BIOCHEM

BIOCHEMISTRY
CHEMISTRY OF LIFE

 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.
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
 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 14, Carbon 13, and Carbon 12
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
o Cation – an ion that loses electrons so becomes positively charged
o 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
History of Cell Discovery
Microscope view of cells

 Robert Hooke
 first to see cells
 designed microscope that he was able to view cork cells with (1665).
 Named “Cells” because they look like monk quarters

 Anton Van Leeuwenhoek

 first to see living cells
 improved design, and was able to view red blood cells and bacteria.
 Called them "animalcules"

Scientists of Cell Theory

 Theodore Schwann – zoologist who observed that the tissues of animals had cells
(1839)
 Mattias Schleiden – botanist who observed that the tissues of plants had cells (1845)
  Rudolf Virchow – reported that every living thing is made up of cells, and that these cells
must come from other cells.
Cell Theory
1. All living things are made of one or more cells.
2. Cells are the basic unit of structure and function in organisms.
 (the smallest unit that can perform life functions)
3. All cells come from pre - existing cells.
Terms

 Cell – the smallest unit that can carry on the processes of life.
 Unicellular – consists of only one cell
 Multicellular – consists of more than one cell
Basic cell structures

Two basic cell types

 Prokaryotic - lacks internal structures surrounded by membranes.

 Has a cell membrane & a cell wall
 Has NO nucleus.
-Means “before the nucleus”
 Usually, Unicellular organisms
 Ex: Bacteria
 Eukaryotic - contains internal membrane bound structures.
 Has a nucleus
 Has a cell membrane
 Usually, multicellular organisms
 Ex: Plants, animals, and protists
Cell Membrane
 The thin layer of protein and fat that surrounds the cell.
The cell membrane is semi permeable, allowing some
substances to pass into the cell and blocking others.
Nucleus
 Surrounded by a nuclear envelope with nuclear pores
 Contains the genetic information (DNA) which exists
as chromatin in a non-dividing cell
 Controls all cell activities
Nucleolus
 In the center of the nucleus
 Produces the ribosomes
Cytoplasm
 fluid filled interior of cell
 suspends cell organelles
Nucleoplasm
 It is also called as nuclear matrix. It contains enzymes involved in the synthesis of DNA
and RNA.
Chromosomes
 Eukaryotes (cells with nuclei such as those found in plants, yeast, and animals) possess
multiple large linear chromosomes contained in the cell's nucleus.
 In the nuclear chromosomes of eukaryotes, the uncondensed DNA exists in a semi-
ordered structure, where it is wrapped around histones (structural proteins), forming a
composite material called chromatin.
Mitochondria
 Produces cellular energy in the form of ATP through a process called cellular respiration
(metabolizes glucose)

Lysosomes
 digests and recycles old cell parts, sometimes bacteria
 contain high levels of enzymes

Peroxisomes
 Are also small vesicles surrounded by a membrane. They are also called as
microbodies.
 Functions:
1. They contain enzymes of H2O2 metabolism. The concentration of protein in
peroxisomes is very high and they may occur in crystallines form. The enzymes of
H2O2 catabolism present in peroxisomes are peroxidase and catalase.
Ribosomes
 site of protein synthesis
 links amino acids together to form proteins

Endoplasmic Reticulum
 Transport system within the cell
 Transport cell materials
 Two types: Rough (With Ribosomes) and Smooth

 Rough ER
 It has ribosomes which give it its “rough”
appearance
 Functions in protein synthesis
 Smooth ER
 Mostly contains enzymes that function in lipid
synthesis
Golgi Apparatus
 Flattened stacks of membranes
 Collects, packages and modifies cell
materials to be used in other parts of
the cell or transported out of the cell
Vacuole/Vesicles
 storage

Centrioles
 Used during cell division and separate
chromosomes
 Only found in animal cells

Cytoskeleton
- These are filament like structures made up of proteins present in cytoplasm. Non-muscle
cells perform mechanical work with these intracellular networks of proteins.
 Microfilaments. They are actin like filaments. They form loose web beneath cell
membrane.
 Intermediate filaments-fixing positions
 Microtubules. Tubulin is the building block of microtubules. Dendrites, axons of nerve
cells and sperm cells contain microtubules. The sperm cell moves with the help of
flagellum, a microtubule. These cytoskeletons are involved in the maintenance of cell
shape, cell division, cell motility, phagocytosis, endocytosis and exocytosis.
The Cell Cycle

 Somatic Cells
 Cells that make your organs and tissues
 Sex Cells
 The ONLY cells that are not somatic – sperm and egg (Gametes)
Cell Division

 In eukaryotes, cell division occurs in two major stages.

 The first stage, division of the cell nucleus, is called mitosis.
 The second stage, division of the cell cytoplasm, is called cytokinesis.
 The cell cycle is the series of events that cells go through as they grow and divide.
 Interphase is the period of growth that occurs between cell divisions.
 Cell spends most of its life in this phase.
Cell Cycle
During Cell Cycle:
1. a cell grows
2. prepares for division
3. divides to form two daughter cells, each of which begins the cycle again
The cell cycle consists of four phases:

 G1 (First Gap Phase)

 S Phase
 G2 (Second Gap Phase)
 M Phase
Events in the Cell Cycle
During G1, the cell
 increases in size (cell grows)
 synthesizes new proteins and
organelles (cell develops)
During the S phase, (DNA replication)
 chromosomes are replicated
 DNA synthesis takes place
 Once a cell enters the S phase, it
usually completes the rest of the cell
cycle
The G2 Phase (Second Gap Phase)
 organelles and molecules required for
cell division are produced
 Once G2 is complete, the cell is ready to start
the M phase—Mitosis

Stages of the Cell Cycle

Remember: IPMAT
Mitosis is after Interphase
Prophase

 the first phase in mitosis

 THREE THINGS TO LOOK FOR:
1. chromosomes can be seen as two chromatids, in the
shape of an “X”
2. Nuclear envelope dissolves
3. Centrioles are present with some spindle fibers
Metaphase

 Second phase in Mitosis

 THREE THINGS TO LOOK FOR:
1. chromosomes line up in the middle
2. Nuclear envelope is gone (no nucleus)
3. Spindle fibers (on opposite poles) are stretching towards the chromosomes
Anaphase

 Third phase of Mitosis

 THREE THINGS TO LOOK FOR:
1. Spindle fibers pull chromosomes towards the separate
poles
2. Chromosomes are split in HALF
3. Sister chromatids are now their OWN chromosome.
Telophase

 the final stage of Mitosis

 THREE THINGS TO LOOK FOR:
1. The nuclear envelope reforms around each set of
chromosomes (so daughter cells each have one) and
chromosomes straighten out (uncoil)
2. Spindle fibers are gone
3. Cleavage furrow is forming between the cells
Cytokinesis

 Interphase  Mitosis  Cytokinesis

 Final step in the Cell Cycle
 Actually means “cell moving”
 The final pinching of the cell into two complete
identical cells!

Molecular Composition of Cell

 Water
- Water accounts for about 70-75% of the weight of the cell. Other cellular constituents are
either dissolved or suspended in water.
 Organic Compounds
 1. Organic compounds accounts for 25-30% of the cell weight.
2. 2. They are nucleic acids, proteins, polysaccharides (carbohydrates) and lipids.
Proteins account 10-20% of the weight of the cell. Nucleic acids account 7-10%
of the cell weight.
3. Polysaccharides usually account for 2-5% of the cell weight. About 3% of cell
weight is due to lipids. Lipids content may be higher in adipocytes or fat cells.
Proteins may account more of cell weight in cells like erythrocytes.
4. Other low molecular weight organic compounds may account for 4% of cell
weight. They
5. are monosaccharides, amino acids, fatty acids, purine and pyrimidine
nucleotides, peptides, hormones, vitamins and coenzymes.
 Inorganic Compounds
1. Inorganic compounds account for the rest of the cell weight.
2. They are cations like sodium, potassium, calcium, magnesium, copper, iron and
anions like chloride, phosphate, bicarbonate, sulfate, iodide and fluoride.
Why do multicellular organisms need to regulate the death of their cells?

 To regulate the sizes of cell populations in adult bodies cell proliferation must be
balanced with cell death.
 This allows organisms to precisely control the sizes of their tissues and organs.
Three types of Cell Death
1. Necrosis
 It is also termed as cell murder. Cells undergo necrotic death if cell membrane is
damaged or due to decreased oxygen supply and if energy (ATP) production is
blocked.
2. Apoptosis
 This type of cell death occurs in tissue turnover. Individual cells or groups of cells
undergo this type of death. Aged cells in the body are removed by apoptosis.
 It is a genetically programmed cell death. In the initial stages of apoptosis, cell
shrinks, followed by fragmentation and finally these fragments are eliminated by
phagocytosis.
3. Atrophy
 This type of cell death occurs in the absence of essential survival factors.
 Survival factors required by the cell are produced by other cells. Absence of
nerve
 growth factor leads to atrophy of nerves. It is also genetically programmed cell
death.
Medical and Biological Importance

 Cells are not immortal i.e., they have finite life span. In the body, cells are formed and
destroyed. So, cells are in dynamic state.
 Cell division and cell death are two opposite processes required to maintain constant
tissue volume (tissue homeostasis).
 Further cell death plays an important role in shaping tissues and organs during
development or during recovery from injuries.
 Cell death may occur due to several external factors also.