BIOCHEMISTRY…

Barrozo, Princes P, LPT

Instructor

The Chemistry of Life

BIOCHEMISTRY
I. COURSE DESCRIPTION: This course covers
the structural chemistry of the components of
living matter and how this relates to biological
function. It also covers the structure-function,
kinetics and regulation of biological catalysts.
II. COURSE CREDIT: 5 units: 3 units lecture, 2
units laboratory
III. PREREQUISITES: None
 GRADING SYSTEM
LECTURE LABORATORY
Lecture exam 50% Laboratory exam 50%

Lecture quizzes 30% Laboratory activities 50%

Lecture activities 20% Total laboratory (%) 100%

Total lecture (%) 100%

 GRADING SYSTEM
PRELIM/MIDTERM/FINAL %
GRADE
Lecture Grade 60%
Laboratory Grade 40%
Final Grade 100%

PRELIM MIDTERM FINAL AVE. FINAL

GRADE GRADE GRADE GRADE
30% 30% 40% 100%
BIOCHEMISTRY BSN 1- 7
Bio-Chemistry
 What do you think of when you see the word
Biochemistry?
 List the first 5 things that you think of in your
notebook.
Bio Chemistry
 Bio= life
 Chemistry = how things interact
 Biochemistry= the branch of science in which you
study the chemical and physical processes that
occur in an organism.
Biochemist
 focus heavily on studying the structure and
function of biomolecules
 Biomolecules they are also known as the biological
building blocks of life.
 There are four main classes of biomolecules
1. carbohydrates
2. proteins
3. lipids
4. nucleic acid
I can…
 Identify the parts of an atom AND understand how
atoms interact
Matter…
 All matter, whether living or nonliving, is made of the same
type building blocks called atoms
 An atom is the smallest basic unit of matter
 All atoms have the same basic structure, composed of three
smaller particles
 Proton – a positively charged particle in an atom’s nucleus
 Neutron – a neutral (no charge) particle which has about the
same mass as a proton and is also in the nucleus
 Electron – a negatively charged particle found outside the
nucleus. Electrons are much, much smaller than proton and
neutrons
Elements…
 Different types of atoms are called elements, which
cannot be broken down by ordinary chemical means
 Which element an atom is depends on the number of
protons in the atom’s nucleus
 For example… all hydrogen atoms have 1proton and all
oxygen atoms have 8 protons
 Only about 25 different elements are found in
organisms
 However, atoms of different elements can “link” or bond
together to form compounds
ISOTOPE
 Elements can have a different number of neutrons.
 This is called an isotope
 Carbon 12, Carbon 13, and Carbon 14
ISOTOPE OF HYDROGEN
Compounds…
 Atoms form compounds in two ways
1. Ionic bonds – consists of ions and forms through the
electrical force between oppositely charged ions
 An ion is an atom that has lost or gained electrons
 Cation – an ion that loses electrons so becomes positively charged
 Anion – an ion that gains electrons so becomes negatively charged
2. Covalent bonds – forms when atoms share one or more
pairs of electrons
 A molecule consists of two or more atoms held together by
covalent bonds
Why elements bond the way they
do…
 All atoms want 8 electrons in their outer most
energy level (shell) This is called the octet rule.
 That is why they do what they do
 Ionic bonds – gain or lose electrons
 Covalent share electrons
 How do we identify each type
 Ionic compound – metal + non-metal
 Covalent compound – non-metal + non-metal
Bell Ringer…
1. How is an atom different from a compound?
2. What does the number of protons tell us about an
element?
3. Identify the following as ionic or covalent
compounds
a. Cl2F4
b. CuF2
c. AlBr3
d. CO2
4. Compare and contrast ionic and covalent bonds
Carbon based molecules
 Carbon based molecules are the foundation for life
 Many of these molecules are large and called
polymers. Poly- many
 A repeating unit of the same small molecule
(monomer)
 There are four main types of carbon-based
molecules in living things
1. Carbohydrates
2. Proteins
3. Lipids
4. Nucleic acids
Bell Ringer…
 What is the main element in an “organic”
molecule?
 How are monomers related to polymers?
 What are the four main “organic” molecules living
organisms need?
Carbohydrates…
 Known as sugars and starches
 Also include cellulose and glycogen
 Made up of monosaccharides (monomer) which
can be put together to form disaccharides and
polysaccharides
 Disaccharides – maltose, lactose, and sucrose (table
sugar)
 Polysaccharides – starch, cellulose (cell wall
component), and glycogen (storage of carbs in the liver
and muscle)
 Glycogen is important for insulin in humans
Why carbs are important to living
organisms…
 Short-term storage energy storage
 Plant cell wall components – strength
 Component of cell membranes – glycogen
 It helps identify the type of cell
Proteins…
 Known as meat to us
 Made up of amino acids (monomer) which can

be put together to form polypeptides (50-300

a.a.)
 20 different amino acids are found in human
proteins
Amino acids are organic molecules that, when
linked together with other amino acids, form
a protein
Key takeaways
 Almost all cell functions involve proteins. These
proteins are composed of organic molecules called
amino acids.
 While there are many different amino acids in
nature, our proteins are formed from twenty amino
acids
 amino acids are typically composed of
1. carbon atom 4. an amino group
2. hydrogen atom 5. variable group
3. carboxyl group
Key takeaways
 nonessential amino acids
made naturally by the body 
 Amino acids that can not be naturally made by the
body are called essential amino acids.
Generally, amino acids have the following structural
properties:

 A carbon (the alpha carbon)

 A hydrogen atom (H)
 A Carboxyl group (-COOH)
 An Amino group (-NH2)
 A "variable" group
or "R" group
Nonpolar amino acid
 Ala: Alanine           
 Gly: Glycine         
 Ile: Isoleucine         
 Leu: Leucine
 Met: Methionine 
 Trp: Tryptophan    
 Phe: Phenylalanine   
 Pro: Proline
 Val: Valine
Polar Amino Acids

 Cys: Cysteine        
  Ser: Serine          
  Thr: Threonine
 Tyr: Tyrosine       
 Asn: Asparagine
  Gln: Glutamine
POLAR BASIC AMINO ACIDS
(POSITIVELY CHARGED)
 His: Histidine      
 Lys: Lysine           
 Arg: Arginine
POLAR ACIDIC AMINO ACIDS
(NEGATIVELY CHARGED)
 Asp: Aspartate 
 Glu: Glutamate
Why proteins are important to
living organism…
 Form body tissue
 Skin, hair, muscles
 Important for immune response
 Antibodies – fight off foreign invaders
 All enzymes in the body
 Biological catalysts – they speed chemical reactions
inside the body
Lipids…
 Known as fats, oils and waxes
 Made up of glycerol and fatty acids
 Saturated fatty acids
 Single bonds join carbon (carbon – carbon) together
 Are oils at room temperatures
 Unsaturated fatty acids
 Has at least one carbon = carbon (joined by double bonds)
 3 fatty acids + 1 glycerol = triglyceride
Excessive amounts of lipids
 cholesterol and triglycerides,
Can lead to diseases such as:
 atherosclerosis ("hardening of the arteries")
 hypertension (high blood pressure)
 coronary artery disease
Why lipids are important to living
organisms…
 Long term storage of energy
 Fat is the storage mechanism
 Formation of cell membranes
 Nerves and brain tissue
 Phospholipids and cholesterol
 Phospholipids have hydrophobic heads and hydrophilic tails
 Hormones
 Made of steroids
Types of Lipids and Where They Are Found

The three main types of lipids in your body are:

1. Phospholipids
make up the outer layer of cells in the bodies of animals
and humans. 
2. Sterols
known as steroid alcohols
 plant sterols or phytosterols found in foods and offer

many health benefits.4

  Phytosterols are similar to the main sterol in humans

called cholesterol.
 Cholesterol is also key for making bile salts, the
substances that help the body break down fat and absorb
vitamins.
The two most commonly known types of proteins that carry
cholesterol are
  high-density lipoprotein (HDL) 

“good” cholesterol because it absorbs cholesterol and

brings it back to the liver
 low-density lipoprotein (LDL)

“bad” cholesterol because it can build up in the blood

3. Triglycerides
are the most common form of fat in the bloodstream.
They consist of three fatty acid chains linked by a
molecule called glycerol
 saturated fats typically derived from animal

products such as meat, butter, and cheese.

 Unsaturated fats have essential nutrients as 

omega-3 fatty acids, and are found in foods like tuna,

salmon, nuts, seeds, avocados, and leafy vegetables
 Trans fats, or "partially hydrogenated oils," 
What foods raise triglyceride levels?

from food and drinks, especially

• alcohol and carbohydrates, that end up stored in the

form of triglycerides in our fat (adipose) tissue.

Role of Lipids in the Body

 Supporting cells and aiding in essential

functions
 Protecting nerve cells

 Helping the body absorb certain vitamins

 Helping produce hormones, including

estrogen, testosterone, and cortisol

Vitamin absorption
 Vitamin A - immune system, vision, and
reproduction.14
 Vitamin D - immune health and bone strength
 Vitamin E - boosts the immune system, helps
prevent blood clots, and protects cells from
unstable molecules that can cause disease (
free radicals).16
 Vitamin K - bone health. It also allows you to heal
safely from injuries by helping your body form
blood clots.17
 Hormone production
 including estrogen, testosterone, and cortisol
Here are a few important jobs that hormones have:
 Key players in sexual development and reproduction

 Help control the immune system and metabolism

 Keep water and salt (sodium) levels in the body

balanced
 Control inflammation and promote healing

 Regulate the body's stress response

 Regulate circadian rhythms.

Risks Associated With High
Lipids
 liver disease and heart disease
Cardiovascular disease is the leading cause of death
 Atherosclerosis- clog the arteries
Lipid panel test
A lipid panel is also called a cholesterol test
Nucleic Acids…
 chain of nucleotides which stores genetic
information in biological systems. It creates DNA
and RNA, which store the information needed by
cells to create proteins. This information is stored
in multiple sets of three nucleotides, known as
codons
 Known as DNA and RNA
 Made up of nucleotides
 A nucleotide consists of
 Phosphate group
 Pentose sugar (5-carbon sugar)
How Nucleic Acids Work
  molecules are acids 
  “source code” for making cells.
  “messenger” that could carry copies of the
instructions found in DNA.
 first discovered in the nuclei of our cells.
Why nucleic acids are important to
living things…
 DNA
 Blueprint for life
 Our genes
 RNA
 Translates DNA to make PROTEINS
RNA, or ribonucleic acid – acted as a “messenger”
that could carry copies of the instructions found in
DNA.
 Function of Nucleic Acids
 Nucleic Acids Store Information Like Computer
Code
Cells also use nucleic acids for other purposes. 
Ribosomes – the cellular machines that make protein
– and some enzymes are made out of RNA
the nucleotides that are strung together to create
nucleic acids consist of :
 five-carbon sugar,

 phosphate group

 nitrogen-containing base. 
Nucleic Acids are Polymers of Nucleotides

 The term “polymer” comes from “poly” for

“many” and “mer” for parts, referring to the fact
that each nucleic acid is made of many nucleotides.
 Nucleic Acid Structure

Nucleic acids are formed mainly with the elements

 Carbon

 oxygen,

 hydrogen,

 nitrogen, and

 phosphorus.
 Monomer of Nucleic Acids

There are four basic types of nucleotide,

 adenine (A),

 guanine (G),

 cytosine (C),

 thymine (T).
Chemical Reactions in the body…
 Chemical reactions require the addition of energy,
called activation energy , to take place
 Even if a chemical reactions starts, it may not
happen very quickly
 However, both the activation energy and the rate of
a chemical reaction can be changed by a catalyst
 A catalyst is a substance that decreases the activation
energy for a reaction and increases the rate of reaction
 Enzymes are biological catalysts
Enzymes…
 Almost all enzymes are proteins and almost every
process in living things needs enzymes
 The function of each enzyme depends on its
structure
 A change in biological conditions can affect the shape
of an enzyme, which can decrease or prevent an
enzyme from working properly
 For example, enzymes function best in a small range around
an organism’s normal temperature and pH
Shapes of enzymes…
 The shape of an enzyme is important because it
allows only certain molecules to bind to the
enzyme
 The specific molecules that an enzyme acts on are
called substrates
 It works like a puzzle or lock and key – only certain
pieces fit together for it to work
 If an enzymes structure changes, the substrate cannot bind
to the enzyme
Bell Ringer…
 What does the activation energy tell us for a
particular reaction?
 How does a catalyst affect a chemical reaction?
 Why would enzymes be called a “lock and key” or
“puzzle piece”?
One more thing about chemical
reactions and enzymes…
 There are two types of energy changes that can
occur with chemical reactions
 enzymes do not change this for an reaction
 Exothermic reactions
 Releases energy (usually in the form of heat or light)
 Energy in the reactant bonds are higher than in the
product bonds
 Endothermic reactions
 Absorbs energy
 Energy in the reactant bonds are lower than in the
product bonds
CHEMISTRY LABORATORY GENERAL DIRECTIONS
HAZARDS SYMBOLS AND MEANINGS

1. Poisonous

2. Environmental hazard

3. Corrosive
HAZARDS SYMBOLS AND MEANINGS

4. Explosive

5. Flammable

6. Harmful or irritant
HAZARDS SYMBOLS AND MEANINGS

7. Oxidizing chemical

8. Dangerous when wet

9. Flammable solid
HAZARDS SYMBOLS AND MEANINGS

10. Flammable gas

11. Flammable liquid

12. Non Flammable gas

 HAZARDS SYMBOLS AND MEANINGS

13. Organic peroxide

14. Spontaneously
combustible

15. Stow away from foodstuffs

 HAZARDS SYMBOLS AND MEANINGS

16. Inhalation hazard

17. Marine pollutant

CHEMISTRY LABORATORY SAFETY RULES
CHEMISTRY LABORATORY FIRST AID