Biochem test 2 Flashcards
Southern blots identify
DNA
Western blots identify
protein
northern blots identify
RNA
what amino acids are hydrophobic
alanine, valine, leucine,
Isoleucine
Methionine, Phenylalanine,
Tryptophan
Tyrosine
Methionine
Met, M
Phenylalanine
Phe, F
pI (isoelectric point):
pH when a.a has no net charge
Valine
V, Val
Tryptophan
Trp, W
linear tripeptide has
3 amino acids and 2 peptide bonds
Peptide bond is also known as
amide bond
Peptide bond formation is the reaction
NH2 and COOH from a.a.
In the side chane of Lys what group is attached to the c group
amino group
What are the hydrophilic amino acids
Asparagine, Glutamine, Serine, Threonine
What are the acidic amino acids
aspartic acid, glutamic acid
What are the basic amino acids
Lysine, Histidine, arginine
chaperonins such as the GroEl/Es system
requires ATP hydrolysis
What is the name of disease caused by a missense mutation in the B chain of hemoglobin
sickle cell anemia
the formation of a dipeptide from two amino acids involves
loss of water
the classic experiment demonstrating that reduced and denatured RNase A could refold into the native form demonstrates that
1 primary structure can demtermine a 3 tertiary structure
In general, molecular chaperone proteins function by
preventing premature folding by binding hydrophobic regions of the proteins
What is true about peptide bonds
it results in linear polymer of amino acids
How are peptide bonds synthesized
synthesized N-terminus to C-terminus
peptide bond formation is achieved by the dehydration condensation of how many amino acids
2 amino acids
Mass spectrometry has emerged as a technique for
protein sequencing.
ELISA
enzyme linked immunosorbent assay
What factors are used for protein sequencing
affinity, high salt concentration, ionic strength, size
Membrane spanning contains
hydrophobic amino acids in the central region
What does membrane spanning allow the protein to do
allow the protein to cross the bilayer membrane
what are the two of Categorization of homologous sequences
Paralogs and orthologs
Orthologs similar sequence is found in
different specicies
Orthologs mode of evolution
conventional divergence -speciation
Paralogs i Similar seq is found within the
the same species
Paralogs Mode of evolution is
gene duplication
What are some properities of hemoglobin
binds 4 O2
moderate affintiy to O2
What is the elution order for ion exhange chromatography
weakly-charged → moderate → strongly-charge
the column for ion Exhange chromatography is selected based on the
type and strength of charge
affinity chromatography separates by
separates by molecular conformation
affinity chromograhy frequntly generates
a single peak while all other in the sample is unretained
.Bradford assay uses colorimetics to
measure the total amount of proteins.
SDS-PAGE uses the charge to
separate proteins in different sizes.
in gel filtration chromatography what particle elutes faster
Larger proteins elute first and smaller ones elute later.
porus gels of gel filtration
separate small, denatured, or solubilized proteins
a technique used to determine the tertiary structure of a protein is -
x-ray crystallography
Asparagine
Asn, N
What is true about protein domains
they may retain their correct shape even when seperated from the rest of the proteins
Carbon monoxide binds to heme-
with a higher affinity than oxygen
Glutamine
Gln, Q
Serine
Ser, S
Threonine
Thr, T
pI equivalence point
pI = (pK1 + pK2)/2
pI for acidic a.a. (D, E
pI = (pK1 + pKR )/2
Aspartic acid
Asp, d
Glutamic acid
E,Glu
pI for basic a.a. (K, R, H)
(pK2 + pKR )/2
What are the 10 essential amino acids
Phenylalanine (F)
Lysine (K)
Leucine (L)
Tryptophan (w)
Arginine (R)
Methionine (M)
Valine (V)
Histidine (H)
Threonine (T)
Isoleucine (I)
Bovine insulin
two polypeptide chains A and B joined by disulfide (S–S) bonds
How much rotation is there on plane polorzed light
0
What are some of the planer characteristics of a peptide bond
partial double bound character
no rotation around the peptide bond
α-carbon is
the point of flexibility along the backbone
Φ and Ψ describe the
conformation of the backbone
DNA binding fits perfectly to the
major groove of dsDNA
What does DNA binding recognize?
- Recognize a specific DNA sequence and bind to it via H-bonds
Whats a monomer
long a helix
every 4th residue is hydrophobic
What amino acids are in kertain
Large # of cys
Why are their large # of cys in kertain
they stabilize the filament
What does myoglobin do to O2
it stores O2
Protein has minimal solubility at
pH=PI — precipitation
What are the 2 types of B sheets strucutres
parallel & antiparallel)
What are the similarities between of parallel & antiparallel
Inter-strand H-bonding between C=O & N-H
What are the differences between parallel and antiparallel
the direction of the associated β strands and the length of loop
what amino acids have ionizable side chains
arginine, aspartic acid, cysteine, glutamic acid, histidine, lysine and tyrosine
In Keratin, pairs of helices wind about each other in what fashion
left hand fashion
Sigmoidal O 2-binding curve:
very efficient in O 2 transport
Heme causes the structural change, how
Binding of O 2 → Fe(III) into heme plane → Pull on helix F → Conformational
change