Biochemistry 460/660

Lecture #2

Foundations of Biochemistry
Learning goals:
FUNCTIONAL GROUPS

Biochemistry: Unique Role of Carbon

30 Elements Essential for Life

Other than carbon, elements H, O, N, P, S are also

common
Metal ions (e.g., K+, Na+, Ca++, Mg++, Zn++, Fe++) play
important roles in metabolism

Biomolecules have several functional groups

Location of Functional Group is Important

The difference is
a hydroxygroup ( -OH ) on 2'C in RNAversus a single
proton ( -H)in DNA.

The extra -O- in

the ribose
backbone prevents
formation of stable
long double-helical
regions in RNA

Hydrocarbon Functional Groups

Hydrocarbon Functional GroupsNatural Uses (Amino Acids)

Common Aliphatic
Amino Acid
Functional GroupNonpolar GroupProvide a good core
(inside) of a protein
because they are
hydrophobic.

Functional
Groups
Methylation is a common
regulatory element for
Transcription and
Replication.

https://www.resverlogix.com/programs/rvx-208-moa/epigenetics/

cytosine and adenine, can be methylated

Hydrocarbon Functional GroupsNatural Uses

Common Aliphatic
Amino Acid Functional
GroupNonpolar GroupProvide a good core
(inside) of a protein
because of
hydrophobicity.

Hydrocarbon Functional GroupsBiotech/Biochem Uses

Phenyl Ring absorbs
UV light- foundation
for numerous
quantitative assays.

Hydrocarbon Functional GroupsBiotech Uses

Therapeutic
Applications
High-Throughput
Fragment Drug
Screening

http://pubs.rsc.org/en/content/chapterhtml/2015/9781782620938-00001?isbn=978-1-78262-093-8

Phosphate-Based Functional Groups

Phosphate Functional Groups-Natural Uses

High Energy Bonds

Phosphate Functional
Groups-Natural Uses
(Energy Transfer)

Phosphate Functional
Groups-Natural Uses
(Regulation)

https://www.researchgate.net/figure/236086700_fig3_Fig-3-N-terminal-and-C-terminal-tails-fl-ank-the-kinase-core-of-PKA-The-conserved-N

Phosphate Functional Groups

Natural Uses (Energy)

ATP: Chemical Currency of Energy

Oxygen Functional Groups

Oxygen Functional Groups

Natural Uses (Regulation)

Oxygen Functional Groups

Natural Uses (Bonds)

Oxygen Functional Groups

Natural Uses (Acidic Amino Acids)

Aceticacid,whichgivesvinegar
itssourtaste
FUNCTIONALPROPERTIES
Hasacidicpropertiesbecauseitis
asourceofhydrogenions.

Thecovalentbondbetween
oxygenandhydrogenissopolar
thathydrogenions(H+)tendto
dissociatereversibly;forexample,

Aceticacid

Acetateion

Incells,foundintheionicform,
whichiscalledacarboxylategroup.

Ethers
No -OH bonds
Not soluble in water
Anesthetics

Esters: sweet aromas and flavours

Sweet aroma in pineapples,

jasmine
Synthetic versions are very
common

Sulfur Functional Groups

Oxygen Functional Groups

Natural Uses (Acidic Amino Acids)

Carbon Functional Groups

Sulfur Functional Groups

Oxygen Functional Groups

Natural Uses (Acidic Amino Acids)

Nitrogen Functional Groups

Nitrogen Functional Groups

Natural Uses (Bonds)

Nitrogen Functional Groups

Natural Uses (Acidic Amino Acids)

Uses of Antibodies

Protein Story- IgG

What is an
antibody?
An antibody is a protein
produced by the immune
system to identify and
neutralize foreign
objects like bacteria and
viruses. Each antibody
recognizes a specific
antigen unique to its

Oxygen Functional Groups

Natural Uses (Acidic Amino Acids)

http://what-when-how.com/acp-medicine/adaptive-immunity-antigens-antibodies-and-t-cell-and-b-cell-receptors-part-1/

Antigen-Antibody interactions

Interactions between
biomolecules are specific

Interactions between
biomolecules are specific

Interactions between
biomolecules are specific
Macromolecules have unique binding
pockets
Only certain molecules fit in well and can
bind
Binding of chiral biomolecules is
stereospecific
FUNCTIONAL GROUPS PROVIDE THAT

Ag-Ab interactions
Bonds:

Hydrogen
Ionic
Hydrophobic
interactions
Van der Waals forces

Each bond is weak;

many are
strong
To hold they must be
close requiring
high amts of
complementarity!

Summary
In this Lecture, we learned:
To realize that the structure of
biomolecules often gives them
specific functions
To recognize important functional
groups and their applications

Fail Fast,
Succeed Faster!