Flashcards in Amino Acids and Protein Structure Deck (69):
L-alpha-AA is a ___ acid with an amino group on carbon ___
carboxylic; 2 (the alpha carbon)
What is the role of the Hydrogen on an AA
prevents bulkiness and allows side chains to fit
Almost all AAs are ___ AAs
How many AAs are coded for by DNA?
What are the non polar AAs?
glycine, alanine, proline, valine, leucine, isoleucine
What are the aromatic AAs?
phenylalanine, tyrosine, tryptophan
What are the polar, uncharged AAs?
asparagine, glutamine, serine, threonine
What are the sulfur-containing AAs?
What are the negatively charged AAs?
What are the positively charged AAs?
arginine, lysine, histidine
Aspartate has a pKa of 3.9. Give the ratio of COOH to COO- at a pKa of 2.9, 1.9, and 4.9
pKa 2.9: 10 times more COOH
pKa 1.9: 100 times more COOH
pKa 4.9: 10 times more COO- or 10 times less COOH
What is the isoelectric point?
at a certain pH, there will be an equal number of postive and negative charges
In regards to protein structure, what is unique about the isoelectric point
proteins are least stable at pI
This AA forms disulfides
cysteine, between 2 cysteine molecules
disulfide bridges have what affect on protein structure?
This is found in only a few enzymes and is incorporated via a specialized tRNA which is then incorporated into a protein
At any given pH, a peptide will have a characteristic charge. Changes in a pH will do what?
change the charge on the peptide
Which AAs are involved in carbohydrate addition, specifically O-glycosylation?
serine, tyrosine, and threonine
Which AAs are involved in carbohydrate addition, specifically N-glycosylation?
Which AAs are involved in lipid addition, specifically palmitoylation?
Which AAs are involved in lipid addition, specifically prenylation?
Which AAs are involved in lipid addition, specifically myristoylation?
Which AAs are involved in regulation, specifically phosphorylation?
Serine, Threonine, and Tyrosine
Which AAs are involved in regulation, specifically ADP-ribosylation?
arginine, glutamine, cysteine
Which AAs are involved in regulation, specifically Acetylation?
Which AAs are involved in modification, specifically oxidation?
Which AAs are involved in modification, specifically carboxylation?
This is the bond between the alpha-carboxyl group of one amino acid and the alpha-amino group of another amino acid
The peptide bond is ___, with the alpha-carbon, the carbonyl carbon, the carbonyl oxygen, the nitrogen, the nitrogen-hydrogen and the second alpha-carbon all in the same plane
Adjacent R groups of two amino acyl residues are almost always in the ___ configuration
What is primary structure of a protein
sequence of AAs
Residue #1 is the amino terminal or ___-terminal; The last residue is the carboxyl terminal or ___-terminal
Different protein isoforms or isozymes may be expressed at different developmental stages. true or false?
true, ex: HbF, HbA
Give an example of different protein isoforms or isozymes expressed simultaneously but restricted to different tissue
creatine kinase isoenzymes and lactate dehydrogenase isozymes
In regards to primary structure, give an example of species variation
What is secondary protein structure
recurring, localized structures found within regions of a polypeptide chain - primarily alpha helix and beta sheets
The alpha helix is stabilized by ___ bonds between the amide hydrogen of an amino acyl residue and the carbonyl oxygen atom of a second amino acyl residue located four amino acyl residues down the chain
Which AA can't be part of an alpha helix
True or false? beta sheets form a planar surface
The surfaces formed by B-pleated sheets are often ___
What are some other secondary structures that are less repetitive and uniform than alpha helices and beta sheets?
bends, loops, and turns
patterns of secondary structures are frequently found in several different proteins. These repeating patterns often function similarly to each other and represent what?
motifs and domains
ex: nucleotide binding domains are found in many proteins which bind and hydrolyze ATP
What is tertiary protein structure?
the folding pattern of the secondary structural elements into a 3D conformation
What five forces are involved in tertiary protein structure?
1. hydrogen bonds
2. salt bridges
3. hydrophobic interactions
4. van der waals forces
5. disulfide bridges
Globular proteins soluble in aqueous environment are part of tertiary structure. The "core" of a soluble globular protein usually contains a high proportion of ____ amino acyl residues and ____ ____ amino acyl residues are usually concentrated on the surface of soluble globular proteins
hydrophobic; charged polar
Globular proteins in tertiary structure interact with a polar aqueous environment to form ___ ___ to stabilize structure
In regards to tertiary structure, transmembrane proteins are membrane spanning domains made up of what?
alpha helices and hydrophobic residues that are exposed to the lipid environment
In transmembrane proteins, extracellular and intracellular domains may be more characteristic of ___ interactions
What is quaternary protein structure?
association of individual polypeptide chain subunits into one functional protein
In regards to quaternary structure, what are the four forces involved in globular proteins
1. hydrogen bonding
2. hydrophobic interactions
3. salt bridges
4. rarely disulfide bonds
In regards to quaternary structure, in fibrous (connective tissue) and other structural proteins, there may be extensive ___ linkages to other proteins
What is an example of cooperativity between subunits?
The ___ structure of a protein specifies the folding of the mature protein
What do heat shock proteins do?
prevent improper folding of proteins
Other heat shock proteins that require energy do what?
promote proper folding
The following describes a technique used in protein purification and analysis:
separations of compounds based on the relative affinity of the compounds for a given stationary phase and for the mobile phase
This chromatography medium is porous beads. The protein mixture flows through a column. Smaller proteins can enter the pores of the beads, and therefore take longer to flow through the column. Larger proteins elute first.
size exclusion chromatography
In ion exchange chromatography, the medium is resin beads with covalently bound chemicals which bear a charged group. Explain the difference between cation exchange and anion exchange
1. the bound chemicals have a negative charge
2. positively charged compounds (cations) will adhere to the column
1. chemicals have a positive charge
2. negatively charged compounds (anions) will adhere to the column
Describe hydrophobic interaction chromatography
medium contains hydrophobic groups; proteins with exposed hydrophobic surfaces will adhere to column; adhering proteins are eluted by decreasing polarity of the eleuent
The following describes what type of chromatography?
medium contains a bound ligand; proteins which bind ligand will adhere to column; adhering proteins may be eluted by adding excess ligand
In this type of chromatography, eluent is pumped under high pressure - separation is faster and at a higher resolution and usually uses hydrophobic interaction.
high-pressure liquid chromatography
Separation based on migration of charged molecules in an applied electrical field is called what?
ex: hemoglobin isoforms
Describe what happens in an SDS-PAGE
large number of SDS (detergent) molecules interact with each protein molecule, producing proteins of approximately equal charge-to-mass ratios, also disrupting quaternary structure and separation into monomers - then migration through the PA gel is based on sized, smaller proteins migrating faster
Special, proprietary buffers are used to generate a pH gradient within a PA gel. proteins will migrate to the pH which is equal to the protein's pI. Once at the pH which equals the pI, the protein will no longer migrate. What technique is this?
Give the first and second dimension of two-dimensional electrophoresis
Describe a western blot
1. proteins separated by electrophoresis (usually SDS-PAGE) are transferred to synthetic membrane
2. membrane is incubated with antibody (primary antibody) to a specific protein
3. a second antibody (to the primary antibody) conjugated with a reporter molecule is added to visualize the specific protein
The following description is of what technique:
1. penylisothiocyanate reacts with N-terminal
2. derivative can be removed, analyzed, and AA identified
3. a new N-terminal is produced which is subjected to a 2nd round of the reaction
4. process may be repeated multiple times to determine the AA sequence of a peptide
Mass spec separates molecules based on what?