Biochemistry Course

Ho Thien Hoang

8/2018
 The World of Elements

C N O

Na Mg P S

K Ca

Different kinds of atoms = elements

 Hydrogen
1 proton
1 electron

Oxygen
8 protons
8 neutrons
8 electrons

Proton + Neutron 0 Electron –

Most Common Elements in all life
forms
 Life requires ~25 chemical elements
• About 25 elements are essential for life
– Four elements make up 96% of living matter:
• carbon (C) • hydrogen (H)
• oxygen (O) • nitrogen (N)
– Four elements make up most of remaining 4%:
• phosphorus (P) • calcium (Ca)
• sulfur (S) • potassium (K)
4 Phân tử sinh học đa chức năng bao gồm?
 Proteine

Proteins play many roles, such as signal molecules, receptors for signal molecules
and enzymes, biological catalysts.
Protein’s Natural Form
Amino Acid Formation
Nucleic Acids are the Information Molecules of the Cell
Nucleotides are the building blocks of nucleic acids. There are two types of nucleic
acids:
•Deoxyribonucleic acid (DNA) consists of a double helix of polymers made up of
deoxyribose, phosphate, and four bases: A, G, C, and T. In the double helix, A pairs
with T, and G pairs with C.
•Ribonucleic acid (RNA) is a single-stranded polymer made up of ribose; phosphate ;
and the bases A, G, C and U.
Nucleic Acid Formation
Molecular energy
Cordycepin
 Lipid
• Lipids Are a Storage Form of Fuel and Serve As
a Barrier
• A key property of lipids is that they have
hydrophilic and hydrophobic properties. Lipids
form barriers, called membranes, that allow
compartmentalization.
• Lipids also function as fuel molecules and
signal molecules.
Phospholipid Formation
 Carbonhydrates
• Carbohydrates Are Fuels and Informational
Molecules
• Carbohydrates are an important fuel source.
Glucose is a common carbohydrate.
• Glucose is stored as glycogen in animals.
• Carbohydrates are also important signal
molecules, notably in cell-cell recognition.
Monosaccharides Combining
Học thuyết trung tâm
DNA Replicating
Construction of mRNA from DNA
Constructing Chromosomes
 -
Membrane Formation

WATER

Hydrophilic
head

Hydrophobic
tail

WATER
Representation of a Protobionts
Stanley Miller
LE 26-2
CH4
Water vapor
Electrode

Condenser

Cold
water

Cooled water
containing
organic
H2 O molecules

Sample for
chemical analysis
Early Earth
Energy Source
Prokaryotic Cell (Bacteria)
Stromatalites in Shark Bay,
Australia
Eukaryotic Cell (animal)
Eukaryotic Cell (plant)
Lynn Margulis
Endosymbiotic Hypothesis
(thuyết nội cộng sinh)
 Modern Day Eukaryotic Cells
Animal Plants
Prokaryotic cell size as compared to
Eukaryotic Cell size
Surface Area vs. Volume
Cocci Bacteria
Bacilli Bacteria
Helical Bacteria
Cell Wall and Gram Stain
Sticky Bacterial Capsule
Prokaryotic Cell (Bacteria)
LE 2-4
Cloud of negative
charge (2 electrons) Electrons

Nucleus
Molecule: Same element
Molecule: Different elements
 Energy and Atoms

Third energy level (shell)

Energy
Second energy level (shell)
absorbed

First energy level (shell)

Energy
lost

Atomic
nucleus
Valence Electrons (Electron hoá trị)
Covalent Bonds
POLAR MOLECULE
–

H H

+ +
H2O
 Ionic Bonds

Liên kết ion là một liên kết hoá học có bản chất là lực hut tĩnh điện giữa 2
ion mang điện tích trái dấu.
Thường là liên kết giữa các nguyên tử nguyên tố phi kim với các nguyên tử
nguyên tố kim loại
SALT

Na+
Cl–
Hydrogen Bonds Form Between an Electronegative Atom
and Hydrogen
Hydrogen bonds are not unique to water molecules and can occur whenever
hydrogen is covalently bonded to an electronegative atom.

Water disrupts hydrogen bonds between two molecules by competing for the
hydrogen bonding capability.
HYDROGEN BONDS – +

Water
(H2O)

+
Hydrogen bond
–

Ammonia
(NH3)

+ +

+
 Van der Waals Interactions

e-
e- e- e-

e- e-

e- e-

NUCLEUS

Là lực tương tác giữa các phân tử khi được tiếp xúc với nhau. Cụ thể nó
là lực hút giữa các phân tử.
Bichemsistry course

Water Part 1
Earth
States of Water
Water Cycle

Transport
over land
Solar energy

Net movement of
water vapor by wind

Precipitation
Precipitation Evaporation over land
over ocean from ocean
Evapotranspiration
from land

Percolation
through
soil
Runoff and
groundwater
Water and Polarity

Hydrogen
bonds
Water and Cohesion

Water-conducting cells

100 µm
Adhesion
Earth and Temperature
Water and Temperature

Hydrogen
bonds
What happens to the ice?
Evaporative Cooling
Evaporative Cooling in plants
Hydrogen Bond angles
Life below the water
 Unit 1
1.5 Biochemistry: Water Part 2
Universal Solvent
Solution
Suspension
 Colloid
This is why you should shake milk first
Moles of Substances
pH and pOH scales
Buffering by Bicarbonate in blood
Acid Rain Source
Acid rain effects on plants
Acid Rain and Concrete
Early Earth
 Carbon Bonding

Molecular Structural Ball-and-Stick Space-Filling

Formula Formula Model Model

Methane

Ethane

Ethene (ethylene)
Hydrocarbon tails
Hydrocarbon Tails of a
Phospholipid

Choline

Phosphate

Glycerol

Fatty acids

Hydrophilic
head

Hydrophobic
tails

Structural formula Space-filling model Phospholipid symbol

Cell Membranes
Functional groups serve important
purposes in molecules

Estradiol

Female lion

Testosterone

Male lion
 LE 4-10aa

STRUCTURE

(may be written HO—)

Ethanol, the alcohol present in

alcoholic beverages

NAME OF COMPOUNDS FUNCTIONAL PROPERTIES

Alcohols (their specific names Is polar as a result of the

usually end in -ol) electronegative oxygen atom
drawing electrons toward itself.
Attracts water molecules, helping
dissolve organic compounds such
as sugars (see Figure 5.3).
 LE 4-10ab
STRUCTURE
NAME OF COMPOUNDS
Ketones if the carbonyl group is
within a carbon skeleton
Aldehydes if the carbonyl group is
at the end of the carbon skeleton
Acetone, the simplest ketone
EXAMPLE
Acetone, the simplest ketone
Propanal, an aldehyde
FUNCTIONAL PROPERTIES
A ketone and an aldehyde may
be structural isomers with
different properties, as is the case
for acetone and propanal.
LE 4-10ac

STRUCTURE EXAMPLE

Acetic acid, which gives vinegar

its sour taste

NAME OF COMPOUNDS FUNCTIONAL PROPERTIES

Carboxylic acids, or organic acids Has acidic properties because it is

a source of hydrogen ions.
The covalent bond between
oxygen and hydrogen is so polar
that hydrogen ions (H+) tend to
dissociate reversibly; for example,

Acetic acid Acetate ion

In cells, found in the ionic form,
which is called a carboxylate group.
LE 4-10ba

STRUCTURE EXAMPLE

Glycine

Because it also has a carboxyl

group, glycine is both an amine and
a carboxylic acid; compounds with
both groups are called amino acids.

NAME OF COMPOUNDS FUNCTIONAL PROPERTIES

Amine Acts as a base; can pick up a

proton from the surrounding
solution:

(nonionized) (ionized)

Ionized, with a charge of 1+,

under cellular conditions
 LE 4-10bb

STRUCTURE EXAMPLE

(may be written HS—)

Ethanethiol

NAME OF COMPOUNDS FUNCTIONAL PROPERTIES

Thiols Two sulfhydryl groups can

interact to help stabilize protein
structure (see Figure 5.20).
 LE 4-10bc

STRUCTURE EXAMPLE

Glycerol phosphate

NAME OF COMPOUNDS FUNCTIONAL PROPERTIES

Organic phosphates Makes the molecule of which it

is a part an anion (negatively
charged ion).

Can transfer energy between

organic molecules.
Dehydration and
Hydrolysis Short polymer Unlinked monomer
Reactions
Dehydration removes a water
molecule, forming a new bond

Longer polymer
Dehydration reaction in the synthesis of a polymer

Hydrolysis adds a water

molecule, breaking a bond

Hydrolysis of a polymer
Proteins
Chapter 3 Outline
LE 5-UN78

a carbon

Amino Carboxyl
group group
Two Different Ways of Depicting How Biomolecules Will Be Used

Fischer projections are useful for visualizing the constituent atoms of the molecule.

Every atom is identified, and the bonds to the central atom are depicted as vertical
and horizontal lines. The horizontal bonds are taken to project out of the plane
toward the viewer, whereas the vertical bonds are assumed to project behind the
viewer.
 Most Amino Acids Exist in Two Mirror-Image Forms

When four different groups are bonded to the a-carbon, the amino
acids are chiral, which means that they exist as two mirror-image
forms called the L isomer and the D isomer.

Only the L isomers are found in proteins.

The 20 amino acids found in proteins contain unique side chains
that vary in size, shape, charge, hydrogen-bonding capacity,
hydrophobic character, and chemical reactivity.

Amino acids have three-letter abbreviations and one-letter symbols.

Hydrophobic Amino Acids Have Mainly Hydrocarbon
Side chains
Nonpolar amino acid
Polar and Electrically charged
The Ionizable Side Chains Enhance Reactivity
and Bonding
3.3 Essential Amino Acids Must be Obtained from the
Diet

Kwashiorkor is a form of malnutrition resulting from

inadequate consumption of amino acids usually ingested as
proteins.
Dehydration and
Hydrolysis
Short polymer Unlinked monomer
Reactions again
Dehydration removes a water
molecule, forming a new bond

Longer polymer
Dehydration reaction in the synthesis of a polymer

Hydrolysis adds a water

molecule, breaking a bond

Hydrolysis of a polymer
Peptide Bonding
Primary (1’) sequence
Primary Structure is IMPORTANT
 Sickle Cell and Oxygen
transport
Normal hemoglobin Sickle-cell hemoglobin
Primary Val His Leu Thr Pro Glu Glu Primary Val His Leu Thr Pro Val Glu
structure 1 2 3 4 5 6 7 structure 1 2 3 4 5 6 7
Exposed
Secondary Secondary hydrophobic
and tertiary  subunit and tertiary region  subunit
structures structures

 a
a

Quaternary Normal Quaternary Sickle-cell
structure hemoglobin structure hemoglobin a
(top view) 
 a

Function Molecules do Function Molecules

not associate interact with
with one one another to
another; each crystallize into
carries oxygen. a fiber; capacity
to carry oxygen
is greatly reduced.
2’ structure
3’ Structure
4’ Structure
Protein’s Natural Form
Denaturation of a protein
Chaperonin
Nitrogen Cycle and
Proteins

N2 in atmosphere

Assimilation
Denitrifying
bacteria
NO3–
Nitrogen-fixing
bacteria in root
nodules of legumes Decomposers Nitrifying
Ammonification bacteria
Nitrification
NH3 NH4+ NO2–
Nitrogen-fixing Nitrifying
soil bacteria bacteria
Thank you for your listening