Biochem Exam 1 Flashcards
Name the Amino Acids with Nonpolar, Aliphatic R groups and describe their unique characteristic.
1.) glycine 2.) alanine 3.) valine 4.) leucine 5.) isoleucine
R groups consist of CH groups.
Name the Amino Acids with Nonpolar, Aromatic R groups and describe their unique characteristic.
1.) Phenylalanine 2.) Tyrosine 3.) Tryptophan
All have aromatic rings.
Tyrosine has OH group
Tryptophan has an NH group
Name the Amino Acids with Uncharged, Polar R groups and describe their unique characteristic.
1.) threonine 2.) serine 3.) asparagine 4.) glutamine
All have an OH or C=ONH2 attached to their R groups.
Name the Amino Acids with Acidic R groups and describe their unique characteristic.
1.) aspartic acid 2.) glutamic acid
Both have COOH group attached to R group.
Name the Amino Acids with Basic R groups and describe their unique characteristic.
1.) histidine 2.) lysine 3.) arginine
All have NH2 or NH3 attached to their R group.
Name the cyclic imino acid and describe some of its unique characteristics.
proline
- Proline does not form a conventional peptide bond
- Very constrained compared to other aa
- The sidechain is aliphatic with no functional groups
- The sidechain covalently bonds to the amide nitrogen eliminating the opportunity for hydrogen bonding at that position
- Its α-imino group is bonded to its side chain
- hydrophobic
Name the Amino Acids with sulfur-containing R groups:
1.) cysteine 2.) methionine
Amino Acids with aliphatic hydroxyl R groups:
1.) serine 2.) threonine
Describe primary protein structure:
Primary protein structure is sequence of a chain of amino acids (often thought of as beads on a string).
Describe secondary protein strucutre:
2 types of secondary protein structure: 1.) Alpha Helix-hydrogen bonds between the “backbone” amide (NH) and carboxyl (C=O) groups stabilize the alpha helix. There are 3.6 amino acids per turn. 2.) Beta Sheet- the “backbone of the polypeptide chain is extended into a zigzag structure. When the zigzag polypeptide chains are arranged side by side, they form a structure resembling a series of pleats.
Amino Acid with an Amide Derivative R group:
1.) asparagine 2.) glutamine
Describe tertiary protein structure:
-Tertiary structure refers to the overall 3D structure of the protein. -Amino Acid side chain interactions contribute to protein folding seen in tertiary structure. -4 types of side chain interactions: 1.) disulfide bonds 2.) hydrogen bonds 3.) salt bridges 4.) hydrophobic interactions
Describe quaternary protein structure:
Can be composed of multiple polypeptide chains. Quaternary structure refers to the number and arrangement of protein subunits.
Define ionization state:
-The ionization state of an amino acid depends on pH. -Amino acids are amphoteric (can act as a base and as an acid). -At low pH, the carboxyl group accepts a proton and becomes uncharged, and the overall charge on the molecule is positive -At high pH, the amino group loses its proton and becomes uncharged, and the overall charge on the molecule is negative +H3N—CH2—COOH ↔ +H3N—CH2—COO- ↔ H2N—CH2–COO-
Define the Henderson Hasselbalch equation:
- Describes the derivation of pH as a measure of acidity in biological and chemical systems
- useful for estimating the pH of a buffer solution
- widely used to calculate the isoelectric point of proteins (point at which protein neither accept nor yield proton)
Define zwitterion:
- a molecule or ion that has both positively charged and negatively charged groups
- in aqueous solution, the amino acid exists as a dipolar molecule
Define pI
- pI is the Isoelectric point.
- It is the pH at which a protein neither accepts nor yields a proton. (The protein has no net electrical charge.)
Define peptide:
-consisting of two or more amino acids linked in a chain, the carboxyl group of each acid being joined to the amino group of the next
Describe Homocysteinuria
- disorder of methionine metabolism
- leading to an abnormal accumulation (excess) of homocysteine and its metabolites in blood and urine
- clinical presentation: downward dislocation of the lens (ectopia lentis), long limbs, mental retardation, and/or seizures due to low abundance of fibrin protein fibers in lens (disulfide bonds required for lens structure).
Describe Sulfite Oxidase Deficiency
-Sulfite oxidase is required to metabolize the sulfur-containing amino acids cysteine and methionine in foods. -Lack of functional sulfite oxidase causes a disease known as sulfite oxidase deficiency. -This rare but fatal disease causes neurological disorders, mental retardation, physical deformities, the degradation of the brain, and death. -Reasons for the lack of functional sulfite oxidase include a genetic defect
Describe Marfan Syndrome
-involves a mutation to the gene that makes fibrillin, which results in abnormal connective tissue -specifically, it can result in lens dislocation, where the lens is shifted out of its normal position. This occurs because of weakness in the ciliary zonules, the connective tissue strands which suspend the lens within the eye.
Describe Hyperbilirubinemia
- Heme oxygenase converts heme to biliverdin, which is ultimately converted to bilirubin.
- If heme oxygenase is overactive you get higher levels of bilirubin resulting in discoloration of teeth
What is the approximate pH of an amino acid that has 2 ionizable groups and is fully protonated?
pH<2.4
What is the approximate pH of an amino acid that has 2 ionizable groups and only one group is protonated?
between 2.4 and 9.8
What is the approximate pH of an amino acid that has 2 ionizable groups and neither group is protonated?
pH>9.8
The isoelectric points for most amino acids is between 5 and about 6.5. There are 5 whose pI fall outside of this range. What are the five and what are their corresponding pI?
- ) Arginine at 10.76
- ) Aspartic Acid at 2.77
- ) Glutamic Acid at 3.22
- ) Lysine at 9.74
- ) Histidine at 7.59
Describe Solubility-Based Purification Methods
Salting in- increasing the ionic strength of a solution so that the protein of interest stays in solution. (solubility increases)
Salting out- increasing the ionic strength of a solution so that the protein of interest crashes out of solution. (solubility decreases)
Describe purification of proteins by chromatography
Chromatography- purifies and concentrates biomolecules (proteins) based on chemical or physical differences
- ) Size- Size Exlusion chromatography
- ) Surface Charge-Ion Exchange chromatography
- ) Biorecognition (ligand specificity)- Affinity chromatography
Describe Dialysis and Ultrafiltration
Proteins of interest is in solution. The membrane of the dialysis tubing has molecular weight cut off. Choose a size of membrane based on what your are trying to accomplish. EX if have 100 kilodalton protein, choose 50 kilodalton membrane. Smaller molecules move in and out of membrane, protein is trapped inside of membrane. Used for buffer exchange and purification
Describe Size Exclusion Chromatography
Have resin beads of specific size in column. Pour solution containing protein of interest through the column. Small molecules can slowly travel through beads. Larger molecules (proteins) are too large to move through the beads so they have to move around beads. The result is that larger molecules moves through column faster and elude first. Get a buffer exchange solution.
Describe Ion Exhange Chromatography
With a cation exchanger (Resin), has ligand attached that is negatively charged and binds with the positively charged protein
Anion exchanger (Resin), has ligand attached that is positively charged and binds with the negatively charged protein
DEAE (anion exchanger, positively charged). If solution is at pH 7.5, albumin has a negative charge so it will be retained, but immunoglobulin has positive charge at pH 7.5 so it will elude out.
Describe Affinity Chromatography (AC)
In AC, a specific interaction of substrate with ligand occurs. An antibody is attached to the resin in the column. When you pour the protein solution through the column, the protein of interest will bind to the resin. Used to purify IgG from blood.
Explain an example of pI protein purification.
Isoelectric Focusing (IEF)
IEF Gels have pH gradient.
A protein that is in a pH region below its pI (protein has a positive charge) will migrate towards the cathode (left to right) until it stops at its pI.
A protein that is in a pH region above its pI (protein has a negative charge) it will migrate towards the anode (right to left) until it stop at its pI.
What are some ways to characterize proteins by separation methods?
1.) Once purified for determination for aa composition, the protein is subjected to hydrolysis
- 6 M HCl
- 110 ºC
- 24-48 hours
Chromatogram from an aa analysis by cation exchange chromatography shows relative fluorescence of different amino acids.
- ) Edman degradation - N-terminal residue is labeled and cleaved from the peptide sequentially without disrupting the peptide bonds between other amino acid residues
- ) Mass Spectrometry- Can do this with mix of proteins or purified. Chop up protein with protease, get peptides, put in liquid chromatography column, separates peptides out. Mass spectrometer will give you intact mass, this will tell you the mass of your peptide which gives clues as to what peptide it might be. Peptide gets fragmented again and get msms spectrum. This is a fragmentation of origin peptide.
What is botulinum toxin and what does it do?
- Botulinum toxin is a proteinaceous toxin produced by the microorganism clostridium botulinum
- it is internalized and in acid environments the toxic and non-toxic components separate
- Toxic fragments prevent release of Ach neurotransmitter and cleaves the proteins involved in docking of neurotransmitter vesicles.
- This causes FLACCID (sagging) PARALYSIS of muscles.
- Cranial nerves affected first (double vision, difficulty swallowing) then
- Paralysis descends resulting in respiratory failure
Explain Carbohydrate Chirality
- Numbering of the carbons begins from the end containing the aldehyde or ketone functional group
- D or L assignment is based on the configuration around the highest numbered asymmetric center (anomeric carbon) (farthest from the aldehyde or keto group)
- If the hydroxyl (OH) group in the projection formula points to the right, it is defined as a member of the D-family. A left-directed hydroxyl group (the mirror image) represents the L-family
- NEARLY ALL SUGARS FOUND IN THE BODY HAVE THE D CONFIGURATION
- AMINO ACIDS HAVE THE L CONFIGURATION
Of the 8 D-aldohexoses, only 3 are found in significant amounts in the body:
- ) glucos (blood sugar)
- ) Mannose
- ) Galactose
_______ is the only ketohexose present in siginificant concentration in our diet or in the body
fructose
What is the most aboundant carbohydrate in nature?
Cellulose
What is the difference between starch and glycogen?
- Starch = amylose + amylopectin
- It is the most common storage polysaccharide in PLANTS
- Glucose storage in polymeric form minimizes osmotic effects
- Starch adopts a helical form in water
- Glycogen is the animal equivalent to starch.
- It has more alpha (1-6) brances than starch
- It promotes rapid glucose release during exercise
- It is stored in muscle and liver cells as high MW granules
- It is hydrolyzed by amylases and other enzymes
What is an amino sugar?
- A sugar molecule in which a hydroxyl group has been replaced with an amine group.
- More than 60 amino sugars are known, with one of the most abundant being N-Acetyl-d-glucosamine, which is the main component of chitin.
Do lipids or carbohydrates yield more energy? Why?
- gram for gram, fats provide more energy than carbohydrates
- The reason for this is the amount of oxidation that takes place as these compounds are converted to carbon dioxide and water.
- Carbon for carbon, fats require more oxidation to become CO2 and H2O than do carbohydrates
- More energy is present in fats - fatty acids are more “reduced” than carbohydrates
- Fatty acids are nonpolar and not hydrated by water
How many stereoisomers (D and L) can be made from aldoses containing XX carbons with XX asymmetric centers?
- The number of stereoisomers is 2n (n = number of asymmetric centers).
- 6-C aldoses have 4 asymmetric centers for a total of 16 stereoisomers (8 D-sugars and 8 L-sugars).
Why has glucose been evolutionarily selected as blood sugar?
- Glucose exists largely in nonreactive, inert, cyclic hemiacetal conformations (>99.99% in aqueous solution at pH 7.4 and 37°C)
- Of all the D-sugars in the world, D-glucose exists to the greatest extent in these cyclic conformations
- Least oxidizable and least reactive with protein
- The relative chemical inertness of glucose is the reason for its evolutionary selection as blood sugar.
Explain the relationship between sugars and blood types?
- The blood types are named after antigens that are found on the surface of of the red blood cells, and these antigens are simple chains of sugars.
- The types of oligosaccharides present on the surface of the red blood cells determine a person’s blood type: if only the 0-type antigen is present, the blood type is 0, if only the antigen A or B is found, the blood is type A or B, respectively, and if both A and B antigens are present, the blood type is AB [1]. The A and B antigens differ only in a sidechain on the terminal sugar.