Biochemistry Notes

By: Aldo Voto

Chapter
what is biochemistry ?
↳ bio Chem is the chemical
of
study the molecules and the

reactions of life

Example of a model organism

:

↳ E. coli da yeast

the work done

species can lot about
on one
say a

the other
species
processes s occurring in

ThetwomajorbreakthroughsinbiochoIDEnzyme.es
were noted catalyst to
as
-
biochemical reactions

e) Nucleic acids as
genetic material
↳ central : information
dogma flow of

. DNA → RNA →
proteins

it , C. N , O , P s
six major elements in bio : ,

what are
biopolymers ?
↳
macromolecules created
by organic molecules
or monomers ;
through condensation dehydration reactions

what is the difference b/w bio polymer and monomers

↳ polymers have directionality : one end is

chemically different than the other

polymers have distinct eg DNA store info nucleotides cannot

properties i . can
,
triply polysaccharides , poly nucleotides 4 polypeptides
topos store info
geneticacids in nucleotide sequence
-
monomers i Nucleic acids → nucleotides of nucleic
*

guanine cytosine thy min ( uracil

o
polymer : DNA , RNA ↳ adenine
, , ,

structureofnvcleotide.gs
phosphate
aromatic
↳ purines
G double
base : N
o-
containing
-

pyrimidine
↳
- ring single
group
5 carbon
.mg
-
sugar
adenine
purines : ,
guanine
pyrimidines
:
cytosine thymine,

StructureofAT

→ high in potential energy adenine base

,

gamma phosphoryl
Y -

B beta phosphoryl
-

bond

y p a
→ lyocidic
→
sugar

what are nucleic acids ?

↳ of linked 3 's 5
'

polymers nucleotides
by a
phosphodiester bond
' '

Directionality of
poly nucleotides
: 5 phosphategroup 4 3
hydroxyl
H
, it
-
group
Y
⇐T it adenine
1¥
H N
 '
5

phosphodiester
/ linkage

-
-

phosphate group → ribose or

linked to CS of
p
3
' deoxyribose
of next nucleotide
sugar

How does the structure of DNA relate to its function ?

↳ due to its form .
it is able to replicate ,
store
genetic information
and undergo sequence specific interactions with proteins

and double stranded will prevent

base
pairing errors in the sequence
•

Proteins
polymer -

proteins
-
all amino acids

are chiral , except

acids for
monomer -
amino
glycine
• condensation reactions
↳ bonds
peptide
I
aminoacidstruc.tv#

why is the
primary structure so
important ?
determines the
folding of polypeptides and thus its shape The protein's
-

, .

function is determined by its 3-D structure .

Why proper conformation important ?

is

Most proteins are enzymes and contain an active site where chemical

reactions takes place .

If not folded properly , protein loses its

conformation and substrates would not be able to bind .

The protein
would unable to its function
be
undergo
.
How can protein misfolding cause diseases ?
Misfolding alters the proteins properties ,
in most cases making them

wrong folded proteins

insoluble . This can cause accumulation of
and cause
neurological issues; in the case of Alzheimers .

Carbohydrates
what are 3 functions of carbohydrates ?
↳ involved in
storage of
provide structure ( cellulose) and are
energy ,

involved in metabolism as intermediates .

StofD :

I ✓
H

Hl_ OH

H0/-
H

HT
-
H

OH

OH

CHZOH

FormationofD-gluc with
.

hydroxyl group opposite

tide : respect to CHZOH

hydroxyl same direction

group
B-glycosidc.ci as CHZOH

structural polymer : cellulose

storage polymer : starch

, glycogen

>

joined by glycosidic bonds

 How does glycosidic linkage allow for starch fwnct ?
and
glycogen carry
its
↳ Cassio really
o
1,6 y glycosidic linkage will allow
a - - for
branching to occur

for of
which
packing together increases surface
more area
storage energy
se → structural
polymer → p -

1,4 -

glycosidic repeating
Compare and contrast the structure 4 function of different carbohydrate
polymers

oe-as.%4a-n.GL?9.sj dic/B-t4glyaosidic
T
Starch Glycogen Cellulose

Fass! :L
"

storage polymer storage polymer structural

polymer
"
. '

allow allow
glycosidic linkage glycosidic linkage glycosidic linkage allows it
•

branching
for
energy storage
to increase S.a .

yo
branching
for
energy storage
to increase S.a

g.
to be linear stack ,

and allow more H bonds -

together
(stronger)

Lipids → cnuaeic ) acids

'

How do lipids differ from proteins ,

n a
,
and
.
carbohydrates ?

↳ unlike the other macromolecules

, lipids do not form
polymers ,
but instead
aggregates
L-pidcharacen.sc :D hydrophobic (insoluble in )
Hzo
2) soluble in non -

polar solvents

3) some are
amphipathic

Lipids:D energy storage

2) membrane structure → insolubility di flexibility
3) involved transmission
in
signal

Cleassesoflipids fatty : acids

, triglycerides , phospholipids (phosphoglycerides )
How do
phospholipids interact in aqueous solution ?
↳ they spontaneously form micelles or bilayers; the hydrophilic heads face
the aqueous environment and hydrophobic portion face hydrophobic environ .
Functionality: 1) act as a barrier
separating inside components
from outside environment

2) impermeable to most water soluble

compounds

3) provides flexibility
•
The basic features of all cells include a plasma membrane ,
cytosol ,

chromosomes
containing genes
and ribosomes which assist in
making
proteins .

The
-
cell
'
ribosomal RNA synthesis occurs in the nucleolus

a
chromatin is made up of DNA and proteins ( histones)

•
3 locations for protein processing
:
DRER 2) golgi 3) cytoplasm
•
Both mitochondria and chloroplasts have their own ribosomes 4 DNA

that
peroxisomes metabolic compartments containing specialized enzymes

break reactive into H2O

down
oxygen species 4 oxygen

?
why is the
cytoskeleton also considered an
organelle
↳ cytoskeleton is an
organelle as it is membrane -
bound
Chapter c
T

÷÷÷÷÷÷÷÷÷÷÷:i÷÷÷:
•
V -

shape molecule

polar ( electronegativity of
Oxygen)

n .

t:÷÷÷÷¥÷÷
-
-
tetrahedron

Hydrogen hence
why AHF kjfmol
•

bonding
releases
for
energy ,
e -
20 ,
as
you
H -
bondsenergy is
being released
How would
energy
of a covalent bond compare to a
hydrogen bond ?

↳ the
energy of a covalent bond would be
greater than a
hydrogen bond

1..is?eIth/.initssolidfGoms4hydNgmbonds
water can form
• 4 H bonds -

Heieabnnndesga atoms 775.17

Know how to draw

Why does ice float ?

its solid form the volume
hydrogen bondsthe
form in increases ;
↳ as water 4 ,
and as the volume increases ,
density decreases
D=
MVT
Difference b/w cohesion & adhesion

↳ cohesion type
is the
adhesion is molecules of different
tendency
of molecules of the same to stick
together and
types sticking together
*
high a
cohesion
lot of
=
high is
surface
required
tension
to break H bonds and lot of
energy energy
↳
-
a

is released when H -
bonds form

what is the difference b/w heat 4 temp ? .

↳ heat is the amount of

energy
associated w/ movement of atoms , temperature
measures the
intensity of heat .

What enables water to be an excellent solvent ?

↳ due to its
polarity water forms ,
a
hydration sphere around the solute ;
ionic compounds dissolve water in

ie .

glucose can form H - bonds w/ H2O due to its OH

groups

Explain the hydrophobic effect

↳ water molecules
tend
non -

to
polar molecules
associate w/
aggregate rather
each together
other
,
than
due
with
to
non -

polar molecules
surrounding them

Non-covalentinterac.to#

charge charge ofinteractions

-

covalent
: electrostatic interactions b/w two
charged particles
↳ 1) strongest
non interactions

2) bridges ( opposite charge groups)

H2o but salt
charge charge interactions
weakens -

contribute to
stability of hydrophobic interior
site has interactions
enzyme active
charge charge
-

Hydrogen bonds i electrostatic interaction

↳ denaturation is the disruption of intramolecular H - bonds → altered structure

Van der Waals : attraction b/w nuclei of an atom and e- of adjacent atoms .

of
Also, repulsion e- b/w adjacent atoms

↳
.

weaker than H -
bonds
Hydrophobic interactions
solution
aqueous
relatively
:
nonpolar groups associating together in

↳ of system
thermodynamic stability :
increase in
entropy ; minimizing number of
ordered hydrophobic portion
molecules
water
surrounding

strategies for
maintains osmo
regulation !

1) polymerizing monomers into macromolecules → decrease Csolute]

2) plant cells have cell walls and vacuoles which
pump water out

pI : pH at which a molecule or surface carries no electric charge

zwitterion : both
neutral molecule
containing positive and
negative charge
Chapters
R varies b/w amino
group
-
-

General structure acids

>
of amino acid -

properties of side chains influence

the conformation of
protein

AlipathicR-grou# → non - aromatic

hydrocarbons

Glycine ② ly G) Alanine (Ala AT Valine [Val V]

H H It
① ①
Hz IN - L - COOH Hsiu -
d
l
- c - OH Hz - I - coat
l l
CH
H 3 CH
' t
not chiral carbon -
no reactive functional c c#
-
µ z
- ,
-
H side chain
go p functional
- no reactive

group

Leucine dev ,
L] Isoleucine file I]
,
Proline ④ no
, ]
P

H H

Hz
⑦ I ① I
COOH
Hz N OH COO H Hg N c
-

- C -
c
- - -

kHz l
H
l l
Hsc g y
-

da
-

l \ cHz
l
Hsc C
Hz C Hz
- no reactive functional - has 2 chiral C's

group
-
absorb UV @ 280mm

A-romaticR-g.ro# containing Trp higher absorption to

-

→ due delocalize
ring e
-

Phenylalanine Phd Tyrosine Cyr Y] , Tryptophan p, W ]

Hsiu -
I -
coat Hsiu -
tic - coat
Hs
-
E -
coo H

l l l
Hz C H2
c

l
C
Hz
l l
X A ¥7
Ex ¥4
-

it

Tpoig p
-
has a benzene
. :

less hydrophobic
than Phe
 Sulphurcontainingivethininec Met, ]
M Cysteine( Cys ,
C)
H H
① I ⑤ I

HzN -
C - COOH HSN -
C - COOH
l l
CHZ
C
Hz I
(
SH
Hz
{
S -
more nucleophilic than methionine
1
(
Hz
forms disulfide
bridges
-

CHS
bulky
-

AlcoholR-goupsserinecser.SI Threonine Ehr , ]

T
H It

⑦ I ① I
coat COOH
HzN c -

HzN C
-
- -

l l
Chez H -
C - OH
I 1
OH
( Hz

AcidicR-groups-A-spartale-CAsp.to ] Glutamate u
,
E] Asparagine n
, ]
N

tic
H

Hsiu -
d -
coo
-0
Hs -
tic -
coo
-0 Hsiu -
-
coo -0

l l l
Chez cHz CHZ
l l
l
( 00-0 che y o
too -0 HCN

Glutamine @In ,
Histidine
'

I HIN I
-0
cool
-
-

Hs - -
coo
I
C Hz
C
Hz
l l
'

Hz
'

c. N

I µ -1
C H
1 To
HZN
 ✓ scale
Hydropathy
Corelative hydrophobicity

⑦ requires energy isoleucine 3. I Kj moi!

having it
: we notice
Ile the hydrophobic environment requires
- since likes
, energy
to move it to water
y

→ these
regions mostly composed of

hydrophobic amino acids

what post translational modifications →

are chemical modifications
happening
to a a 's

after translation
protein

↳
↳ eg hydroxy proline hydroxy lysine, thyroxine
.

these chemical activities

modifications
derived from
can
produce compounds with other

eg GABA glutamate
.
→

its back bone COO rid of -0

loses
getting charge
→
,

Peptidebonds

§aryce
linked
: linear sequence
of amino acids

by dehydrationreactions : t -

carboxyl group of one amino acid

,
with
£ amino of another
group
-

Peptide bond has partial double bond characteristic

what prevents free rotation around the bond ?

↳ e- delocalization 4 characteristic
partial double bend

→
rotation allowed around N -
ca and each co -
C bond

to hindrance
* trans conformation preferred due steric
Analyticaltechniques
→ first step
Protein Purification : determine structure crystals
primary ,
mate to determine

§n
3 -
D structure

detect
protein
assayiyge.es#qepnoper+y
of that to its in
presence

↳ eg .
enzyme → track disappearance of substrate or appearance of
products

step: prepare solution of proteins →

homogenizer ; this will
disrupt cells

step fractionation → crude

separation of
homogenates into fractions

↳ differential
↳ salting centrifugation (separate
method that
on mass
,
density
of
)
protein solubility
purification makes use
out :

*
salting
out followed
by dialysis

steps : column
chromatography
→ filled with insoluble matrix
with matrix
↳ rate at which
proteins elude depend on its interaction

→ ring
struckres
The fractions can be quantified
using (
A 280 absorbance of
light
not contain these ads
* the problem with this is that some proteins might .

followed
* column
chromatography by protein assay
Gel filtration separates proteins based
chromatography on size
-

↳ small proteins become trapped in

pores
of beads →
large proteins
elude first

ton exchange chromatography proteins will interact with

positively charged
-

bead (anion exchanger) or negatively charged beads

(cation exchanger)
↳ electrostatic bound proteins M [salt]
via interactions * a re eluded
by
→
selective 4 specific 's
Affinity chromatography ; uses
properties of
protein
interactions
↳binding be antibody
ligand can other or
⇐electrophoresis -

separates proteins based on their

migration in an electric
field
↳ alkaline solution → mates all proteins anionic

PAGE →
separates on size and
charge
SDS PAGE →
separates based on size
only ( SDS denatures 4 adds ①
charge )
Determining amino acid composition of proteins :
: bonds
step 1 acid
hydrolysis breaks peptide
→

step 2 : bind each amino acid to PITC

step 3 :
separation of PTC -
amino acids
by chromatography ( HPLC)
will react of
4 absorb 280mm
↳ PITC w/ amino
group
aa 's allow ads to at

later

-17¥
will bind, elute
'
I * hydrophobic aa

He *
hydrophilic will elute faster
↳ N

column
hydrocarbon
chain
① allows absorbance

Why PITC →
② prevents reversible reactions
by blocking amino
group
¥noli reagent used to cleave disulfide bonds

i#ai that
prevents reformation of disulfide bonds
reagent
lproteasesdareagentsl IMPORTANT
bromide : cleaves peptide bonds at carbonyl side of methionine
cyanogen

trypsin : cleaves peptide bonds on

carbonyl side of lysine 4 arginine

S .
aureus V8 : cleaves peptide bonds on
carbonyl side of
glutamate 4 aspartate

chymotrypsin :
cleaves peptide bonds on carbonyl side of aromatic amino acids