Biochemistry - Chemistry of Amino Acids, Peptides and Protein
3-d structure of a protein
3-d structure is related to ___
tertiary structure determines function, what is an example?
the enzyme catalytic site which forms a pocket for a specific substrate
4 examples of tertiary structures
quaternary structure involves more than 1 ___ subunit (aka monomer)
3 examples of quaternary structure
in quaternary structure, the degree of subunit ___ affects function
found in RBCs; hemoprotein
hemoglobin: ___ polypeptides of 2 classes; each subunit has a ___
adult HbA: alpha2beta2
fetal HbF: alpha2___2
4; heme; gamma
8 ___-handed alpha-helices in each alpha subunit
___ right-handed alpha-helices in each beta subunit
functions of hemoglobin
O2 and CO2 transport, buffer
what binds O2 as it relates to hemoglobin function?
His (E7) --> specifically hinders CO binding
hemoglobin contains 4 subunits held by ___ bonds --> ___ structure
___ and ___ hemoglobin structures are flexible
___-form of hemoglobin binds O2, ___-form cannot
binding of first O2 takes the longest time...the rest get progressively faster. this is b/c binding O2 changes conformation of other subunits, facilitating further O2 binding
T-conformation has a ___ O2 affinity; R-conformation has a ___ O2 affinity
sickle-cell anemia = ?
reduced O-carrying capacity of blood
myoglobin found in ___; hemo___; 1 polypeptide of ___ amino acids; ___ right-handed alpha-helices (A-H) with heme b/t helices ___ and ___
muscle; protein; 153; E; F
O2 bound to ___ is a reserve for when pO2 of tissues is low...it is then released for ___ synthesis
most abundant protein in the body
mature ___ composed of 3 alpha-chain subunits
collagen consists of ___ subunits held together by ___-bonds
re: collagen, different tissues have different ___ ___ compositions, e.g. type I collagen is ___ alpha-1 and ___ alpha-2 chain
amino acid; 2; 1
___ is the most abundant amino acid in collagen, with lots of proline and ___
amino acids definition
monomeric unit of peptides and proteins
most amino acids occur as?
L-alpha amino acids
ideal formula of amino acid has ___ charges and practical formula has ___ and ___ charges and the ___ from the carboxyl group shifts
zero; +; -; hydrogen
acronym to describe the essential amino acids is?
essential amino acids ___ be synthesized by the body
adults can synthesize which 2 essential amino acids (children cannot)?
histidine and arginine
amino acid classification by nutritional criteria includes the ___ amino acids
what are the 12 non-essential AAs?
which 2 AAs are not required for protein synthesis since they are formed after protein is synthesized?
hydroxyproline & hydroxylysine
amino acid classification by chemical criteria incorporates the use of ___ ___ properties (R-group)
AA classification by chemical criteria includes which 7 groups of amino acids?
5 aliphatic AAs
Gly, Ala, Val, Leu, Ile
5 hydroxyl AAs
Ser, Thr, Tyr, Hyl, Hyp
2 sulfur AAs
3 carboxyl/amide AAs
Asp, Glu/Asn, Gln
4 basic AAs
Lys, Arg, His, Hyl
4 aromatic AAs
His, Phe, Tyr, Trp
2 pyrrolidine AAs
which 4 AAs DON'T occur in proteins?
req'd for Met synthesis
functions with Vit B12
high levels associated with atherosclerosis
intermediates in biosynthesis of urea
ornithine, citrulline, arginosuccinic acid
precursor for biosynthesis of catecholamines
what are the 3 most abundant catecholamines?
the most abundant catecholamines are all produced by which 2 AAs?
phenylalanine & tyrosine
when the 4 groups on a carbon are different
3 non-alpha amino acids
GABA (gamma-aminobutryic acid)
part of pantothenic acid (Vit B5)
resp. for integrity and function of retina
part of a bile acid (taurocholic acid)
inhibitory neurotransmitter from glutamate
when the 4 groups on a carbon are different
there is more ___ charge at low pH and more ___ charge at high pH
a pH with lots of protons would favor the ___ form at the bottom of the ratio and would be ___ 1 and for a higher pH it would be the opposite
uncharged; less than
if R-groups are hydrocarbons then they are ___ and can form ___ bonds
if R-groups are polar (COOH, NH3, OH) then they are ___ and can form ___ bonds (salt bridge) or ___ bonds
hydrophilic; ionic; hydrogen
if r-groups are aromatic then they possess strong ___ absorption; this is used for quantitation of ___ in solution
if r-groups are -OH then they become esterified by ___
phosphorylation alters ___ function; major role is in phosphorylation ___
if r-groups are -SH (usually Cys) then they are oxidized to form ___ bonds
if a compound has hydrogen it's in ___ form and w/o hydrogen it's ___
b/t COOH and NH3
in vivo, catalyzed by enzymes
aka peptide bond
usually formed b/t 2 cysteines
involved in redox reactions
general 3D protein structure
if r-groups are -OH or -NH2 they can form ___ by covalently bonding carbohydrates via ___ bonds
HbA1c stands for?
1 carbohydrate attached
glycohemoglobin is ___ or ___ hemoglobin
less than/equal to 10 amino acids
more than 10 AAs
may be comprised of multiple polypeptides
N-terminal aka? C-terminal aka?
intracellular antioxidant; will prevent oxidation of other compounds, thus it must reduce other compounds while it is being oxidized
tripeptide of glutathione
Glu Cys Gly; Cys contains S so can possibly form disulfide bond
tripeptide form hypothalamus, stimulates pituitary
thyrotropin-releasing hormone (TRH)
pain neurotransmitter; 11 AA peptide in gut, SC and brain
vasodilating; derived form proteolytic cleavage
kinins (bradykinin and kallidin)
analgesic action like opiates
3 types of opiopeptides are?
Leu and Met are part of which sub-group?
30 AA polypeptide derived from lipotropin about 60x stronger than opium
an opiopeptide in the SC
specific amino acid sequence
in primary structure:
connected by ___ bond (covalent amide bond) which can be hydrolyzed by ___ or boiling
dictated by ___ in genes
dictates subsequent ___
peptide; proteases; codons; organization
4 types of secondary structure
beta pleated sheet
alpha helix and beta pleated sheet are examples of ___ bonding
3 steps of collagen synthesis
1.translation of mRNA into pro-alpha chain in fibroblasts
2.hydroxylation of pro-alpha chains
proline by prolyl hydroxyls
lysine by lysyl hydroxylase
3.three hydroxylated pro-alpha-chains H-bond to form pro-collagen (hydroxyproline, hydroxylysine, glycine)
4. secretion of pro collagen out of cell by exocytosis
5. cleavage of N and C-terminal segments by procollagne peptidases -->tropocollagens
6. oxidation of some lysine's to lysyl aldehydes by lysyl oxidase
both reactions in the collagen synthesis 2nd step require which 3 components?
vit C, iron, O2
genetic mutation where Gly is replaced by Cys; easy bone bending and fracture, humpback (twisted spine); delayed wound healing
step 6 of collagen synthesis requires which 3 components?
Cu, vit B6, O2
re: step 6 of collagen synthesis, the ___ functional group leads to cross linking of tropocollagen-->collagen fibrils (the ___ structure)
due to deficiency of lysyl oxidase; deformed spine; bone demineralization; joint dislocation; aortic aneurysms
protein classification based on which 4 factors?
which 4 contractile proteins are resp. for contraction & relaxation?
actin, myosin, tropomyosin, troponins
globular actin polymerizes into actin ___
G-actin =? F-actin=?
globular actin; actin filaments
f-actin is wrapped with a dimer of rope-shaped ___ and is attached by ___ troponins-->thin filament of the ___
tropomyosin; 3; sarcomere
___ is the thick filament
found in lung, large aa., skin and other CT
many random coils (2 degree structure) --> elasticity and extensibility
pralines are hydroxylated (as in collagen)
some lysine's oxidized to aldehydes (as in collagen)
___ formed from condensation of ___ lysine aldehydes plus ___ unmodified lysine-->marker of elastin metabolism/turnover (i.e. emphysema); comes out of ___
desmosine; 3; 1; urine
due to lack of ATP; actin cannot be released; the actin-myosin complex remains contractd
whenever you see ATP there's going to be ___ involved
albumins are ___, e.g. serum albumin
globulins are ___ ___ solutions with low water solubility, e.g. antibodies
glutelins are ___ or ___ soluble, e.g. gluten
basic proteins are ___ or ___ soluble, e.g. histones
water-soluble; dilute salt; acid or base; acid or salt
most proteins, when classified according to shape, belong to this class
elongated proteins, generally structural e.g. actin, myosin, collagen, elastin, keratin, etc.
no attachment of non-protein component
apoprotein + prosthetic group
conjugated (complex) proteins
5 conjugated proteins
hemo Hb, cytochromes
glyco antibodies, glycophorin
lipo chylomicrons, LDL, HDL, VLDL
metallo some hemoproteins (Fe), IGFBP-5 protease
9 types of proteins based on function
enzymes; structural proteins; contraction; transport; hormones; protection; storage; receptor; cross-membrane transporter
2 protein sub-classifications based on conjugation
simple & conjugated
2 sub-classes of protein based on shape
globular & fibrous