quiz 1.1 intro to proteins Flashcards
bonds affected by water
ionic
hydrogen
bonds not affected by water
covalent
van der vaals
electrons per sheel
2-8-8-18
atomic numbers of H, C, N, O
1-6-7-8
unequal sharing of electrons
polar
____________ accounts for 70% of cell’s weight
water
which are nonpolar and unreactive?
carbon carbon
carbon hydrogen
carbon ocygen
carbon nitrogen?
C-C
C-H
which are polar and more reactive
carbon carbon
carbon hydrogen
carbon ocygen
carbon nitrogen?
C-O
C-N
identify the functional group
C = O nonterminal
ketone
identify the functional group
OH - C = O
carboxylic acid
identify the functional group
O=C-O-C=O
acid anhydride
identify the functional group
-OH
alcohol
identify the functional group
O=C-H
aldehyde
identify the functional group
-SH
sulfhydryl
identify the functional group
S-S
disulfide
identify the functional group
-NH2
amino
identify the functional group
N with three methyls attached
quaternary amine
identify the functional group
O=C-O
ester
identify the functional group
O=C-S
thioester
identify the functional group
O=C-NH
amide
phases in subcellular fractionation
extraction/cell disruprion
homogenization
centrifugation
phase that aims to get maximum disruption of cell and minimal subcelllar damage
extration/cell disruption
resulting suspension is a cell free system containing intact organells known as
homogenate
cells disrupted will be liberated into the _____
sucrose solution
layers after 3rd phase of fractionation
nuclear fraction
mitochondrial
microsomal
soluble fraction
included in mitochondrial fraction of centrifugate
mitochondria
chlorophyll
lysosomes
peroxisome
included in microsomal fraction of centrifugate
ER
ribosomes
plasma membrane
included in the soluble fraction of centrifugate
cytoplasm
used in the assessment of purity after fractionatiojn
marker molecules
marker molecule for sample of nucleus
DNA
marker molecule for sample of mitochondrion
glutamic dehydrogenase
marker molecule for sample of ribosomes
high content of RNA
marker molecule for sample of endoplasmic reticulum
G6P
marker molecule for sample of lysosomes
ACP
marker molecule for sample of plasma membrane
Na-K ATPase
5’-nucleotidase
marker molecule for sample of golgi apparatus
galactosyl transferase
marker molecule for sample of peroxisomes
catalse
uric acid oxidase
marker molecule for sample of cytoskeleton
none
marker molecule for sample of cytosol
lactate dehydrogenase
difference of aldehyde and ketone
aldehyde @ C1 (terminal)
ketone @ C2
suffix for aldoses
-ose
suffix for ketoses
-lose
aldoses that are hexose
glucose
galactose
mannose
ketoses that are hexose
fructose
sucrose is formed by
glucose + fructose
lactose is formed by
glucose + galactose
maltose is formed by
glucose + glucose
an example of trisacch
raffinose
composed of 2-10 saccharides
oligosacch
made up of more than 10 sacchs
polysacch
shows sugars in their open chain form
Fischer projection
three variations of Fischer projection
convetional
linear
zigzag
formed when the hydroxyl group attacks the carbonyl group
cyclic structure
which cyclic structure is more stable
boat and chair
as a rule in Haworth, hydroxyl on the right are ____ on the rings
down
shown in a way that the bonds nearest are bold and thickened and the hydroxyls are either up and down
haworth
how are cycic structures formed
when hydroxyl attacks carbonyl group
when alcohol adds to an aldehyde the results is called
hemiacetal
when an alcohol adds to a ketone the result is called
hemiketal
in the presence of an acid, another alcohol group can add to hemiacetal or hemiketal to form
ketal or acetal
refers to a six membered ring consisting of _____ and _______
pyranose; 5 C and 1 O
refers to a five mmbered ring consisting of ___ and ____
furanose; 4 C and 1 O
most important monosacchs
5 and 6-carbon
means having four diff groups attached to it
chiral/asymmetric carbon
properties if monosacchs
chirality stereoisomerism optical activity mutarotation reducing properties
having same functional groups and connectivity but differ in arrangments of atoms and bonds in space
stereoisomers
number of possible stereoisomers depend on
number of chiral carbons (2 raised to n)
stereoisomers that are mirror images
enantiomers/ D and L isomer
said to be D form when OH at penultimate carbon is _____
at the right
____ are naturally occuring sugars
D-sugars
stereosiomers that are not mirror images
diastereomers
diastereomers that differ at only one specific carbon
epimers
are D-glucose and D-galastose epimers?
yes
are D-galactose and D-mannose epimers?
no
monosacchs that differ in configuration only around the carbonyl group that has undergone attack
anomers/ alpha beta isomers
pnemonics ng alpha beta isomers
dra. lab
2 isomers have the same struc. formula but differ in carbonyl groyp
aldose-ketose isomerism
percentage of carbon-oxygen-hydrogen
50-20-10
percentage of nitrogen-calcium-phosphorus
8.5-4-2.5
ability to rotate plane polarized light to the right or left
optical activity
two types of optical activity
dextrorotatory and levorotatory
the angle of rotation in optical activity is measured by
polarimeter
optical actiity of gluose and fructose
+52.5
-91
result from spontaneous change of alpha to beta forms and vice versa
mutarotation
mutarotation is commonly seen in
freshly prepared solution
this is the carbon attacked by hydroxyl
anomer
what confers or how is reducing property conferred to a monosacch
if hydroxyl group in anomer is not linked to another compound
what are the derivatives of monosacc
glucose fam amino sugar deoxysugars acidic sugars sugar alcohols sugar phosphate
part of the glycolysis and pentose phosphate pathway
glucose-6-phosphate
commonly used for osteoarthritis
glucosamine
found in peptidoglycans of bacterial cell walls
N-acetylmuramic acid
allows virus to enter
sialic acid/n-acetylmuraminic acid
sugars that have had a hydroxyl group replaced by a hydrogen atom
deoxyribose
monosacchs with a carboxyl group (-COOH)
sugar acids
example of sugar acids
aldonic acid
ulosonic acid
uronic acid
aldaric acid
sugars that contain hydroxyl group in place of a carbonyl group
sugar alcohols
an osmotic diuretic to reduce cerebral edema
mannitol
accumulates in the lenses of diabetic patients and causes cataracts
sorbitol
type of covalent bond that joins a carb group with another that may or may not be a carb
glycosidic bond
types of glycosidic bond based on anomeric hydroxyl group
alpha
beta
sweetest artificial
aspartane
standard sugar
sucrose
sweetest natural sugar
fructose
bond of lactose
beta 1-4
bond of maltose
alpha 1-4
bond of sucrose
alpha 1-2
an essentialy linear homo polysacch
amylose
highly branched homo polysacc
amylopectin
occurence of branches in amylopectin every
24-30 glucose units
bond of amylose
alpha 1-4
bonds of amylopectin
alpha 1-4; alpha 1-6 at branches
polysaccg ore branched than amylopectin
glycogen
occurence of branches in glycogen
every 8-12
material in plant cell wall that provides strength and rigidity
cellulose
major form of storage carb in plants
starch
major form of storage carb in animal
glycogen
glycogen with an alternating above and below of CH2OH
cellulose
used in glomerular filtration rate
fructans
found in fungi, considered a derivative of cellulose
chitin
difference of proteoglycans and glycoproteins
proteoglycan: carb > protein
glycoprotein: protein > carb
formed by the repetition of a disacch unit of an amino sugar and a sugar acid
GAGs
lubricant in the synovial fluid, consistency to vitreous humor, tensile strength and elasticity of cartilages and tendons
hyaluronic acid
tensile strength and elasticity of cartilages, ligaments, tendons, walls of aorta
chondroitin sulfate
found in cornea, cartilage, hair and nails
keratan sulfate
an anticoagulant
heparin
two ways carbos are linked to rpoteins
o-link
n-link
o-link when carbo are attached ti hydroxyl side chains of __________
serine
threonine
hydroxylysine residues
n-link when carbo are attched to amide nitrogen of _______
asparagine residues
extracelular matrix protein or integral transmembrane
proteoglycans
glycoconjugate only found in bacterial cell wall
peptidoglycan/murein
murein contains _____ and not proteins
oligopeptides
what are the components in a ‘peptidoglycan”
peptido: tetrapeptide and pentaglycine
glycan: NAG and NAM
covanlently bound to peptidoglycans of bacte
teichoic acid
what is the tetrapeptide bridge of gram pos bacte
L ala - D glu - L lys - D ala
an intrinsic membrane protein of the outer cell wall that attaches to the peptidogkycan layer in gram neg
Braun lipoprotein
determines the antigenicity of bacte
LPS
protein word first coined by
Mulder, 1838
“____ dictates ____”
structure dictates function
two function of proteins
dynamic
structural
the form found in most proteins
L form
form found in bacteria cell wall and some antibiotics
D form
amino acids exist as _________ in solution
zwitterion
essential amino acids
PVT TIM HALL
phenylalanine
valine
theronine
tyrosine
isoleucine
methionine
histidine
arginine
lysine
leucine
amino acid essential only to infants not adults
arginine
considered the 21st amino acid
selenocysteine
a structural analog of cysteine
selenocysteine
considered the 22nd amino acid
1-pyrorolysine
found in freshwater microbe, translated using the stop codon
1-pyrrolysine
AA with the phenol ring
phenylalanine
AA witht he phenolic group
tyrosine
AA with the indole ring
tryptophan
AA with the thioether group
methionine
AA with the sulfhydryl group
cysteine
AA with the guanidine group
arginine
AA with the imidazole group
histidine
AA with the amide group
asparagine
a test that produces polypeptide with one less amino acid that the original
Sangers DFNB
end product in ninhydrin test
Ruhemann’s purple
peptide bonds are seen in what parts
amino and carboxyl group
allowa the measurement of carboxyl groups
Sorensen’s titration
test for quantitative amino groups in proteins based on nitrogen gas released
Van Syke’s
tests/ rxns for R group that produce red product
Sakaguchi
nitroprusside
Sullivans
bond between alpha carbon and carbonyl carbon atom
psi bond
bond between alpha carbon and nitrogen
phi bond
in the amide plane of amino acids, H and O are always in ____
trans configuration
what is the repeating backbone of polypeptide chains
Calpha-C-N-Calpha-C-N
short segments of amino acids that serve to reverse the direction
bends
regions containing beyond the inimum number necessary to connect adjacent regions of econdary structures
loops
left handed helical strands are wound into a super coiled triple helix, preventing alpha or beta configs
collagen helix
the fundamental functional and three dimensional structural units are called
domains
aids in the final folding of proteins
heat shock proteins or chaperones
each chain in protein is (quaternary) called a
subunit/component/domain
the pKa of -COOH
~2 (greater acidity)
the pKa of -NH3
~9-10 (lesser acidity)
in neutrAL SOLUTION, PkA OF AMINO GROUP IS ______ TO CARBOXYLIC
greater
if pH > pI, amino acid is
negative
if pH
psotive
the loss of native conformation
denaturation
what is retaine in denaturation
primary strucure only
in this denaturation process, solubility is dependent on
salt conc.
increase the solubility by adding salt at ___
low conc
rapid technique for conc of proteins and removal os small contaminant
ultrafilt.
in gel filtration, which are eluted first
larger molecules
method that uses anion or cation exchange
ion exchange chrom
aka molecular sieving
column gel filtration
denaturating agent used in SDS PAGE
sodium dodecyl sulfate
bands in PAGE are visulaized using
Coomasie blue
in SDS PAGE, which are eluted first
smaller molecules
