Carbohydrates common sugars

Defintion: (C)m(H2O)n

Fischer projection to ring structure conversion:

MECHANISM: 1. Draw the backbone:
nb orbitals on alcohol 5 or 6 sugar (minimize C/C
attacks the pi* orbitals clashes, syn-pent interactions,
of the carbonyl chair conformations)
2. Number carbons:
+H+, -H+ start with anomeric carbon

3. Assign D or L:
D: furthest Carbon goes up
L: furthest Carbon goes down
+H+, -H+
4. Assign α or β:
α: OH OPPOSITE as furthest carbon
β: OH SAME as furthest carbon
preferred preferred
by ketose
5. Remaining carbons:
by aldose
OH left: OH UP
pyrannose furanose OH right: OH DOWN

6. 3D conformation:
6C adopt CHAIR conformation.
maximize # of equatoriaol
f(x) groups
***preferred*** bind
hemoglobin
can adopt (A1C)
stereogenicity
(R or S)

each stereogenic center is OPPOSITE

of the other in the mirror image
Carbohydrates carbohydrates attached to proteins
glycoproteins mostly protein by weight
reducing sugars:

proper secretion
indicative of
healthy cells

monosaccharides are versatile and form polymers

join to alcohols join to amino acids

Join to phosphate groups >> STORE ENERGY proteoglycans mostly carbohydrate by weight

water bind
to CS and KS

forms cushion
structural roless
ECM for cartilage >> Keratin + Aggrecan

monosaccharides form polysaccharides

glycosidic linkages exist

ONLY on the ANOMERIC
carbon (C1) mucins (glycoprotein) form mucus

anything else is just

an ETHER

common polysaccharides
STARCH
Starch = same as glycogen EXCEPT
contains either:
Amylose = only alpha-1,4
linkages and is linear
Amylopectin = mostly alpha-1,4,
but 1/30 residues contain glycosolation
alpha-1,6 so branches, but less occurs in ER
so than glycogen
sandwhich structure make
GLYCOGEN it harder to digest; need
every 1 in 10 sugars >>
cellulase (microorganisms) easier for enzymes to
alpha 1-6 linkages,
interact with (curved)
leading to branching

amylose

amylopectin
Cellobiose >> Glucose
beta 1,4 Glucose.
ALPHA linkages: OH opposite
Important!!! beta-1,4
side of CH2OH (C1)
polymer of glucose is
cellulose (not digestible BETA linkages: OH same side of
by higher animals) CH2OH (C1)
Carbohydrates

aldoses

sugars you should know

ketoses
Lipids palmitate (16 C)
n-hexadecanoate
membrane features: CH3(Ch2)14COO-
form compartments
form bilayers stearate (18 C)
form due to hydrophobic effect
n-octadecanoate
proteins have specific functions
asymmetrical (external face diff. from
CH3(Ch2)16COO-
internal face)
fluid
palmitoleate (16 C)
electrically polarized
know cis-∆9-hexadecenoate
fatty acids: CH3(Ch2)5CH=CH(CH2)7COO-
these ω-7 family
STRUCTURE:
Hydrocarbons but OXIDIZED! lipids
have a carboxyl group
saturation: maximum # of hydrogens?
NOMENCLATURE:
oleate (18 C)
[# carbons] : [ # of double bond]
cis-∆9-hexadecenoate
CH3(Ch2)7CH=CH(CH2)7COO-
omega (ω): carbon at methyl end
ω-9 family
alpha (ɑ): 1 C away from carboxyl
beta (β): 2 C away from carboxyl
∆ [# of carbons away from carboxyl group]

omega (ω): double bond position

# of carbons from methyl end
ω [# of carbons away from carboxyl group]

Example:
ω-6 family
[n + 6]: ∆ [1 + n + 2]
ω-3 family

[stereochem]-[ ][#],[ ][#]-[#carbons] linoleate (18 C)

[#bond type][bond type][oate] cis, cis-∆9,∆12-octadecadienoate
CH3(Ch2)7CH=CH(CH2)7COO-
Example#1:
ω-3 family
cis

arachidonate (18 C)
ω-6 family
cis,cis,cis- all-cis-∆5,∆8,∆11,∆14-
cis cis
∆9,∆12,∆15- eicosatetraenoate
octodecatrienoate
linolenate CH3(Ch2)4(CH=CHCH2)4(CH2)2COO-
phospholipids
components:
Membrane Lipids named after Sphinx in
Egypt by Johann Ludwig
Thudichum in 1884
(homie found it
1. platform/tether: perplexing)
a. glycerol of sphingosine
2. fatty acids in charge of membrane fluidity
3. phosphate
4. alcohol (connected to phosphate) lecithin imposter

cholesterol

phosphatidyl lipid
ceramide (found in beauty cream)
simplest
phosphogylceride
gangliosides:
fatty acids
branched
esterified to C1 chains with up
and C2 to 7 sugars

found in membranes of mitochondria

(prevalent in the heart)

most
abundant
in
Phosphatidylglycerol
eukaryotic
membranes

lecithin

prevalent in
prokaryotic
membranes
important in eukaryotic signaling
fatty acids
branched!

fatty acids
ETHERIFIED to C2
and C3
phospholipids are Membrane Lipids
amphipathic
fatty acids form:
phosphilipids
to prevent soap
traingular/rect- interaction
property
angular, so form: with water,
close in and
form:

no strength

Soaps: traditionally made

soaponfication rxn: by boiling animal fat (e.g.,
beef tallow) in lye (NaOH).

Salts with Na+ or K+ are

soluble in water, but Mg2+
or Ca2+ soaps precipitate
forming “scum”.

“hard water” >> difficulty washing

cuz low solubility of salts
solve this problem with
“water softeners” that
SOAP remove the Mg2+ and Ca2+
Soaps solubilize oil, cells, and dirt in from the water.
micelles: cheap and easy to make.

Na dodecylsulfate (SDS):
used in laundry
invented to mitigate the hard water problem detergents to food
common detergents: branched additivies
(discontinuted, not biodegradable) and
linear akylbenzenesulfonates that
resist binding Mg2+ and Ca2+

Sodium triphosphate: Na-EDTA

measure how much
chelating agent (sequester metals) (ethylenediaminetetraacetic acid)
of a subtstance
BANNED! promote algal growth in sequesters heavy metals: Ca2+, Mg2+, Fe2+, Cs+
crosses the plasma
wastewaters > deplete oxygen safer chelator membrane over
time
great for drug delivery (small uncharged gr
moklecules great
permeabilty)

also great for drug delivery

 common RE Nucleic Acid
Methods

palindromic!
f(x) of enzymes: provide a
primitive immune system
against invading viruses.
bacterial RE sites methylated >>
prevent cleavage

polymorphisms: genetic variation

PCR:
restriction fragment length polymorphisms
Denaturation (72)
(RFLP): change the length of the gene!
Annealing (60)
Elongation (98)

clone 25kb fragments

deletion! insertion!

cloning of eukaryotic genes in

prokaryotes: RNA transcript >> Reverse
Transcriptase >>> cDNA >> insert
 CH10 assess: how
ortho: same f(x)
random is this
diff species Sequence
alignment alignment?
para: similar DEFAULT:
structure match: + 10
SAME species gap: -25

homologs!

(sequester oxygen
in root nodules >>
improve N2
fixation)

Different functions
BUT very similar
structures!

100% correspondence >> synteny

folds very different
evolutionary relationship not
1) similar active guaranteed!
site (His-Ser-Asp)
spatial
arrangement
2) similar
mechanism
3) cut peptide
bonds
sweet bitter umami
smell
vision (rhodopsin)