8.1.16 Lecture Flashcards
Name 3 functions of proteins (of 7 possible)
- Enzymatic (catalysis) 2. Tissue and cell structure 3. Hormones and hormone receptors 4. Ion channels 5. Transporters 6. Transcription factors 7. Contraction in muscles
What is the central dogma?
- In the nucleus, DNA/genes are transcribed to mRNA. 2. The mRNA is transported to the cytosol, where it is translated into a protein. 3. This protein may be modified further.
What is the proteome? Describe its makeup.
The proteome is the catalog of all proteins. The genome is composed of 20-25,000 genes. The genome is transcribed into 100,000 possible mRNA (transcripts) to make up the transcriptome. This occurs via alternative promoters, splicing, and mRNA editing. Finally, these are translated into the proteome, which is made up of over 1 million proteins.
Draw an amino acid in its original form.
Draw an amino acid in its Zwitterionic form. At what pH does this form occur?
Physiological pH = ~7.4
What is the only amino acid isomer found in proteins?
L-isomer
What are the characteristics of hydrophobic vs. hydrophilic amino acids?
Hydrophobic: non-polar, no water interactions, found in interior of proteins
Hydrophilic: polar and/or charged, interact with water via hydrogen bonds, found on the surface of a protein.
Glycine
Gly
pKa of R: n/a
Alanine
Ala
pKa of R: n/a
Valine
Val
pKa of R = n/a
Leucine
Leu
pKa of R = n/a
Isoleucine
Ile
pKa of R = n/a
Serine
Ser
pKa of R = n/a
Threonine
Thr
pKa of R = n/a
Cysteine
Cys
pKa = 8.37
Methionine
Met
pKa of R = n/a
Phenylalanine
Phe
pKa of R = n/a
Tyrosine
Tyr
pKa of R = 10.46
Tryptophan
Trp
pKa of R = n/a
Aspartate
Asp
pKa of R = 3.65
Asparagine
Asn
pKa of R = n/a
Glutamate
Glu
pKa of R = 4.3
Glutamine
Gln
pKa of R = n/a
Lysine
Lys
pKa of R = 10.8
Arginine
Arg
pKa of R = 12.5
Histidine
His
pKa of R = 6.0
Proline
Pro
pKa of R = n/a
Name the two amino acids categorized as small.
Glycine and Alanine
Name the three amino acids categorized as branched chain.
Valine, Leucine, and Isoleucine
Name the two amino acids categorized as hydroxyl.
Serine and Threonine
Name the two amino acids categorized as sulfuric.
Cysteine and Methionine
Name the three amino acids categorized as aromatic.
Phenylalanine, Tyrosine, and Tryptophan
Name the four acidic amino acids.
Aspartate, Asparagine, Glutamate, and Glutamine
Name the three basic amino acids.
Lysine, Arginine, and Histidine.
Name the amino acid categorized as imino.
Proline
What 5 amino acids are charged at physiological pH?
Aspartate, Glutamate, Lysine, Arginine, and Histidine
What are the characteristics of a peptide bond?
Amide, planar, trans
What is cystine?
A derived amino acid, created by oxidizing two cysteines; these two amino acids are joined by a covalent disulfide bond
What two proteins involve cystine?
Vasopressin (antidiuretic hormone) and insulin
Define acid and base.
Acid: H+ donor, Base: H+ receptor
What is Ka?
The acid dissociation equilibrium constant; it measures the strength of an acid.
Ka = ?
[H+][A-]/[HA]
Derive the Henderson-Hasselbach Equation.
A low pKa indicates ____. A high pKa indicates ____.
an acid; a base
On a titration curve, a flat portion (m~0) indicates ____.
pH = pKa; [A-] ~ [HA]
What is the isoelectric point (pI)? How can it be calculated?
The pH at which there are an equal number of + and - charges. It is calculated by averaging the pKa values that border the Zwitterion form.
Describe 2-D electrophoresis.
First, run the specimen on a pH gradient. It will move to its pI and stop. Then, run the specimin on a second gel to separate it by size.
After 2-D electrophoresis, how is a particular protein studied?
First, cut out the protein. Then, digest it with trypsin. Separate it by HPLC. Measure the mass and determine the amino acid sequence.
