Exam 4 Flashcards
Amino acids contain a central _________ carbon
tetrahedral
Is water lost or gain in peptide bind formation?
loose water
What kind of bond is a peptide bond?
covalent
What enzyme catalyzes peptide bond formation?
Peptidyl transferase
What does a peptide bond join?
amino acids
What are the 4 types of amino acids?
- nonpolar/hydrophobic
- polar/hydrophilic
- acidic
- basic
Selenocysteine (SEC, U) is a rare amino acid, what does it look like?
cysteine with selenium replacing the sulfur
What are proteins that depend on Selenocysteines catalytic activity?
selenoenzymes
Pyrrolysine (Pyl, O) is a rare amino acid, what synthesized it?
synthesized from 2 L-lysine
Is the rare amino acid, Pyrrolysine (Pyl, O), positive or negative?
positive
The rare amino acids, Hydroxylysine (Hyl) and Hydroxyproline (Hyp) are post-translationally modified and are found in _____________
connective tissue (collagen)
The rare amino acid, Carboxyglutamic acid, is post-transcriptionally modified how?
glutamic acid undergoes carboxylation
The rare amino acid, Carboxyglutamic acid, is important for _____________
clotting factors
The rare amino acid, Pyroglutamic acid (PCA), is a cyclic form of __________
glutamic acid (glutamine)
Amino acids that do not occur in proteins are know to be responsible for __________ and ____________
hormones and neurotransmitters
What are essential amino acids?
cannot be synthesized from scratch by humans
What are conditionally essential amino acids?
obtained from diet
What are dispensable amino acids?
can be synthesized by humans
How many possible triplets (codons) are possible?
64
(63 without stop codon)
Why are there 64 possible triplets but only 20 amino acids?
Give 2 reasons
- If you increased the number of amino acids beyond 20 then it would be difficult to create suitable tRNA molecules that could be distinguished between one another by the aminoacyl-tRNA synthetase so that the correct amino acid could be added
- these 20 amino acids are fairly stable
What is known as the 21st amino acid and why is it not present anymore in organisms?
it was apart of the anaerobic world before there was oxygen present, but now there is lots of oxygen so its not useful
SELENOCYSTEINE
What is the cationic form of amino acids?
NH3+
COOH
What is the anionic form of amino acids?
NH2
COO-
What is the Zwitterion form of amino acids?
NH3+
COO-
amino acids are weakly _________ acids
polyprotic
What is a polyprotic acid?
has more than one acidic H+ so it can donate for than one H+
The degree of dissociation of amino acids depends on the ______ of the medium
pH
For amino acids that don’t have a dissociable side chain, the first thing to dissociate is _______________ and the second thing is _________
alpha carbonyl group
alpha amino group
What is the pKa of alpha carboxyl group?
2 (acidic)
What is the pKa of alpha amino group?
9 (basic)
What are optically active molecules?
can rotate the plane of polarized light
Optically active molecules are __________
chiral
What amino acid does not have a chiral carbon?
glycine
Chiral centers of amino acids allow for _____________(mirror images but not superimposable)
stereoisomerism (mirror images but not superimposable)
What are the mirror images of chiral amino acids called?
enantiomers
____-amino acids are the most common
L-amino acids
All amino acids absorb __________ wavelengths
infrared
What 3 amino acids absorb UV?
Phe
Tyr
Trp
_______ spectra are characteristic for each amino acid residue in proteins
NMR
What can NMR spectra tell you about a protein?
its 3D structure
Proteins are ______ polymers of amino acids
unbranched
amino acids join head-to-tail through formation of ____________ bonds (peptide)
covalent
The peptide backbone of a protein consists of the repeated sequence ___________
–N–C(alpha)–C(o)
In the peptide backbone sequence, –N–C(alpha)–C(o), what does the N stand for?
amide nitrogen (NH3)
In the peptide backbone sequence, –N–C(alpha)–C(o), what does the C(alpha) stand for?
alpha carbon
In the peptide backbone sequence, –N–C(alpha)–C(o), what does the C(o) stand for?
carbonyl carbon (COOH)
What conformation is the peptide bond usually found in?
trans
What is positive and negative in the peptide bond?
positive: N
negative: O
The peptide bond is ______ than single bonds but ______ than double bonds
shorter
longer
Due to the double bond character of the peptide bond, the size atoms of the bond define a ________ plane
amide plane
Is the double bond in peptide bonds usually on the O or N?
neither; it moves between both
What is each amino acid unit called?
residue
What is 2 residues called?
dipeptide
What is 3 residues called?
tripeptide
What is 12-20 residues called?
oligopeptide
What is 20+ (many) residues called?
polypeptide
What is one polypeptide chain called?
monomeric protein
What is more than one polypeptide chain called?
multimeric protein
What is a protein with one kind of chain called?
homomultimeric
What is a protein with two or more kinds of chains called?
heteromultimer
What is an example of a heteromultimer protein?
beta globin has 2 alpha nd 2 beta chains
Is the sequence if amino acids in a protein considered genetic information?
yes
What direction is the amino acid sequence read in?
amino to carboxyl terminus
What 2 groups interact to form a peptide bond?
alpha COOH and alpha NH3+
Peptide formation is the creation of an _________ bond between the carboxyl and amino group
amide bond
Peptide bonds are ___-planar
co-planar
What is the 2 planes (angles) on either side of the alpha carbon formed when a peptide bond occurs?
phi and psi
What are the 2 shapes of proteins?
fibrous
globular
What is the primary structure of proteins?
sequence
What are 3 example of secondary structures of proteins?
helix
sheet
loop/turns
What is the tertiary structure of proteins?
3D shapes (domains)
Are fibrous proteins water soluble or insoluble?
insoluble
What bridges are formed in primary structures of proteins?
disulfide bridges
Disulfide bonds occur in the primary structure of proteins between what amino acid and itself?
Cys
Can multiple secondary structures come together to form a unit?
yes
What is an example of a tetramer (quaternary structure)?
hemoglobin
What is the difference between configuration and conformation?
configuration: breaking bonds
conformation: no bond breaking
Proteins tend to be least soluble at thier ____________ point
isoelectric point
During protein purification, what happens first salting in or out?
salting in
Does salting in or our increase solubility?
salting in
What is the protein purification, Ion exchange?
separates proteins based on their net charge
What is the protein purification, Size exclusion?
separates proteins based on their size
During protein purification, what dramatically increases as the protein is purified?
specific activity
What is specific activity of a protein?
activity of the enzyme per mg of protein
What are 3 methods estimating protein concentrations?
Bradford assay
Lowry assay
BCA (purple complex)
Several methods of estimating protein concentration rely on the reduction of ______ to ______
Cu2+
Cu+
Determination of protein concentration by UV absorption depends on the presence of ____________
aromatic amino acids in proteins
__________ and ________ absorb UV light at 280nm (the very end of spectrum)
tyrosine
tryptophan
What 2 ways can proteins be sequenced?
- real amino acid sequencing
- sequencing the corresponding DNA in the gene
What are the 2 methods of amino acid sequencing that are used together ?
Sanger Method (one at a time)
Mass Spec (cleaves into fragments)
What are the steps of determining protein sequence?
- separate polypeptide chains
- remove S-S (disulfide bonds)
- identify N and C end residues
- cleave each polypeptide into smaller pieces and sequence (Edman and Mass Spec)
- repeat step 4 with different cleavage procedures to make different overlapping fragments
- using overlapping fragments to reconstruct the protein sequence
What end of the residue is susceptible to cleavage by Trypsin, Chymotrypsin, Clostripaon, Staph, and Cyanogen bromide in protein sequencing?
C
What part of the residue is susceptible to cleavage by pH 2.5?
Asp-Pro bonds
What are some uses of amino acid sequences?
- function of protein
- domain structure
- mosaicism in primary structure
- facilitate predications on higher order of structures
- facilitate construction of proves for genes
- evaluation of relationships between proteins (in a species of between species)
What are some biological function of proteins?
- enzymes
- control metabolism and gene expression
- transport proteins
- storage proteins
- movement
- structure
What are 3 structural methods to characterize proteins at atomic resolution?
- X-ray crystallography
- NMR
- Cryo-electron microscopy
Protein function depends on _________ and _______forces
structure
weak, non-covalent forces
The number of protein folding patterns is large but _________
finite
Structures of globular proteins are marginally __________
stable
marginal stability facilitates ________
motion
__________ enables function
motion
What are 4 examples of non-protein amino acids? (neurotransmitteres and hormones)
GABA
epinepherine
histamine
serotonin
Why do polar and non polar amino acids only have 2 pKa values?
one from the carboxyl and one from the amino group
Why do basic and acidic amino acids have 3 pKa values?
one for COOH
one for NH3
one for side chain
What wavelength do amino acids absorb at?
280
What is the length of peptide bonds?
0.133nm
What are the possible phi and psi angles?
nothing with a 0
180 and 180
-60 and 180
Secondary, tertiary, and quaternary structures of proteins are formed and stabilized by ________ forces
weak forces
