Biochemistry

College of Arts and Sciences

Chapter 1
Eukaryotic Cells and Protein

BERLIN E. AGSALOG
Faculty-in-Charge
1st Semester I AY 2024-2025

Biochem
The 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.
At the end of the semester, the students are expected to:
1.Recognize, write formulas and describe the chemical structures that make up the
components of living matter proteins and carbohydrates
2.Describe the interactions of these components of living matter, proteins carbohydrtaes,
lipids and nucleic acids
3.Describe the interactions of these components that give rise to the organized
supramolecular structures
4.Explain how enzyme work and they are regulated
5.Explain how chemical reactions are regulated inside living cells.
6.Apply key concepts in biochemistry to explain the practical applications in the field of
agriculture medicine, pharmacy and allied fields.

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TABLE OF CONTENTS
• Cell Organelles and Function
• Protein, Protein Synthesis

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Cell
Organelles
1. Cell (Plasma membrane)
 Provides shape and flexibility
 Semi-permeable
 Maintains Homeostasis

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2. Cytoplasm
 Jellylike material
 Contains water, salts, and other
chemicals
 Suspends organelles and site for
different chemical reactions
3. Nucleus
where DNA and RNA
are made
DNA directs cell
activities.
The brain of the cell
4. Nucleolus
 Located in the nucleus
 Responsible for making ribosomes

5. Chromatin
 Located in the nucleus
 The long strands of DNA
6. Endoplasmic Reticulum
Membrane system of folded sacs and tunnels
Moves material around the cell
Rough E.R – Covered with ribosomes, protein
synthesis
Smooth E.R – no ribosomes
7. Ribosomes
Helps the cell make its own protein
8. Golgi Bodies
Stacks of membrane-covered sacs
Sorts, packages, and sends proteins outside the cell
9. Mitochondria
Provides energy for
the cell
Has its own DNA
The power plant of
the cell
10.Lysosome
Small and spherical
structures
Contains digestive enzymes
that digest food particles,
bacteria, and worn out or
broken cell parts
11.Cell Wall
Found in plants cells
Very rigid structure that
surrounds the cell membrane
Helps support and protect the
cell
12.Chloroplast
In plants cells
Captures light energy
and produces food for
the plant
Contains green
pigment called
chlorophyll
13.Vacuoles
 Temporary storage
areas in cells
 Stores food,
enzymes, and
waste products
 Cell Parts- Support and Locomotion

1. Cytoskeleton
a. Microtubules
b. Microfilaments

2. Cilia & Flagella

Introduction to Proteins and Amino Acids

Twenty percent of the human body is made up of

proteins. Proteins are the large, complex molecules

that are critical for normal functioning of cells. IMAGE MAY BE PLACED HERE
• They are essential for the structure, function, and
regulation of the body’s tissues and organs.
• Proteins are made up of smaller units called amino
acids, which are building blocks of proteins. They
are attached to one another by peptide bonds
forming a long chain of proteins.

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Introduction to Proteins and Amino Acids

• An amino acid contains both a carboxylic group and

an amino group. Amino acids that have an amino
group bonded directly to the alpha-carbon are referred
to as alpha amino acids.
• Every alpha amino acid has a carbon atom, called an
alpha carbon, Cα ; bonded to a carboxylic acid, –
COOH group; an amino, –NH2 group; a hydrogen
atom; and an R group that is unique for every amino
acid.

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Introduction to Proteins and Amino Acids

Classification of amino acids

• There are 20 amino acids. Based on the nature of their
‘R’ group, they are classified based on their polarity as:

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Introduction to Proteins and Amino Acids

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Classification based on essentiality:
Essential amino acids are the amino acids which you
need through your diet because your body cannot make
them. Whereas non essential amino acids are the amino
acids which are not an essential part of your diet because
they can be synthesized by your body.
Essential Non essential
Histidine Alanine
Isoleucine Leucine Arginine
Methionine Aspargine
Phenyl alanine Aspartate
Threonine Cystine
Tryptophan Valine Glutamic acid
Glycine
Ornithine
Proline
Serine
Tyrosine
Peptide bonds
• Amino acids are linked together by ‘amide groups’ called peptide bonds.
• During protein synthesis, the carboxyl group of amino acid at the end of the
growing polypeptide chain reacts with the amino group of an incoming amino
acid, releasing a molecule of water. The resulting bond between the amino
acids is a peptide bond.
 Primary Structure
• The simplest level of protein structure, primary structure is simply the sequence of amino acids in a polypeptide
chain.
• The hormone insulin has two polypeptide chains A, and B. The sequence of the A chain, and the sequence of the
chain can be considered as an example for primary structure.
Secondary structure
secondary structure, refers to local folded structures that form within a
polypeptide due to interactions between atoms.
• The most common types of secondary structures are the α helix and the β
pleated sheet. Both structures are held in shape by hydrogen bonds, which
form between the carbonyl O of one amino acid and the amino H of another.
 Tertiary structure
• The overall three-dimensional structure of a polypeptide is called its tertiary structure.
The tertiary structure is primarily due to interactions between the R groups of the amino
acids that make up the protein.
• Important to tertiary structure are hydrophobic interactions, in which amino acids with
nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving
hydrophilic amino acids on the outside to interact with surrounding water molecules.
Also, Disulfide bonds, covalent linkages between the sulfurcontaining side chains of
cysteines, are much stronger than the other types of bonds that contribute to tertiary
structure
 Quaternary structure
• When multiple polypeptide chain subunits come together, then the
protein attains its quaternary structure.
• An example for quaternary structure is hemoglobin. The hemoglobin
carries oxygen in the blood and is made up of four subunits, two
each of the α and β types.
 Denaturation and protein folding
• Each protein has its own unique shape. If the temperature or pH of
a protein's environment is changed, or if it is exposed to chemicals,
these interactions may be disrupted, causing the protein to lose its
three-dimensional structure and turn back into an unstructured
string of amino acids.
• When a protein loses its higher-order structure, but not its primary
sequence, it is said to be denatured. Denatured proteins are
usually nonfunctional.
 Structure of proteins
• The sequence of a protein is determined by the DNA of the gene
that encodes the protein (or that encodes a portion of the protein,
for multisubunit proteins).
• A change in the gene's DNA sequence may lead to a change in the
amino acid sequence of the protein. Even changing just one amino
acid in a protein’s sequence can affect the protein’s overall
structure and function.
• To understand how a protein gets its final shape or conformation,
we need to understand the four levels of protein structure: primary,
secondary, tertiary, and quaternary
Protein
Synthesis
Refers to the biological processes whereby
amino acids are assembled by peptide bonding
into specific polypeptide sequences in accord
with genetic blueprints encoded by
deoxyribonucleic acid.

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Protein
Synthesis Transcription
Translation
Elongation

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 Biochemistry
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Protei
n
• Large molecules
• Made up of chains of amino acids
• Are found in every cell in the body
• Are involved in most of the body’s functions and
life processes
• The sequence of amino acids is determined by
DNA

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Structure of
Protein
• Made up of chains of amino acids; classified by number of amino acids in a
chain
– Peptides: fewer than 50 amino acids
• Dipeptides: 2 amino acids
• Tripeptides: 3 amino acids
• Polypeptides: more than 10 amino acids
– Proteins: more than 50 amino acids
• Typically 100 to 10,000 amino acids linked together
• Chains are synthesizes based on specific bodily DNA
• Amino acids are composed of carbon, hydrogen, oxygen, and nitrogen

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Structural Differences Between
Carbohydrates, Lipids, and Proteins
Condensation and Hydrolytic Reactions
• Essential – must be consumed in the diet
• Nonessential – can be synthesized in the body
• Conditionally essential – cannot be synthesized due to illness or lack of
necessary precursors
– Premature infants lack sufficient enzymes needed to create arginine
Quick Review
• Proteins are chains of combination of amino acids
• Amino acids contain carbon, hydrogen, oxygen, nitrogen,
and sometimes sulfur
• Unique amino acids consist of a central carbon with a
carboxyl group, a hydrogen, a nitrogen-containing amine
group, and a unique side chain
• There are 20 side chains and 20 unique amino acids
–9 essential amino acids
–11 nonessential amino acids
• At time these become conditionally essential
• Amino acids link together with peptide bonds by
condensation and break apart by hydrolysis
Quick Review

• Attractions and interactions between the side chains cause

the proteins to fold into precise three-dimensional shapes
• Protein shape determines its function
• Proteins are denatured and their shapes changed by
– Heat
– Acids
– Bases
– Salts
– Mechanical agitation
 References
• https://www.khanacademy.org/science/biology/macro molecules/proteins-and-amino-acids/a/orders-ofprotein
-structure

• https://www.khanacademy.org/testprep/mcat/biomolecules/amino-acids-andproteins1/a/chemistry-of-amino-acids-
and-proteinstructure

• https://www.chem.wisc.edu/deptfiles/genchem/netori al/modules/biomolecules/modules/protein1/prot15.ht
m

• http://cbc.arizona.edu/classes/bioc460/spring/460we b/lectures/LEC3_AminoAcids_08-ppt
Image references:
Peptide bond: https://www.chem.wisc.edu/deptfiles/genchem/netorial/modu
les/biomolecules/modules/protein1/prot15.htm Primary and tertiary structures:
https://www.khanacademy.org/science/biology/macromolecul es/proteins-and-amino-acids/a/orders-of-protein-structure
Secondary structure: https://kimberlybiochemist.wordpress.com/category/aminoacids-and-proteins/
Quaternary structure: http://swift.cmbi.ru.nl/gv/students/mtom/QUA_1.html
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B e rlin Ed e r A g sa log , LPT, M A Ed

I n st r u c to r 1

bagsalog@unp.edu.ph

Messenger:Berlin Eder Agsalog