BIOCHEMISTRY LECTURE
BSN 1-J
Chapter 1: Intro – Chapter 3: Proteins (Prelims)
Structural Organization of the Human
Biochemistry Body
- The study of chemical substances found 1. Atoms
in living organisms; and 2. Molecules
- Chemical interactions of these substances 3. Macromolecules
with each other. 4. Organelles
- It is the chemistry of life 5. Cells
o Combines biology and chemistry 6. Tissue
- Studies how cells manufacture the 7. Organ
molecules needed for life and how 8. Organism
chemical reactions occur.
Chemical Foundations of Biochemistry
Organic Chemistry
Biochemistry: An Overview - The study of compounds of carbon and
- All living things:
hydrogen and their derivatives.
o Make use of the same type of
- Biomolecules are part of organic chem.
biomolecules
o Use energy Functional Groups:
- Cells and biomolecules arise from very
simple molecules such as: - Atom / Group of atoms that show
o H2O characteristics of physical and chemical
o CH4 properties.
o NH3
Biomolecules
o N2
- Include large molecules such as proteins,
o H2
nucleic acids, polysaccharides, and lipids.
- Field of biochemistry draws many
- Are Polymers (Greek: poly + meros,
disciplines
many+parts)
- Biochemistry answers questions on the
o Derived from monomers (single +
molecular nature of life
parts)
Biochem Application to the Real World Biological Micromolecules:
1. Medicine
2. Research Science 1. Amino Acids
3. Food and Cosmetics 2. Sugars (monosaccharides)
4. Agriculture 3. Nucleotides
5. Patent Law
Biological Macromolecules:
6. Publishing
7. Education 1. Proteins
8. Pharmaceuticals 2. Carbohydrates
9. Forensic Science 3. Nucleic Acids
4. Lipids
Attributes of Life – Quick Recap
1. Adaptation The Major Groups of Biochemicals
2. Growth & Repair
3. Metabolism Amino Acids
4. Reproduction - The simplest compounds
5. Complexity & Organization - Building blocks of protein
6. Regulation - All contain an amino group and a carboxyl
7. Size & Shape group
8. Respond to stimuli - Basic structure:
9. Locomotion o Central carbon atom is bonded to
10. Variation & Change a, carboxyl group an amino
,BIOCHEMISTRY LECTURE
BSN 1-J
Chapter 1: Intro – Chapter 3: Proteins (Prelims)
group, a hydrogen, and a variable Lipids
group, called R group - The most diverse and cannot be shown
with a simple structure common to all
lipids
- Poorly soluble in water
o Because most of their structure is
composed of long chains of
hydrocarbons
Carbohydrates
- Carbohydrates are compounds made up
of carbon, hydrogen, and oxygen, with a
general formula of (CH2O)n, where n is at
least 3.
- The simplest forms are call
monosaccharides (such as glucose)
- Simple sugars often make up much
larger polymers and are used for energy
Functional Groups
storage and structural components.
- An atom or group of atoms within a
molecule that has similar chemical
properties whenever it appears in various
compounds.
Chapter 1A: Introduction to
Cell
- The total DNA of a cell is called the
genome
- Individual units of heredity, controlling
indiv. traits by coding for a functional
Nucleotides protein or RNA, are genes.
- The basic unit of the hereditary materials
Classification of Living Cells:
DNA and RNA.
- Also form Adenosine Triphosphate (ATP) 1. Prokaryotes (Archaea, Eubacteria,
- Composed of a five-carbon sugar, a Cyanobacteria)
nitrogen-containing ring, and one or more o Lack defined nucleus or internal
phosphate groups membrane structures
- Combine to form nucleic acids o Lack membrane-bound organelles
o DNA is found in Nuclear Region
o Usually unicellular
▪ But may form colonies
o Some live in extreme conditions
o Cytosol has a granular appearance
due to ribosomes
o Plasma membrane is the only
membrane found in prokaryotes
o Size (diameter):
▪ 1-3 µm
,BIOCHEMISTRY LECTURE
BSN 1-J
Chapter 1: Intro – Chapter 3: Proteins (Prelims)
2. Eukaryotes
o Define nucleus and with
membrane-bound organelles
o Eukaryote - “true nucleus”
o Include unicellular organisms
(yeast, paramecium) &
multicellular plants and animals
o Size (diameter):
▪ 10-100 µm
Chapter 1B: Water
Electronegativity
- The tendency of an atom to attract
electrons to itself in a chemical bond
Polarity
- Polar Bonds
o High difference in electronegativity
Main Parts of Prokaryotic Cells: - Nonpolar Bonds
1. DNA o Very small electronegativity
o Single, closed, circular molecule difference
o Attached to cell membrane
2. Ribosomes
o Contribute to the granular
appearance of cytosol
o Consists of RNA & protein
(ribonucleoprotein particles)
▪ Site of protein synthesis
3. Cytosol
o Aqueous portion of cytoplasm
4. Plasma Membrane
o Made of lipid molecules and
proteins Water Structure
5. Cell Wall - Water molecule form dipoles
o Made up of mostly polysaccharide - Strong electronegativity of oxygen attracts
material electrons away from hydrogen
o Serves as protection - Dipole
o A molecule with electrical charge
Main Organelles of Eukaryotic Cells: distributed asymmetrically about
its structure
- Water has a bent structure
- It is a polar molecule
, BIOCHEMISTRY LECTURE
BSN 1-J
Chapter 1: Intro – Chapter 3: Proteins (Prelims)
- Water molecule is an irregular, slightly Biomolecules Fold to Position Polar and
skewed tetrahedron with oxygen as its Charged Groups on Their Surfaces
center
- Proteins fold:
o Hydrophilic portion oriented
outside the molecule
o Hydrophobic portions oriented
inside
- Lipids in cell membranes are arranged so
that:
o Hydrophilic portion is inside; and
o Hydrophobic portions are oriented
outside
4. Hydrophobic Interactions
5. Excellent nucleophile (Donate e- to
electrophiles)
o Nucleophilic attack often results in
hydrolysis
6. Water ionization greatly influence pH of
surrounding environment
o Ex: Blood pH
▪ Acidosis (<7.35)
▪ Alkalosis (>7.45)
Solvent Properties of Water
- Water is an ideal biologic solvent Buffers
- The polar nature of water largely - Something that resists change
determines its solvent properties - Buffers in our body are aqueous solutions
- Polar molecules dissolve in water, - Buffer solutions:
whereas less polar mols don’t. o Has the ability to resist changes
in pH upon the addition of small
amounts of either acid or base
- A buffer solution contains:
o A weak acid or weak base; and
o The salt of the weak acid or base
- Biomedical Importance / Clinical
Correlation:
o Maintaining pH of blood
Biomedical Importance / Clinical
Correlations
1. Predominant component of living things
2. Water is an ideal biologic solvent
o Dissolves inorganic substances Chapter 3A: Protein
o Dissolves polar organic mols due Characteristics of Proteins
to dipolar structure forming - Most abundant substance in cell next to
hydrogen bonds water (15% of cell mass)
o Hydrogen bonding greatly - Typical human cell (9,000) and human
influence its phys. Properties
body (100,000) proteins (HUHH unsa daw?)
3. Influences the structure of biomolecules
- All proteins contain:
o Forms H-bond with other mols
o C, H, O, N
▪ most have Sulfur
- Protein – Unbranched polymer
o Amino Acid – Monomer unit
BSN 1-J
Chapter 1: Intro – Chapter 3: Proteins (Prelims)
Structural Organization of the Human
Biochemistry Body
- The study of chemical substances found 1. Atoms
in living organisms; and 2. Molecules
- Chemical interactions of these substances 3. Macromolecules
with each other. 4. Organelles
- It is the chemistry of life 5. Cells
o Combines biology and chemistry 6. Tissue
- Studies how cells manufacture the 7. Organ
molecules needed for life and how 8. Organism
chemical reactions occur.
Chemical Foundations of Biochemistry
Organic Chemistry
Biochemistry: An Overview - The study of compounds of carbon and
- All living things:
hydrogen and their derivatives.
o Make use of the same type of
- Biomolecules are part of organic chem.
biomolecules
o Use energy Functional Groups:
- Cells and biomolecules arise from very
simple molecules such as: - Atom / Group of atoms that show
o H2O characteristics of physical and chemical
o CH4 properties.
o NH3
Biomolecules
o N2
- Include large molecules such as proteins,
o H2
nucleic acids, polysaccharides, and lipids.
- Field of biochemistry draws many
- Are Polymers (Greek: poly + meros,
disciplines
many+parts)
- Biochemistry answers questions on the
o Derived from monomers (single +
molecular nature of life
parts)
Biochem Application to the Real World Biological Micromolecules:
1. Medicine
2. Research Science 1. Amino Acids
3. Food and Cosmetics 2. Sugars (monosaccharides)
4. Agriculture 3. Nucleotides
5. Patent Law
Biological Macromolecules:
6. Publishing
7. Education 1. Proteins
8. Pharmaceuticals 2. Carbohydrates
9. Forensic Science 3. Nucleic Acids
4. Lipids
Attributes of Life – Quick Recap
1. Adaptation The Major Groups of Biochemicals
2. Growth & Repair
3. Metabolism Amino Acids
4. Reproduction - The simplest compounds
5. Complexity & Organization - Building blocks of protein
6. Regulation - All contain an amino group and a carboxyl
7. Size & Shape group
8. Respond to stimuli - Basic structure:
9. Locomotion o Central carbon atom is bonded to
10. Variation & Change a, carboxyl group an amino
,BIOCHEMISTRY LECTURE
BSN 1-J
Chapter 1: Intro – Chapter 3: Proteins (Prelims)
group, a hydrogen, and a variable Lipids
group, called R group - The most diverse and cannot be shown
with a simple structure common to all
lipids
- Poorly soluble in water
o Because most of their structure is
composed of long chains of
hydrocarbons
Carbohydrates
- Carbohydrates are compounds made up
of carbon, hydrogen, and oxygen, with a
general formula of (CH2O)n, where n is at
least 3.
- The simplest forms are call
monosaccharides (such as glucose)
- Simple sugars often make up much
larger polymers and are used for energy
Functional Groups
storage and structural components.
- An atom or group of atoms within a
molecule that has similar chemical
properties whenever it appears in various
compounds.
Chapter 1A: Introduction to
Cell
- The total DNA of a cell is called the
genome
- Individual units of heredity, controlling
indiv. traits by coding for a functional
Nucleotides protein or RNA, are genes.
- The basic unit of the hereditary materials
Classification of Living Cells:
DNA and RNA.
- Also form Adenosine Triphosphate (ATP) 1. Prokaryotes (Archaea, Eubacteria,
- Composed of a five-carbon sugar, a Cyanobacteria)
nitrogen-containing ring, and one or more o Lack defined nucleus or internal
phosphate groups membrane structures
- Combine to form nucleic acids o Lack membrane-bound organelles
o DNA is found in Nuclear Region
o Usually unicellular
▪ But may form colonies
o Some live in extreme conditions
o Cytosol has a granular appearance
due to ribosomes
o Plasma membrane is the only
membrane found in prokaryotes
o Size (diameter):
▪ 1-3 µm
,BIOCHEMISTRY LECTURE
BSN 1-J
Chapter 1: Intro – Chapter 3: Proteins (Prelims)
2. Eukaryotes
o Define nucleus and with
membrane-bound organelles
o Eukaryote - “true nucleus”
o Include unicellular organisms
(yeast, paramecium) &
multicellular plants and animals
o Size (diameter):
▪ 10-100 µm
Chapter 1B: Water
Electronegativity
- The tendency of an atom to attract
electrons to itself in a chemical bond
Polarity
- Polar Bonds
o High difference in electronegativity
Main Parts of Prokaryotic Cells: - Nonpolar Bonds
1. DNA o Very small electronegativity
o Single, closed, circular molecule difference
o Attached to cell membrane
2. Ribosomes
o Contribute to the granular
appearance of cytosol
o Consists of RNA & protein
(ribonucleoprotein particles)
▪ Site of protein synthesis
3. Cytosol
o Aqueous portion of cytoplasm
4. Plasma Membrane
o Made of lipid molecules and
proteins Water Structure
5. Cell Wall - Water molecule form dipoles
o Made up of mostly polysaccharide - Strong electronegativity of oxygen attracts
material electrons away from hydrogen
o Serves as protection - Dipole
o A molecule with electrical charge
Main Organelles of Eukaryotic Cells: distributed asymmetrically about
its structure
- Water has a bent structure
- It is a polar molecule
, BIOCHEMISTRY LECTURE
BSN 1-J
Chapter 1: Intro – Chapter 3: Proteins (Prelims)
- Water molecule is an irregular, slightly Biomolecules Fold to Position Polar and
skewed tetrahedron with oxygen as its Charged Groups on Their Surfaces
center
- Proteins fold:
o Hydrophilic portion oriented
outside the molecule
o Hydrophobic portions oriented
inside
- Lipids in cell membranes are arranged so
that:
o Hydrophilic portion is inside; and
o Hydrophobic portions are oriented
outside
4. Hydrophobic Interactions
5. Excellent nucleophile (Donate e- to
electrophiles)
o Nucleophilic attack often results in
hydrolysis
6. Water ionization greatly influence pH of
surrounding environment
o Ex: Blood pH
▪ Acidosis (<7.35)
▪ Alkalosis (>7.45)
Solvent Properties of Water
- Water is an ideal biologic solvent Buffers
- The polar nature of water largely - Something that resists change
determines its solvent properties - Buffers in our body are aqueous solutions
- Polar molecules dissolve in water, - Buffer solutions:
whereas less polar mols don’t. o Has the ability to resist changes
in pH upon the addition of small
amounts of either acid or base
- A buffer solution contains:
o A weak acid or weak base; and
o The salt of the weak acid or base
- Biomedical Importance / Clinical
Correlation:
o Maintaining pH of blood
Biomedical Importance / Clinical
Correlations
1. Predominant component of living things
2. Water is an ideal biologic solvent
o Dissolves inorganic substances Chapter 3A: Protein
o Dissolves polar organic mols due Characteristics of Proteins
to dipolar structure forming - Most abundant substance in cell next to
hydrogen bonds water (15% of cell mass)
o Hydrogen bonding greatly - Typical human cell (9,000) and human
influence its phys. Properties
body (100,000) proteins (HUHH unsa daw?)
3. Influences the structure of biomolecules
- All proteins contain:
o Forms H-bond with other mols
o C, H, O, N
▪ most have Sulfur
- Protein – Unbranched polymer
o Amino Acid – Monomer unit
