Biochemistry Flashcards
If a molecule has n chiral centers, how many possible stereoisomers are there?
2^n
What property is different between enantiomers? (Shape doesn’t count)
Polarization of light
What is the term for a mixture that contains a 50/50 combination of enantiomers
Racemic
What kind of bond is broken in ATP when utilizing it as an energy source?
Phosphoanhydride
What term describes two genes of the same origin in the same organism?
Paralogs
What term describes two genes of the same origin in different organisms?
Orthologs
What term describes two genes of the same origin? (Produced from duplication)
Homologs
What term describes the structure taken by amphipathic molecules when they aggregate and form a hydrophilic interface
Micelles
The pH of a buffer solution is determined by what equation?
Henderson-Hassalbalch
What kind of buffer system is employed by our circulatory system for our blood?
Bicarbonate Buffer System
What kind of buffer system is employed by our cells for our cytosol?
Phosphate Buffer System
What part of an amino acid is its chiral center?
Alpha carbon
Assuming the R group is at the bottom and the H group is at the top, what term describes an amino acid with its amine on the left?
L-Amino Acid
Assuming the R group is at the bottom and the H group is at the top, what term describes an amino acid with its amine on the right?
D-Amino Acid
In what form are most biological enantiomers of amino acids?
L Stereoisomer
What term describes the dimeric amino acid formed from two cysteine residues covalently bound at sulfur?
Cystine
What term describes the amino acid composed of four lysine reduces found in elastin?
Desmosine
What term describes an amino acid that has charges but a net zero charge
Zwitterion
What term describes an amino acid that can act as both an acid and base?
Ampholyte
The pH at which most ions exist in their zwitterion form is referred to as what?
Isoelectric pH (pI)
What constant describes the extent that an acid dissociates in solution
Acid dissociation constant
What equation describes how to calculate the acid dissociation constant
[CB] * [H+] / [Acid]
What term relates the acid dissociation constant to pH by converting it to a -log of 10?
pKa
What is the Henderson-Hasselbalch equation?
pH = pKa + log([CB]/[WA)
When pH = pKa and the pH causes equal amounts of weak acid and its conjugate base, what is this point known as?
Half Equivalence Point
In a titration curve, the X axis measures?
Volume of Strong Base
In a titration curve, the Y axis measures?
pH
Are buffers most effective at
a) Half-Equivalence Points
b) Isoelectric Points
c) Neither
a) Half-Equivalence Points
All amino acids have at least how many half-equivalence points and why?
Two because they all have at least an amine group and carboxyl group?
How many half equivalence points does glycine have?
2
Multi-subunit proteins with at least two identical polypeptides are called what?
Oligomers
What term describes the relationship between the two identical polypeptides in an oligomer?
Protomers
Conjugated Proteins consist of what two elements?
Protein + Prosthetic Group
What method involves slowly separating out unwanted substances from a crude extract through a semipermeable membrane?
Dialysis
What compound is utilized for the process of salting out due to its extremely high solubility?
Ammonium Sulfate
What kinds of specialized chromatography amplifies small distances by multiplying the speed that substances travel through a column?
High-Performance Liquid Chromatography (HPLC)
What chemical process can be utilized to sequence the primary structure of proteins by removing the N-terminus amino acid of the peptide?
Edman Degradation
What type of mass spectrometry utilizes a laser (that inhibits fragmentation) [soft ionization]
MALDI MS
What type of mass spectrometry applies a high voltage charge to a liquid for soft ionization?
ESI MS (Electrospray Ionization)
What type of mass spectrometry breaks down proteins into peptides and then fragments specific peptides into y-type ions or b-type ions which can be compared to analyze amino acid differences and can sequence them?
Tandem MS (MS/MS)
In synthesis of peptides, what kind of column anchors the amino acid?
Polystyrene
The amine group is protected during peptide synthesis by what chemical compound?
FMOC
An amino acid with FMOC is attached to the polypeptide chain using what chemical compound?
DCC
What sulfur-based reducing agent is very common in the cell?
Glutathione
What amino acids make up glutathione?
Glutamate, Glycine, Cysteine
The phi angle is between what two parts of a peptide?
The amine group and alpha carbon
The psi angle is between what two parts of a peptide?
The carboxyl group and alpha carbon
The omega angle is between what two parts of a peptide?
The carboxyl group and amine group between two amino acids
What kind of plot graphs psi angle against the phi angle?
Ramachandran Plot
What amino acid can occupy white spaces in a Ramachandran Plot?
Glycine
What type of secondary structures can be found in the 1nd quadrant of a Ramachandran plot?
Left-handed alpha helix
What type of secondary structures can be found in the 3nd quadrant of a Ramachandran plot?
Right-handed alpha helix
What type of secondary structures can be found in the 2nd quadrant of a Ramachandran plot?
Antiparallel and Parallel beta sheets, collagen triple helix.
What amino acid has the greatest tendency to form alpha helices?
Alanine
What two amino acids are “helix disruptors” that are not found in alpha helices?
Glycine and Proline
What kind of charge is typically exhibited towards the C terminus and N terminus respectively?
Positive and Negative
What kind of beta sheets are longer?
Antiparallel
What kind of beta sheets are more stable structurally?
Antiparallel
What amino acid is typically found in its cis form in beta turns?
Proline
How many amino acid residues do Type 1 and Type 2 beta turns have? What about gamma turns?
4 and 3
Chiral molecules do not have mirrored properties, and so what kind of method can measure the difference in properties between enantiomers to determine structure composition?
Structural Dichroism
In N-acetylglucosamine, instead of a ___ group there is a ____
Hydroxyl; Amine group bound to acetate
What kind of carbohydrate acid is formed from oxidizing the aldehyde group
Aldonic acid
What kind of carbohydrate acid is formed from oxidizing the hydroxyl group of the terminal carbon
Uronic acid
What kind of carbohydrate acid is formed from oxidizing both the hydroxyl group of the terminal carbon and aldehyde
Aldaric acid
Some monosaccharides can be oxidized by mild oxidizing agents such as?
Cu2+ (cupric ion)
When the anomeric carbon of a saccharide forms a glycosidic linkage with oxygen of another compound, what kind of glycosidic linkage is it?
O-glycosyl bond
When the anomeric carbon is joined to a nitrogen in a protein or nitrogenous base, what kind of linkage is formed?
N-glycosyl bond
In a polysaccharide, the end that has a free anomeric carbon is described by what term?
Reducing End
What kind of macromolecular storage molecule found in bacteria and yeasts is composed of 1’6 alpha linkages and 1’3, 1’4, and sometimes 1’2 alpha linkages for branches?
Dextrans
In Chitin, subunits of N-acetylglucosamine are connected in what kind of arrangement and resemble what other kind of polysaccharide?
1’4 Beta Linkage, Cellulose
What are the two conformations of a polysaccharide in solution?
Boat and Chair
What is the most stable conformation for a polysaccharide in solution
Chair Conformation
Lysozyme hydrolyzes ____ linkages between ____ and ____ breaking down the ____ molecule.
Beta 1’4; N-acetylglucosamine and N-acetylmuramic acid; Peptidoglycan
What polysaccharide is found in red algae and contains a mixture of D-galactose, L-galactose, sulfate, and pyruvate?
Agar
The six-membered ring found in carbohydrates is described by what term?
Pyranose ring
The five-membered ring found in carbohydrates is described by what term?
Furanose ring
Glycosaminoglycans are found in what kinds of organisms?
Animals and Bacteria
What is the term for long strands of carbohydrates found in connective tissue that contain amino groups?
Glycosaminoglycans
Glycosaminoglycans have either N-acetylglucosamine or N-acetylgalactosamine and what other type of compound?
Uronic Acid
Glycosaminoglycans can be attached to proteins to form what kind of molecule?
Proteoglycans
What kind of glycosaminoglycan can be found in vitreous humor and the ECM of tendons? It is also targeted by some pathogenic bacteria.
Hyaluronan
What kind of glycosaminoglycan is common in sharks and contributes to tensile strtength?
Chondroitin Sulfate (Cartilage
What kind of glycosaminoglycan lacks uronic acid, has variable sulfur content, and is common in dead cells such as nails?
Keratan Sulfates
What kind of glycosaminoglycan is responsible for interacting many proteins such as one involved in blood clotting?
Heparan Sulfate
What is the term for oligosaccharides covalently joined to a protein through N-linkages?
Glycoproteins
What is the term for proteins that recognize the specialized informational sequences of oligosaccharides?
Lectins
A plasma membrane component whose hydrophilic headgroup is an oligosaccharide and is rich in the brain is described by what term?
Glycosphingolipid
What amino acid residues are used to link proteoglycans to oligosaccharides in O-linkages?
Threonine or Serine
What amino acid residues are used to link proteoglycans to oligosaccharides in O-linkages?
Asparagine
What heparan-sulfate proteoglycans have a single transmembrane domain, three extracellular domains, and regulate cell communication?
Syndecans
What heparan-sulfate proteoglycans are attached to the membrane by a lipid anchor that is derived from phosphatidylinositol?
Glypicans
What glycans with large numbers of O-linked oligosaccharides are present in mucus secretions?
Mucins
What glycosphingolipids have an oligosaccharide called sialic acid?
Gangliosides
Gangliosides are strongly located in what kind of tissue, in what portion of the membrane, and with what kind of charge?
Nervous, Outer Leaflet, Negative.
Luteinizing Hormone and Thyrotropin have N-linked oligosaccharides, why is this special?
They are recognized by lectins on hepatocytes which causes a cyclic concentration in plasma
What plasma protein carries most blood copper and aids in iron metabolism?
Ceruloplasmin
What special sialic acid residue protects ceruloplasmin and erythrocytes from degradation?
N-acetylneuraminate or Neu5ac
What plasma membrane lectins mediate cell-cell recognition and adhesion?
Selectins
What kind of selectins on endothelial cells and leukocytes respectively are involved in margination?
P and E-selectins; L-selectins.
What sialidase is utilized by influenza?
Neuraminidase
What type of restriction endonuclease is primarily utilized for genetic engineering?
Type II
What is the primary benefit to restriction endonucleases that provide sticky ends over blunt ends?
They facilitate covalent linkage of DNA ligase
What are four/five necessary inclusions within a plasmid that is specifically utilized as a cloning vector?
Ori sequence, relatively small size, linkers / polylinker, selectable markers, screenable markers.
During transformation, plasmid DNA is incubated with E.coli, what are two things utilized to enhance the likelihood of transformation?
Heat Shock and a Calcium Chloride solution.
What kind of method utilizes a high voltage electrical pulse to induce temporary permeability into the membrane for large molecules such as plasmids to travel through?
Electroporation
After creating your plasmid that confers resistance to Tetracycline, you attempt transformation with a batch of E. coli cells, you then transfer your batch of E. coli to a petri dish containing Tetracycline to determine what bacteria successfully received the plasmid, what term describes this process?
Positive Selection
After creating your plasmid that contains a gene that codes for an enzyme that breaks down protein X, you attempt transformation with a batch of E. coli cells, you then transfer your batch of E. coli to a petri dish containing substance Y, which interacts with protein X and promotes cell death. You do this to determine what bacteria successfully received the plasmid, what term describes this process?
Negative Selection
