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BIOCHEMISTRY PROKARYOTIC CELLS

SIGNIFICANCE OF BIOCHEMISTRY
 Medical students who acquire a sound of
knowledge of biochemistry will be in a strong
position to deal with two central concerns of
the health sciences:
(1) the understanding and maintenance of health
(2) the understanding and effective treatment of
disease
 Knowledge on diseases processes  Structurally simpler and smaller
 Diagnosis and management of diseases  Do not contain a nucleus
 Manufacture of biological products  Found in Bacteria and Archaebacteria

BIOCHEMICAL SUBSTANCES DISTINGUISHING CHARACTERISTICS OF A PROKARYOTIC


CELL
Biochemical substance
 DNA is not enclosed within a membrane and is
usually a singular circularly arranged chromosome.
Bioinorganic S. Bioorganic S.  Nucleoid
HISTONES
(continuation pf distinguishing Characteristics..)
Water (about 70%) Proteins (about 15%)
 It lacks membrane enclosed organelles
Inorganic salts (about 5%) Lipids (about 8%)  Theirs cell wall contain Peptidoglycan
Carbohydrates (about 2%)  Its usually divides by binary fission.

Nucleic Acids (about 2%)


EUKARYOTIC CELLS
CHARACTERISTIC OF LIFE
1. Metabolism
 Complex series of essential chemical processes.
 E.g. digestion and assimilation, respiration.
2. Growth
 Development of new parts between or within
older ones
 INTUSSUSCEPTION;
3. Irritability
 Respond to changes in their environment.
4. Reproduction
5. Definite form and size
 They contain a true nucleus, bounded by a
6. Chemical composition
membranous nuclear envelope
 Cardon, hydrogen, oxygen and nitrogen.
 They are generally bigger that Prokaryotic cells
 Plants and animals
PROKARYOTIC VS EUKARYOTIC CELL  Other cellular microbes (fungi, protozoa,
and algae)
Two main forms of cells
DISTINGUSHING CHARACTERISTICS OF A EUKARYOTIC CELLS
 Eukaryotic Cell
 Prokaryotic Cell  DNA is found in the cells nucleus and the DNA is
found in multiple chromosomes
Both contain:  DNA is consistently associated with Histones
 Nucleic acids
 Proteins
 Lipids BACTERIA
 Carbohydrates  Prokaryotes
Some kinds of chemical reactions to:  Cell walls (peptidoglycan)
 Binary fission
 Metabolize food  For energy, use organic chemicals, inorganic
 Build proteins chemicals, or photosynthesis
 Store energy
ARCHEA
 Prokaryotes
 Lack Peptidoglycan
 Live in extreme environments
 Includes THE CELL
 Methanogens
 Extreme halophiles
 Extreme thermophiles
FUNGI
 Eukaryotes
 Cell walls (chitin)
 Use organic chemicals for energy
 Molds and mushrooms
 Multicellular consisting of masses of mycelia,
which are composed of filaments called hyphae.
 Yeasts are unicellular

PROTOZAO
 Eukaryotes
DISCOVERY OF CELLS
 Absorb or ingest organic chemicals
 May be motile via Psedupods, cilia, or flagella  Robert Hooke
 Describes cells as similar to the walled
compartments of a honeycomb ‘cellula’
ALGEA
 Anton Van Leeuwenhoek
 Eukaryotes
 First man to witness
 Cell walls ( cellulose)
a live cells under a
 Use photosynthesis for energy
microscope.
 Produce molecular oxygen and organic compounds
 Animalcules
 First person to
THE REVOLUTIONARY CLASSIFICATION observe bacteria,
protozoa, sperm
cells, red blood cells,
as well ast structure
of plants .
MODERN INTERPRETATION OF THE CELL THEORY
1. the cell is the fundamental unit of structure and function in
living organisms
2. all cells arise from pre existing cells by division (omnis
cellula e cellula)

3. energy flows ( metabolism and biochemistry) occurs within


cells

4. cells contain hereditary information (DNA) which is passed


from cells to cells during cell division

WHITTAKER’S 5-KINGDOM SCHEME 5. all cells are basically the same in chemical composition in
organism of similar species.

6. all know living things are made one or more cells.

7. some organism are made up pf only one cell and are


known as unicellular organism

8. other are multicellular, composed of a number of cells

9. the activity of an organism depends on the total activity of


independent cells.

ROBERT BROWN

 Discovered “an opaque spot “ in cells


 Nucleus
3. nucleolus

- The nucleolus is the largest structure in the nucleus of


eukaryotic cells. It is best known as the site of ribosome
biogenesis

 Ribosomes
DEVELOPMENT OF THE CELL THEORY  Composed of RNA and several proteins
 Synthesize proteins
 Matthias Jakob Schleiden and Theodor Schwann  Can be found along the membranes of nuclear
envelope and endoplasmic reticulum
Matthias Jakob Schleiden  Free ribosomes
 Bound ribosomes are attached to a structure
 German professor of botany known as rough endoplasmic reticulum
 Brought the nucleus to attention

Theodor Schwann

 Professor of Physiology
 Propounded what seen became famous as the CELL
THEORY
 Publish a book where he accept cell structure as the
basis of all vegetable tissues as well as in animal
basis.

Rudolf Virchow

 German physiologist, physician, pathologist and  Endoplasmic Reticulum (ER)


anthropologist.  Continuation of the outer nuclear
 Popularized Omnis Cellula e cellula membrane
 Manufactures membranes and perfroms
many other biosynthetic functions
STRUCTURE OF A EUKARYOTIC CELL

 Cythoplasm
 Aqueous cell contents and suspend particles and
organelles
 Lies internal to the cell membrane

Cytosol – semifluid substance within the membrane


containing the other organelles
 Smooth ER; important in the synthesis of
 Cell Membrane lupids and membrane.
 Selective barrier  Rough ER; important in the sythesis of the
 Nucleus protiens
 Controlling center
 Contains chromosomes
 Golgi Apparatus
 Stack of membrane bound vesicles
 Important in packaging molecules for transport
 Cis and trans side

The possible models explaining the organization of


the Golgi apparatus and the transport of proteins

1. nuclear membrane

- allows direct communication between nuclear content and


cytoplasm through the Nuclear pores

2. Nucleoplasm from one cisterna to the next.

- liquid material in the nucleus


 Vesicles
 Used for transport of materials
 Mitochondria PLANT CELL
 Power centers of the cell
 Have smooth outer membranes and highly
convoluted forming fold inner membrane
(cristae)

 Cytoskeleton
 Network of fibers throughout the cytoplasm
 Organizes the structure and activities of the cell  Cell wall
 A cell wall is a structural layer surrounding some
types of cells, just outside the cell membrane. It
can be tough, flexible, and sometimes rigid. It
provides the cell with both structural support
and protection, and also acts as a filtering
mechanism
 Central vacuole and tonoplast
- A tonoplast is actually the membrane that
surrounds the large vacuole in a mature plant
cell. We get the name 'tonoplast' from Greek,
which translated looks something like 'tone,
tension, stretching, and molded.' This would
 Peroxisomes coincide well with where the tonoplast exists. It
 Contain enzymes that catalyse the removal of is also known as the 'vacuolar membrane.'
electrons and associated hydrogen atoms from,  Chloroplast
for example, hydrogen peroxide - Chloroplasts are organelles that conduct
photosynthesis, where the photosynthetic
pigment chlorophyll captures the energy from
sunlight, converts it, and stores it in the energy-
storage molecules ATP and NADPH while
freeing oxygen from water in plant and algal
cells.

 Plasmodesmata
 Plasmodesmata are microscopic channels
which traverse the cell walls of plant cells
and some algal cells, enabling transport and
communication between them.
ANIMAL CELL

 Centriole
 Framework of the cell
 Contains small microfilaments and larger
microtubes
 They support the cell, giving it its shape and
help with the movement of its organelles
 Lysosome
 Recycling center
-Recyle cellular debris
 Membrane bound organelles containing a
variety of enzymes
 Internal pH is 5
 Help digest food particles inside or out side
the cell.
CELL MEMBRANE 3. surface area ( the larger the faster)

Is a thin semi-permeable membrane that surrounds the 4. type molecule or ion diffusing (the little the molecule,
cytoplasm of a cell (outer covering of a cell) allows only the faster)
certain materials to enter.

FLUID MOSIAC MODEL (SINGER AND NICHOLSON,


B. Facilitated – proteins are required to effect the
1972)
passage of materials across relatively inter-molecule
 Describes the plasma membrane, it is membrane
describe as mosaic because if you look at it
Carrier and channel Protein
from a far, due to the different molecules
found in it, it looks a lot like a mosaic.
 It is also describe as fluid because of the
hydrophile part of the phospholipid has a
fluid consistency because it is constantly
moving.
 Membranes are not homogenous
 Membrane components are highly
asymmetric.

CELL MEMBRANE: COMPOSITION

1. Lipid bilayer:
A. Phospholipid bilayer- what Carrier protein- changes its shape so the
surrounds/makes up the plasma molecule can go in/pass through
membrane.
Channel proteins – just an opening
B. Cholesterol – so that the
phospholipid will not be compact.
2. Proteins
C. Osmosis – movement of water from high
A. integral- protrude on both sides of
concentration to a low concentration
the membrane.
B. peripheral – can only be seen on one - the water or solvent is the one that moves
side
3. Carbohydrates- - needs a semi-permiable membrane or its just diffusion

CELL MEMBRANE: TRANSPORT

A. passive transport

 Diffusion
 Facilitated diffusion
 Osmosis

b. active transport

 Uniport and coupled transport

c. Bulk transport

 Endocytosis
 Exocytosis
Types of Osmosis

1. Passive transport – does not need energy. 1. isotomic – equal number of solute both inside
and outside of the cell
2. hypotonic – low number of molecules in the
A. diffusion – movement of molecules from higher environment
concentration to lower concentration.  water will then transfer inside the cell
- moves constantly and randomly making it swell, then eventually pop!
3. hypertonic – too much molecules in the
4 factors that determine rate of diffusion environment
 will result to the cell shrinking because the
1. steepness of the concentration gradient
water will transfer to the environment to
2. temperature ( the hotter the faster ) try and make it equal.
2. ACTIVE TRANSPORT – requires energy
- cell must require very high or
low levels of some molecules.

Uniport – one molecule is transported

Coupled – two molecules are transported

a. symport – same direction

b. antiport – different directions

3.BULK TRANSPORT – is the transport of


quantities of molecules and food particle to
membrane .

a. endocytosis – into the cell

 phagocytosis – eat
 pinocytosis - drink
 receptor – mediated endocytosis

b. exocytosis – movement out of the cell


BIOMOLECULES  Oligosaccharides
 Polysaccharides

Aldoses - An aldose is a monosaccharide with a carbon


backbone chain with a carbonyl group on the endmost
carbon atom, making it an aldehyde, and hydroxyl groups
connected to all the other carbon atoms.

Ketoses - A ketose is a monosaccharide containing


one ketone group per molecule. The simplest ketose
is dihydroxyacetone, which has only three carbon
atoms, and it is the only one with no optical activity.

MACROMOLECULE MONOMER

Carbohydrates Monosaccharides

Lipids not always the same

Proteins Amino Acids

Nucleic Acid Nucleotides

In condensation Reaction – a molecule of water is


removed, from monomer to macromolecule.
Disaccharide- A disaccharide is the sugar formed
ANABOLIC when two monosaccharides are joined by glycosidic
linkage. Like monosaccharides, disaccharides are
Building Block Macromolecule soluble in water. Three common examples are
sucrose, lactose, and maltose. Disaccharides are one
Simple sugar Polysaccharides
of the four chemical groupings of carbohydrates.
Amino acids Protein (peptide)
Glycosidic bond - A glycosidic bond or glycosidic
Nucleotide DNA or RNA linkage is a type of covalent bond that joins a
carbohydrate molecule to another group, which may
Fatty Acid Lipid or may not be another carbohydrate. A glycosidic
bond is formed between the hemiacetal or hemiketal
CATABOLIC group of a saccharide and the hydroxyl group of some
compound such as an alcohol.

1. Carbohydrates – General formula:


C H O = C (H O)
- most abundant class of
bioorganic molecule.
- People; glycogen
- Plants; starch

Functions

 Production of energy
 Storage of glycogen
 Cell communication
 Component of other biomolecules

Classification

 General formula : Polysaccharides (glycan)


C H C = C (H O)
 Homopolysaccharide – one kind of
Based on molecular size sugar
 Hetoropolysaccharide- different
 Monosaccharides sugars???
2. LIPIDS Steroid hormones being lipid soluble can diffuse
- an organic compound found in living through the plasma membrane of the cell very easily.
things organism that is insoluble in
5. protective – coating lipids (biological waste) –
water but soluble in nonpolar solvents

Functions
3. PROTEINS
 Storage
- amino acids
 Surround and insulate vital body
- peptide bonds
organization and functions
- proteios “ first important”
 Prevent loss of energy

Saturated fatty acids (SPAs) (no double bond presence)


- A saturated fat is a type of fat in which the fatty acid
chains have all or predominantly single bonds. A fat is
WATER
made of two kinds of smaller molecules: glycerol and
fatty acids. Fats are made of long chains of carbon PHYSICAL PROPERTIES
atoms. Some carbon atoms are linked by single bonds
 Colorless
and others are linked by double bonds.
 Odorless
 Transparent

Distilled water is considered pure

Rainwater is not pure, precipitation of any kind (snow,


rain, hail) contains dissolved minerals, gasses, acids,
dust, pollen grains, viruses and microorganism.

STRUCTURE OF THE WATER MOLECULE

H + H + O = H2O (chemical formula)


Monosaturated fatty acid (no double bond)
H H
Polysaturated Fatty acid (no Many double bond)
0

(structural Formula)
5 Categories of Lipids
PROPERTIES OF WATER
1. Energy storage (triacylglycerols) – Description A
triglyceride is an ester derived from glycerol and three 1. Polar molecule
fatty acids. Triglycerides are the main constituents of
body fat in humans and other vertebrates, as well as
vegetable fat.

2. membrane-lipid (phospholipid and cholesterol) - is a


compound which belongs to a group of which form the
double-layered surface of all cells. The three major
classes of membrane lipids are phospholipids, How is a water molecule polar?
glycolipids, and cholesterol. Lipids are amphiphilic: they
have one end that is soluble in water and an ending that Water (H2O) is polar because of the bent shape of
is soluble in fat. themolecule. The shape means most of the
negative charge from the oxygen on side of
3. Emulsification lipids (bile lipids)- When bile enters the molecule and the positive charge of the
the small intestine, it will mix with the fat globules and hydrogen atoms is on the other side of
will cause them to break down into smaller units called the molecule. This is an example of polarcovalent
emulsion droplets. This process is called emulsification. chemical bonding.
Emulsification greatly increases the surface area of the
How do water molecules bond with each other?
fat on which the lipase can actually act on.
 + attracted to –
4. messenger lipids (steroid hormones & eicosanoids) -
 Eache H2O is bonded
Steroid hormone: Steroid hormones are derived from
to its nearest
cholesterol and eicosanoids. ... The gonads and the
neighbor
adrenal cortex are the primary sources of steroid
hormones. Examples of eicosanoids are prostaglandins.
HYDROGEN BONDING What affects Surface tension?

 Gravity
 Changes the shape of droplets as the
fall
 Warmer temperature
 Hot water is a better cleaning agents
because the low surface tension makes
it a better “wetting agent” to get into
 They do not share electrons, so they are pores and fissures rather than bridging
weaker than covalent bonds them with surface tension.
 They easily break and form again  Soaps and detergent
 Breaks the surface tension
HYDROGEN BONDS
ADHESION
 Hold water molecules together
 Each water molecule can from a maximum of 4 The attraction of water to other’s surfaces /substances.
hydrogen bonds
Capillary action
 The hydrogen bonds joining water molecules
are weal, about 1/20th as strong as covalent
bonds.
 They form with great frequency
 Extraordinary Properties that are results of
hydrogen bonds.
- Cohesive behavior
- Resist changes in temperature
- High heat of vaporization  Wettable surfaces cause a film of
- Expands when it freezes water to partially pull away from other
- Versatile solvent water molecule and cling to the
surfaces.
Cohesion
 Capillary action is important in soil and
plant/water relations

Capillary action and adhesion

 Adhesion is the
attraction of water
molecules to stick to
Essentially, cohesion and adhesion are the "stickiness" other substances, and
that water molecules have for each other and for other is also results of its
substances. You can see this in the picture to the right. hydrogen bond.
The water drop is composed of water molecules that like  This property
to stick together, an example of the property of allows water to creep
cohesion. up or flows in tubes,
such a plant’s system and phloem, or human
SURFACE TENSION blood vessels. This is called capillary action and
Surface tension, is important for many life processes.
of the force Did you ever wonder: How does water move from roots
necessary to to leaves
stretch or break when a tree
the surfaces of a doesn’t have
liquid, is related a heart to
to cohesion pump the
water?

Importance Cohesion –
adhesion
- Some insects can walk on water theory
- Formation of water drops and waves
THREE STATES OF WATER  At 0OC, Hydrogen bonds relax to form crystal
lattice.
 Water is the
only naturally
occurring
- When water reaches 0OC, water becomes locked
substance that can
into a crystalline lattice with each molecule
exist in all three
bonded to maximum of four partners.
physical states on
- As ice starts to melt, some of the hydrogen
the planet.
bonds break and some water molecules can slip
closer together than they can while in the ice
state.
- Ice is about 10% less dense than water at 4OC.

Physical states of water

Water phase changes


DENSITY OF WATER
 Freezing
- Water expands when it freezes and  Most dense at 4OC
becomes less dense  Contacts until 4OC
 Melting  Expands from 4OC to 0OC
 Evaporation the density of water:
- When water vapor cools it takes up
less space and contracts, allowing 1. prevents water from freezing from bottom to
water molecules to stick to one up.
another forming clouds and 2. ice forms on the
precipitation surface first – the
 Condensation freezing of the water
- Condensation is the change of the releases het to the water
physical state of matter from the gas below creating
phase into the liquid phase, and is insulation
the reverse of vaporization. The word
most often refers to the water cycle. 3. makes transition
 Sublimation between season less
abrupt.
- Sublimation is the transition of a
substance directly from the solid to
the gas phase, without passing
through the intermediate liquid Specific heat is the amount of heat that must be
phase. absorbed or lost for one gram of a substance to
 Frost formation change its temperature by 1OC.
- Frost forms when an outside
 Three fourths of the earth is covered by
surface cools past the dew point.
water. The water serves as a large het sink
The dew point is the point where
responsible for:
the air gets so cold, the water vapor
- Prevention of temperature
in the atmosphere turns into liquid.
fluctuations that are outside the
This liquid freezes. If it gets cold
range suitable for life
enough, little bits of ice, or frost,
- Coastal areas having a mild climate
form.
- A stable marine environment
DENSITY
Specific heat capacity
The density of water:
 Due to hydrogen bonds
 Increases as temperature decreases, until 4OC  Water has the highest specific heat of all
 Decreases from 4OC until 0OC ( freezing point) natural liquids
 Most of the suns heat energy is used to
break the hydrogen bonds.
- Only a little bit left to increase the
vibrations of the molecules (which
increase the temp)

Water moderates temperature on earth

 Water stabilizes air temperature by


absorbing heat from warmer air and
releasing heat to cooler air
 Water can absorb or release relatively large
amount of heat with only a slight change in
its own temperature.

High specific heat capacity


DISSOCIATION OF WATER MOLECULES
 Crucial for living organism which need to
maintain a particular temperatures in order  Occasionally, a hydrogen atom shared by two
to optimizes enzymes activity water molecules shifts from one molecule to
 The high water content of cells and tissues the other.
helps them to maintain a constant - The hydrogen atom leaves its electron
temperature behind and is transferred as a single
 Water acts as a temperature buffer proton – Hydrogen ion ( H+)
Importance - The water molecule that lost a proton
is now a hydroxide ion (OH-)
 Large bodies of water can absorb and - The water molecule with the extra
release a lot of heat with little temperature proton is a hydronium ion (H3O+)
change
 Plays a major role in ocean currents and
controlling climate through thermal
conductivity

Evaporative cooling

 The cooling of a surface occurs when the


liquid evaporates
 This is responsible for:
- Moderating earth’s climate
- Stabilizes temperature in aquatic
ecosystems  A simpler way to view this process is that a
- Preventing organism from
water molecule dissociates into a hydrogen ion
overheating
and hydroxide ion:
HIGH HEAT OF VAPORIZATION H2O  H+ + OH
- This reaction is reversible
 Takes a lot of energy to make water
 At equilibrium the concentration of water
evaporate
molecules greatly exceeds that of H+ and OH
 Most of the initial energy is use to break the
hydrogen bonds.  In pure water only one water molecule in 554
 This causes water to be resistant to million is dissociated
temperature changes. - At equilibrium, the
concentration of H+ or OH is
107M (25OC)
Water pH

 Pure water (distilled) has a pH of 7


 Seawater is slightly basic, with pH of about
8
 Most natural water has a pH of between 6-8
 Acid rain can have a pH as low as 4
AUTIONIZATION OF WATER

THE ION PRODUCT OF WATER

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