OCHEM important molecules Flashcards
what is the difference between L and D amino acids?
they are enantiomers
how can you identify an L or D amino acid?
with all amino acids, we view them as a Fischer projection with the carboxylic acid on the top. If the amino group points to the LEFT it is then an L amino acid.
Fischer projection. horizontal lines are?
pointing out of page (bow tie)
what amino acid do animals have naturally?
L-amino acids
how do we orient carbohydrates in Fischer projections?
the most oxidized group goes on top –> typically CHO.
how do we assign L and D to carbohydrates?
we look at the Fischer projection. with the CHO group on top.
if the bottom most OH is pointing to the right: this is a D sugar
If the bottom most OH is pointing LEFT: this is an L sugar
what natural carbohydrate exists in animals?
D- sugars (think sugars are Delicious!!)
this opposes L-AA’s
t of f, +/1 system. R/S system, and D/L system are all different
true - ish
\+/- = optical activity R/S = absolute configuration D/L = similar concept as R/S with emphasis on the location of the stereocenter
list the ionizable amino acids
D E R K H Y (pka = 10) C (pka = 8)
what does the strecker synthesis produce?
a racemic mixture of L and D amino acids
what is the general mechanism for the strecker synthesis?
- react an aldehyde with an amine to form an imine
- HCN protonates the nitrogen of the imine making it positive
- CN- then nucleophilic attacks the carbonyl centre
- acid-catalyzed hydrolysis converts the nitrile to carboxylic acid
pg. 211
what is malonic ester synthesis?
another way to form amino acids. the use of phthalimide and malonic ester
still forms a racemic mixture
what is gel electrophoresis?
this separates molecules based on size or charge (and moves molecules based on charge)
i.e. a molecule is given a charge so that it will move in the gel with an electric field.
Often used for amino acids and nucleic acids
in peptide bond formation what is lost?
H2O!
t or f, a dipeptide is at higher energy than 2 lone AA’s
true! this explains the driving force of protein folding.
usually bonds are made since whats being made is favourable. that is not that case here.
what is DCC coupling?
we react incoming amino acids with DCC
(cyclohexane-n=c=n-cyclochexane).
the carboxylic acid attacks the delta positive C. then another AA attacks that AA’s carbonyl centre.
the normal backbone of a peptide goes
{N-C-C-N}-C-C-N etc.
explain the core bonds
draw it.
{N-C-C-N}
the C-C bond can rotate normally
the C-N bond cannot –> this is because the lone pair of e on the nitrogen delocalizes to form a resonance with the C=O bond. this makes it planar and rigid
hydrolysis of peptides are kinetically fast and thermodynamically favourable.
false
favourable yes –> since peptide energy is high
but they are slow!!
how do we number carbons in a simple sugar?
we give number 1 to the most oxidized carbon in the chain. typically the CHO carbon.
what is a pyranose and furanose?
these are cyclic sugars .
pyranose - 6 sugar ring
furanose - five sugar ring
how does a sugar cyclize?
when its penultimate carbon attacks the carbonyl group of the sugar creating a HEMI-ACETAL.
Can a cyclized sugar become linear again?
only when its anomeric carbon is in the hemi-acetal form. if it becomes an acetal, then it cannot be in equilibrium.
what is the difference between a alpha and beta sugar?
alpha and beta sugar depends on the face that the penultimate hydroxyl attacked.
if the cyclized sugars anomeric carbons hydroxyl is pointing up this is the beta config
if the cyclized sugars anomeric carbons hydroxyl is pointing down this is the alpha config
axial and equatorial have nothing to do with alpha and beta.
t or f, the alpha and beta forms of a sugar are anomers
true - these are sugar epimers where an epimer is where a diastereomer occurs in which only one stereo centre has an inverted config.
does the penultimate OH always have to attack the carbonyl centre in ring formation?
no. however, only 5 ring and 6 ring sugars will occur
what is a Haworth representation?
this is when a sugar is drawn as a ring and the bottom have of the ring is pointing out of page.
what is the bond that holds disaccharides together?
glycosidic linkage
is the sugars a hemiacetal or acetal once in a glycosidic linkage?
an acetal
what is the exception to the rule that humans cannot digest beta sugar linkages?
we contain lactase which can digest lactose which has a beta linkage. usually though, we cannot digest beta linkages as seen with cellbiose (cellulose monomer)
what is Benedict’s test?
assay to detect the carbonyl units of sugars.
can the Benedict’s test distinguish between hemi-acetals and acetals?
yes, b/c hemiacetals are in equilibrium with their carbonyl state unlike acetals which cannot mutarotate.
what is the general reaction behind Benedict’s test?
- an oxidized form of copper (Cu++) reacts with the aldehyde or ketone
- it oxidizes the ketone / aldehyde thereby being reduced itself
- the product is copper oxide (Cu2O) which is red
note: although typically when something gains oxygen content it has been oxidized, in the case of copper its actually been reduced from +2 –> +1
what are reducing sugars?
any sugar which gives a positive Benedict’s test since it reduced the copper reagent.
t or f, all monosaccharides are reducing sugars?
true, since they all contain an open form of an aldehyde or ketone
all hemiacetals, aldehydes, and ketones give positive tests
all acetals give negative tests
t or f, the anomeric carbon is #1 for aldoses but #2 for ketoses
true. aldose and ketose refers to aldehyde or ketone based.
note: the anomeric carbon is the carbon in a ring that was previously the carbonyl carbon in a linear form
how long is a fatty acid usually?
14-18 carbons but always an even amount of carbons
can a 17 carbon fatty acid exist in humans
no
how are fatty acids numbered?
starting with the carboxylic acid carbon
what is base catalyzed hydrolysis of triglyceride?
saponification which forms free fatty acids and glycerol
t or f, a detergent is a substance that can efficiently solubilize oils while remaining water soluble.
true, they are like soaps (micelles) but stronger
DP-G (phospholipids) are detergents
what is squalene used for?
this is a triterpene (6 isoprene units) and is used to manufacture steroids
how many isoprene units are in a monoterpene?
two (since if there was only one then its just isoprene, not terpene)
how many protons can phosphoric acid donate?
3
H3PO4 –> H2PO4- –> HPO4– –> PO4—
what is pyrophosphate?
P-O-P
this is called an anhydride linkage
t or f, ATP is an RNA precurser
true
explain the structure of ATP
starting from the left
3 phosphate groups joined by anhydride linkages. the final phosphate makes and ether bond with carbon number 5 of ribose (or deoxyribose which lacks the 2’OH group). then carbon 1 makes a bond with a nitrogen in the nitrogenous base.
what is ELISA?
enzyme linked immuno-sorbent assay (ELISA)
uses antigen-antibody interactions to find the presence of
- an antigen like proteins
- or specific antibodies
we see a color change
what is a radioimmunoassay (RA) ?
this is similar to ELISA except rather than using enzyme-linked antibodies which create a color change when detecting the antigen, we measure radioactivity
this can measure amount of hormones or drugs in blood
what are restriction endonuclease enzymes?
use these to cut pieces of DNA or RNA into smaller fragments
southern, northern, western, eastern blot?
Southern - DNA
Northern - RNA (t r’s in northern for RNA)
Western - Protein
Eastern - post-translational modification
t or f, restriction nucleases recognize palindromic sequences usually
true
what is PCR?
detects and amplifies DNA sequences
what is RT-PCR?
detects relative expression of sp. gene products. measures relative amount of mRNA’s
what is q-PCR?
product is both detected and quantified
what are the pKa’s for phosphoric acid
he three pKa values for phosphoric acid are 2.16, 7.21, and 12.32.
