing C and H
Phenylalanine (Phe, F) Tryptophan (Trp, W) - ANSWER nonpolar amino acids
- contains benzene rinds and are referred to as aromatic amino acids
methionine (Met, M) - ANSWER nonpolar amino acids
- contains a sulphur ring along with carbon and hydrogen in its side chain
proline (Pro, P) - ANSWER nonpolar amino acids
- is the only amino acid whose R group bind to its amino group
- very rigid, and can cause a kink in the amino acid chain, causing a proline kink within a protein
Uncharged Polar Side Chain - ANSWER - have no net charge at a pH around 7
- can participate in hydrogen bonding
- found on the outside of soluble proteins
serine (Ser, S) Threonine (Thr, T) - ANSWER Uncharged Polar Side Chain
- have a hydroxyl group capable of forming H-bonds
Tyrosine (Tyr, T) - ANSWER Uncharged Polar Side Chain
- has a hydroxyl group capable of forming H-bonds
- aslo has a benzene ring (making it the 3rd aromatic amino acid)
- can lose a proton at alkaline pH
asparagine (Asn, N) Glutamine (Gln, Q) - ANSWER Uncharged Polar Side Chain
- have carbonyl and amine that can both participant in H bonds and dipole
molecules
aromatic side chains - ANSWER amino acids with a benzene rings side chain
- phenylalanine
- tryptophan
- tyrosine
- these molecules are very large and cause stindric hindrance (repulsion between atoms because they want more space)
Chirality - ANSWER property of a molecule that is not superimposable on its mirror image
- for a molecule to be chiral, it has to have 4 different groups binded
chirality of amino acids - ANSWER - the 2 forms are the D and the L forms
- enzymes often interact with only 1 of the chiral forms of the amino acid
Post Translational Modifications - ANSWER - disulphide bonds
- glycosylation
- phosphorylation
Post Translational Modifications: Disulphide bonds - ANSWER - disulphide bonds can occur between cysteine amino acids in the same protein or other proteins
- disulphide bonds help stabilize the folded protein, making it more resistant to denaturation
Post Translational Modifications: Glycosylation - ANSWER - a sugar group is attached to a protein
- sugar chains can be attached to the amide group in asparagine (N-linked glycosylation) or to the hydroxyl group in serine or threonine (O-linked glycosylation)
Post Translational Modifications: Phosphorylation - ANSWER - a phosphate group can be attached to the hydroxyl group in serine, threonine, and tyrosine
- phosphoryaltion can be used to turn on and off proteins and enzymes
- this causes a conformational change in the protein
kinases - ANSWER enzymes that add phosphate groups
phosphatases - ANSWER enzymes that remove phosphate groups
deprotonated form
titration of amino acids - ANSWER - free amino acids with a non-ionizable side chain have 2 buffering groups, each with a distinct pKa : 2.3 for carboxylic groups (pK1) 9.1 for the amino groups (pK2)
pH and ionization - ANSWER - the plot shows the concentration of each other different protonated states for an amino acid with a non-ionizable side chain R as a function of pH
- zwitterionic form is where one part of the amino acid is positively charged while the other is negatively charged
- where pink and blue lines intersect, half the protons have been removed from the carboxyl group
- where the blue and green lines intersect, half the protons have been removed from the amine group
Titration of Alanine - ANSWER - at pH 0, all alanine is fully protonated and has a net positive charge
- strong base (OH-) is added, and pH increases, the carboxylic group will start to loose its protons
- at a pH of 2.3, 50% of alanine's carboxylic groups will be protonated and
50% will not be
- when pH= pl (net charge is 0), the alanine will exist in the neutral state
- as pH continues to rise, the amino group of alanine molecules will start to lose their protons, at this pH, half the molecules are deprotonated and half are protonated
isoelectric point (pl) - ANSWER - is the pH where the next charge of the molecule is 0
titration of amino acids with ionizable side chains - ANSWER - acidic, basic, tyrosine, and cystein have 3 buffering regions: pK1, pK2, and pKr
amino acids with ionizable side chains - ANSWER Arginine Lysine Tyrosine Cysteine Histidine Aspartic acid Glutamic acid
medical importance of buffers - ANSWER - pH must be maintained
primary structure- peptide bond - ANSWER - the amino acids are joined together by peptide bonds
- condensation reactions (because condensation reactions produce water, we often refer to single amino acids in a protein as residues)
- peptide bonds are very stable
- look back on notes for image
residues - ANSWER a single unit that makes up a polymer (such as an amino acid)
characteristics of peptide bonds - ANSWER - has a partial double bond character
- this characteristic is due to resonance structures (2 forms of a molecule where chemical connectivity is the same, but only different in the position of their electrons)
- the resulting double bond structure is rigid and doesn't rotate (planar)
Peptide Bond: Cis/Trans Peptide bonds - ANSWER Cis Configuration (the 2 alpha carbons are on the same side of the bond. Bring their R groups close together which due to steric hindrance, is unfavourable) Trans Configuration (the 2 alpha carbons are away from each other, giving the R groups more
space)
Peptide Bond: Polarity - ANSWER - once the peptide bond is formed, the carbonyl and the amino groups from the amino acids can no longer ionize
- this means that only charged groups on a peptide are at the N-terminus (amino group) and the C-terminus (carboxyl group) and on any ionized side chain THEY CAN BE A PART OF HYDROGEN BONDING (which is key to forming the secondary structure)
Secondary Structure - ANSWER - the folding of amino acid chain into a secondary structure
- folds to maximize hydrogen bodning
- alpha helices
- beta sheets
alpha helices - ANSWER - most common
- stabilized by hydrogen bonds
residues on alpha helices - ANSWER - the spiral structure is composed of 3. amino acids per turn
beta-sheets to form super-secondary structures
Tertiary Structure - ANSWER - comprised of beta-sheets and alpha-helices, and sections of unfolded primary structure
- there can be more than 1 domain in a protein, and typically combines fold independently of another
- hydrophobic amino acids pack into the inside of the protein while hydrophilic amino acids stay on the outcomes
Tertiary Structure- Stabilizing Interactions - ANSWER - disulphide bond
- hydrophobic interactions
- hydrogen bonds
- ionic interactions
Tertiary Structure- Stabilizing Interactions: Disulphide Bonds - ANSWER - links between 2 cysteine (either in the same protein or another protein)
- these bonds provide stability for the fold, but aren't a driving force for the fold (they just happen after the protein folds)
Tertiary Structure- Stabilizing Interactions: Hydrophobic Interactions -
ANSWER - This is the main driving force for tertiary protein structures (that is because most interactions are taking place in an aqueous environment where the solvent is water, so all the hydrophobic molecules go into the middle)
Tertiary Structure- Stabilizing Interactions: Hydrogen Bonds - ANSWER - hydrogen bonds form between side chains with oxygen or nitrogen (electron-rich atoms)
- hydrogen bonds between polar groups on the protein's surface make proteins more soluble, and prevent the protein molecules from aggregating together
Tertiary Structure- Stabilizing Interactions: Ionic Interactions - ANSWER - take place when negatively charged side chains (Asp, Glu) interact with positively charged Side chains (Lys, His, Arg)
- these are also called electrostatic interactions or salt-bridges
- these bonds contribute to the stability of the tertiary protein
quaternary Structure - ANSWER - bind or 2 or more tertiary proteins or subunits together
- the proteins may work together or independently during protein function
myoglobin (Mb) - ANSWER - present in the heart and skeletal muscle of the body
- it functions as a resevoir for oxygen and an oxygen carrier
- the structure of Mb creates the right enviroment for heme binding and the reversible binding of oxygen (interior hydrophobic, 80% alpha helices)
- the heme group is is bound to a pocket of non-polar amino acids (His) which are key to myoglobin function (the proximal His binds to the Fe of heme and the distal His stabilized the binding of oxygen to the heme group)
Hemoglobin (Hb) - ANSWER - found only in red blood cells (it functions to transport oxygen from the linings to capillaries in the tissues)
- structurally comprised of 4 peptide chains (2 alpha-chains and 2 beta-chains)
- similar structure to Mb, but more complex
Quaternary structure of hemoglobin - ANSWER - dimer of dimer
- each individual alpha-beta dimer is held together by strong hydrophobic interactions and the 2 dimers are held together by weak H bonds and ionic interactions
oxygen binding to myoglobin and hemoglobin - ANSWER - each Mb protein
reversibly binds a single oxygen. The amount of oxygen bound to the Mb protein is measured as the percent of oxygen in the blood, yielding a hyperbolic binding cirve
- each Hb can reversibly bind 4 oxygen, which indicate subunit cooperatively (the binding on 1 oxygen to a subunit increases the affinity for the other subunits to bind oxygens)
cooperative oxygen binding in Hb - ANSWER - the binding of oxygen to Hb causes a conformational change that breaks some of the ionic interactions between dimers and causes a changed structure
- this causes more electron affinity, allowing more oxygen to bind
physiological relevance of cooperative binding - ANSWER - cooperative binding of Hb allows for complete saturation (100% bound to oxygen)
- cooperation also allows easier release of oxygen in the tissues that oxygen levels are low
- Hb has an ideal oxygen delivery system
- Mb is suited to store oxygen in the muscle until it is needed
Fibrous Collagen - ANSWER - for structural support
- combined from secondary structure alpha-helices
