BIOL 2401 AP I Lecture Notes: Cell

BIOL 2401 AP I Lecture Notes : Cell Dr. Weis

The next level of organization from the molecular....Cellular

CYTOLOGY -- the study of cells, both structural and functional

CELLS structural and functional units of all living things

contain organic compounds (C, H, O atoms, molecules, chemical compounds)
that make up carbohydrates, lipids, proteins, nucleic acids that will be used to build the cell.

Principal Substances that make up the cell ::

1. Water ..... 75-80%

2. Proteins ... 10-20%

3. Lipids ... 2%

4. Carbohydrates 1%

5. Electrolytes

Major parts of the cell -----

1. nucleus

2. Cell (plasma) membrane

3. Cytoplasm

The Plasma membrane............

A. Separate body fluid compartments into

Extracellular fluid ECF

Intracellular fluid ICF (cytosol of the cell cytoplasm)

B. Lipid Bilayer that is a phospholipid

(made up of Fatty acids, glycerol, and phosphate).

The tails are fat soluble and hydrophobic.

The heads love water and therefore are called hydrophilic.

Two groups of phospholipids will line up with tails together (non polar)
and heads to each of the ends (creating a polar, hydrophilic end).

The plasma membrane is a dynamic fluid structure and the lipid molecules are free to move from side to side

C. Contains phospholipids, proteins, cholesterol, and carbohydrates, glycolipids

Integral proteins serve as channels through which water soluble substances can pass. These substances include ions and water.

Peripheral proteins are involved in enzymatic reactions and are normally attached to an integral protein.

Both proteins can serve as structural, specific receptor sites, and are involved in Active Transport.

Carbohydrates will attach themselves to the proteins (called glycoproteins) to form a glycocalyx or attach to lipids (called glycolipids). These structures can be involved in receptor sites for hormones and some are involved with immune reactions to initiate chemical signaling by ligands.

The plasma membrane is selectively permeable and will only allow certain substances to pass through,
such as fat soluble substances like O2, CO2, alcohol.
Whereas the membrane is impermeable to water soluble substances like glucose.

Plasma membrane and cell communication via contact signaling created by membrane junctions

Cells bound closely together by various cell adhesion molecules.

A. Passive processes

Diffusion is a random, free, and passive process. It is the movement of a solute down a gradient, from a high concentration to a low concentration toward equilibrium.

Small molecules will go through channels, ions will also go through channels but are affected by charges.

Lipid soluble substances go through the phospholipid Bilayer more rapidly.

The driving force is the kinetic energy of the various molecules

The rate of diffusion depends on several variables.

Increased concentration, shorter distances the molecules travel, smaller molecules, and increased temperature will increase the rate of diffusion.

Simple diffusion is involved to move nonpolar, lipid soluble substances ::

oxygen, carbon dioxide, fats, sodium, urea, and alcohol

Facilitated diffusion requires a carrier substance and is primarily used for large lipid insoluble molecules such as glucose and most amino acids. Its rate is affected by concentration, from a high level to low level,and the amount of specific carrier protein available and the chemical reactions that occur. The number of available carrier proteins available is called the Transport Maximum. (Tm).

Diffusion of water has a special name OSMOSIS. It is the net movement of water caused by a concentration difference across a membrane toward a higher concentration until the solute concentrations are equal. The rate flow for water is faster than regular diffusion and this rate is termed

Bulk Flow. The force that is created by this flow is known as Osmotic Pressure. Since water goes from a lower concentration to a higher one we need to know the affect of osmotic solutions on living cells.

Tonicity is the ability to change the shape or tone of cells by altering their internal water volume.

An ISOTONIC solution means that the concentration of the solute is equal to the concentratiom of the cytoplasm.

[solute] = [cytoplasm] and therefore NO net movement of water and

therefore cells retain their shape

A HYPERTONIC solution has an increased concentration in the solute as compared to the cytoplasm. Water will flow from the cell's cytoplasm (the site of lower concentration) and the cell will shrink or dehydrate, (crenate).

A HYPOTONIC solution has a decreased concentration of solute in a solution (lower concentration) as compared to the cell's cytoplasm. Therefore water will move from the lower concentration (hypotonic solution) into the cell's cytoplasm (higher concentration) and cause the cell to swell and possibly burst or lyse.

B. ACTIVE PROCESSES in Membrane Transport

requires ATP or GTP ENERGY

1. Bulk (Vesicular) Transport : for large molecules.......

a. ENDOCYTOSIS

substances taken into the cell by the infolding of plasma membrane and then form vesicles.

Types of endocytosis are ::

1. Phagocytosis which is used to ingest large particulate matter such as bacteria, tissue.
White blood cells are a good example.

2. Pincocytosis which ingests small particulate matter, such as extracellular fluid.
Examples involve nutrient absorption in the intestinal track.

3. Receptor mediated which is a more specialized version of pincocytosis and is used for proteins and hormone.
Receptors on the plasma membrane will bind with certain molecules causing the ingestion process to be very selective in this case.
Examples :: insulin, iron, and cholesterol based lipoproteins

b. EXOCYTOSIS -- substances are moved from the cell interior to extracellular space.

These substances are within a membranous sac & migrate to fuse to the membrane, and will rupture to release contents outside of the cell.
e.g. cellular secretion of hormones, mucus, neurotransmitters, wastes.

2. ACTIVE Primary TRANSPORT moves molecules from a low concentration to a high concentration. This requires ENERGY, mainly in the form of ATP.

There are specific carrier molecules and enzymes for each substance.

A substance readily combines to its carrier, because of its natural affinity. It is then transported across the membrane.
To release the carrier from the substance, Energy and enzymes are needed.
The carrier is split from the substance and is recycled to be used again, and the substance enters the cell's cytoplasm.

The most important example of Primary Activated Solute Transport is the Sodium-Potassium pump (or called the Sodium pump).

Sodium ion is in very high concentration in the Extra cellular fluid (ECF) verses Potassium ion which is in high concentrations in the intracellular fluid (ICF).

Both can diffuse continuously through specific channels in the membrane, but more sodium ions come in the ICF, than do potassium ions go out to the ECF. This would create an osmotic gradient with water remember that water will follow sodium, thus affecting the intracellular fluid volume of the cell. As you may recall, most intracellular substances like proteins are electronegative and will tend to draw cations inside. If this happens, water will go into the cells (lower to higher) by osmosis and cause the cells to swell.

In the Sodium pump, more sodium ion is transported out than potassium ion in, which occurs at a 3 : 2 ratio, (Na+ : K+) and thus creates an electric potential with a negative charge on the inside of the cell (more positive charges have been removed) and a positive charge on the outside (created by more positive charges due to more Na+ outside the cell)

This is important in transmission of impulses for nerve and muscle fibers. As sodium ion is moved out, it has the reverse affect of osmosis, so that water is moved out.

The electrical potential that is created by the separation of positive and negative charges is known as the TRANSMEMBRANE POTENTIAL.
It differs in each cell that is at rest and is measured in millivolts. This range is -20 to -200 mV depending on the cell.

Thus all cells are said to be polarized and the charge separation ONLY exists at the membrane.

At rest, all cells will maintain a resting membrane potential

Changing the resting membrane potential involves transient opening of ion channels for sodium ion and potassium ion to change and reverse the charge and cause the cell to be excited.

This electrical signaling is important in cells involved in muscle contraction and neuron impulses.

Secondary Active Transport

Cotransport with sodium. Usually involves solutes such as sugars, amino acids, and other ions.

II. Cytoplasm include the cell's contents and have two parts : the cytosol and the organelles.

A. Cytosol is the potassium rich intracellular fluid.

Can contain inclusions (fat vacuoles, melanin, glycogen) that are the byproducts of cellular metabolism or products of cell secretion.

B. Organelles are the "Living portion" of the cell and are grouped in two categories :

These two groups of organelles are ::

1. Membranous
Endoplasmic reticulum, Golgi complex, mitochondria, nucleus, lysosomes, peroxisomes.

2. Nonmembranous
Ribosomes, microfilaments, microtubules, centrioles, centrosomes.

I. Membranous organelles have same membrane structure, the phospholipid Bilayer.

1. Endoplasmic reticulum (E.R.) is a tubular structure that may be elongated (present in cells that secrete large amounts of protein) or spherical (in cells that secrete steroid hormones). Cross section reveals a space in the center called CISTERNS, and a fluid medium called the MATRIX. The function involves in storage, transport, and synthesis. Its membranes are continuous with the nucleus.

Ribosomes may be associated with the surface of the E. R. and are referred as Rough (granular) Endoplasmic Reticulum, and are involved in protein synthesis for cell membrane or export.

Verses no ribosomes (agranular) known a Smooth E. R., and are involved in lipid metabolism and cholesterol synthesis, detoxification of drugs, and glycogenolysis.

2. Golgi Complex is closely associated to the E.R. and consists of stacked flat membrane vesicles involved in transport from the E.R. It processes (modifies and concentrates) and packages material (secretions, membranes, enzymes) in different vesicles.

3. Mitochondria is found in all portions of the cytoplasm. The number will vary per cell depending on the demand.
They can also vary in size and shape and contain their own DNA and RNA, so they can self replicate.

The structure is a TWO Bilayer lipid membrane. The outer membrane is smooth.

The inner membrane is a folded layer (cristae) in a center matrix and contain enzymes to oxidize nutrients to carbon dioxide and water that will liberate Energy used to synthesize ATP in a process called aerobic cellular respiration (and involves oxidative phosphorylation).

4. Nucleus has double membrane that can fuse to form pores, through which substances may pass.
It controls the chemical reactions and reproduction through the storage and processing of genetic information (DNA).

It's organelle, the NUCLEOLUS contain the genetic instructions for producing RNA and ribosomal proteins.
The nucleolus will enlarge when a cell is actively synthesizing proteins.

5. Lysosomes are formed at the Golgi apparatus and are found throughout the cytoplasm. They contain hydrolytic enzymes (called hydrolases) that cleanup and recycle substances to remove unwanted or damaged structures or remove foreign substances. When membrane is unstable -- rupture of lysosomes can result in cell self-digestion known as Autolysis.

6. Peroxisomes are formed from S.E.R. and contain different enzymes known as peroxidases (oxidases and catalases) that neutralize toxins that are absorbed or generated by chemical reactions converting water to hydrogen peroxide or generating substances such as free radicals.

NONMEMBRANOUS Organelles

1. Ribosomes are found free in the cytoplasm and can also be associated with the endoplasmic reticulum. They are composed of 2 subunits: one large and one small. These subunits are made up of RNA and protein. Ribosomes are involved in protein synthesis.

2. Microfilaments are protein strands (ACTIN) that are synthesized by the ribosomes.
They provided the elastic support of the cell membrane, and are involved with microvilli.

They can be organized into tubular structures called Tublin and then arranged in bundles to give structural support as microtubules.

Microtubules can be arranged in groups to form the structure of cilia, centrioles, mitotic spindle.
Microfilaments/Microtubules are known as the CYTOSKELETON that provide internal support.

Cellular Extensions

Cilia : microtubules with centrioles; used to propel substances

Flagella: microtubules with longer centrioles; used to propel the entire cell

Microvilli: membrane folds; used to increase the surface area of the apical region of the cell

THE CELL CYCLE

is a regular sequence of events that can be divided into various activities and function of the cell.

For a majority of the time, the cell in INTERPHASE the subparts include growth phases (G).

G -0 no active replication functions; carries on normal cell processes

G -1 cytoplasmic growth of fluids and organelle. Metabolically active phase can last hours, days, years

S duplication of DNA

G-2 cell prepares for cell division synthesize proteins

and cell division (M) in two parts

Nuclear division called MITOSIS

Cytoplasmic division called CYTOKINESIS

MITOSIS is further divided into four stages

1. Prophase visualize chromatin and dissolution of nuclear membrane

2. Metaphase chromatids align at the center

3. Anaphase chromatids go to the opposite poles

4. Telophase the reverse of prophase and the completion of cytokinesis

Cell division is important for body growth and tissue repair and in the study of cancer & neoplasia.

YOU ARE WHAT YOU EAT

Foods are used by the body to promote growth, maintenance, and repair, but mainly used as metabolic fuels as they are transformed into ATP.

The major nutrients : carbohydrates, lipids, & proteins make up the bulk of what we eat along with water both in our food and drink, and vitamins and minerals in small amounts.

Carbohydrates (CH2O) :

Sugars and starches, the majority from plants

Breakdown of CHO2 will ultimately allow glucose to be delivered and used by the cell as the major source of fuel used to make ATP.

Lipids :

Neutral fats ....meat, dairy --> saturated

oils, seeds, nuts --> unsaturated

Cholesterol.....egg yolk, meat, milk products

The use of triglycerides and cholesterol are controlled by the liver and adipose tissue.

Fats provide an energy source, cushion, insulate, & allow for absorption of fat soluble vitamins

Cholesterol provides structural basis for bile salts and steroid hormones.

Proteins :

animal products.....best source of all essential amino acids

function

structure --> nonreactive, water insoluble, support

Control Mechanism of Cells

Two important cellular functions include the control of protein synthesis (and therefore other functions) by the genes in the nucleus, and transport of substances through the cell membrane.

Most all of these functions require ENERGY and the principal nutrients from which the cell extracts energy are | Oxygen, Carbohydrates, Fats, Proteins.
The carbohydrates, fats, proteins are further converted into their basic components before entering the cell.

Carbohydrates ----> Glucose, Fats--->Fatty acids, Proteins -----> Amino acids.

These will chemically react with oxygen under the influence of various enzymes that control Energy released from the nutrients used to form high energy compounds, such as ATP.

Remember the nucleotide : adenine + phosphate + ribose called adenosine monophosphate (AMP).
Two more phosphate radicals (PO ) can be added to form high energy phosphate bonds....

AMP + P ----> ADP, ADP + P -----> ATP.

ATP is always available to release energy rapidly, and a major portion of ATP in the cell is formed in the mitochondria. ATP is used in three major cell functions :

1. Membrane transport to transport ions of calcium, phosphate, chloride and hydrogen and the Sodium/Potassium pump.

2. Synthesis of chemical compounds such as protein synthesis by the ribosomes, as well as synthesis of phospholipids, cholesterol, purines, pyrimadines.

3. Mechanical work --- Energy for muscle contraction, including ciliary motion.

Lets go back to the mitochondria and remember the structure as having two membranes : an outer smooth membrane and an inner membrane folded forming cristae in the matrix. Remember the function of the mitochondria....the formation of ATP and look at the several steps.

When glucose enters the cell it is subject to enzymes in the cytoplasm that converts it into 2 molecules of pyruvic acid in a process called glycolysis. Only a small amount of ADP is changed to ATP and accounts for less than 5% of the overall energy metabolism of the cell. The fatty acids, amino acids, and pyruvate are further converted in the mitochondrial matrix into a compound called acetyl-CoA. Enzymes further act on this substance to create a series of chemical reactions called the Krebs cycle (or citric acid cycle). Acetyl-CoA is eventually split into carbon dioxide and hydrogen atoms. The carbon dioxide will diffuse out of the mitochondria and cell.

The hydrogen atoms combine with a carrier substance NAD and are carried to the surface of the selves in the mitochondria. On these shelves are oxidative enzymes and the enzyme ATPase. The oxidative enzymes cause the hydrogen atoms to combine with Oxygen in several sequential chemical reactions.

Hydrogen will donate its electron to the electron transport system. This electron will eventually be accepted by Oxygen. The energy that is released from the combination of the ions of hydrogen and oxygen is used to activate ATPase and drive the reaction to manufacture ATP from ADP. The formation of ATP in this matter is called oxidative phosphorylation. ATP is then transported out of the mitochondria by facilitated and simple diffusion into all parts of the cytoplasm and nucleoplasm where Energy is used for cellular reactions.

Lets revisit GLYCOLYSIS.

1. It takes place in the cytosol in a sequence of reactions that convert glucose to pyruvate with the production of ATP.

2. It is a prelude to the citric acid cycle in AEROBIC respiration in which pyruvate is completely oxidized to carbon dioxide and water.

Glucose---->Pyruvate------> Carbon dioxide + water (with oxygen)

------> LACTIC ACID (when oxygen is limited)

------> Ethanol (by yeast and microorganisms)

Glycolysis is stimulated when the energy charge of the cell is low. The rate is controlled by a kinase enzyme which is inhibited by high levels of ATP. The conversion of pyruvate to Acetyl-CoA in the mitochondria is an IRREVERSIBLE step, therefore the cell must control the activity of the enzyme pyruvate dehydrogenase.

Metabolism Summary

Foods are broken down into components before entering the cell :

proteins ---> AA

fats ---> glycerol, fatty acids

CH2O ---> glucose

These components are then converted to pyruvic acid &/or acetyl CoA in the cytoplasm of the cell.

Acetyl CoA is used in the Krebs Cycle and undergoes an oxidative breakdown in the mitochondria to release carbon dioxide and hydrogen.

DNA review

Synthesis of enzymes and other specific proteins are regulated by DNA, thus determining the structure and functions of the cell.

Series of nucleotides with a variable base sequence that determine the genetic code. The sequence of 3 nitrogen bases called triplets can specify :

1. A single amino acid

2. Initiation site

3. Termination site

The genes of the DNA in the nucleus controls the formation of other substances in the cell's cytoplasm by forming RNA in a process called TRANSCRIPTION.
One strand of DNA acts as a template for synthesis of RNA.

The assembly of the RNA nucleotide (ribose, phosphate, bases : A,G,C,U) is under the influence of the enzyme RNA polymerase.

Three types of RNA can be formed. They are :

1. Messenger RNA (mRNA) a long single strand that carries the codons to the cytoplasm for formation of proteins.

2. Ribosomal RNA (rRNA) stored in the nucleolus and is used in the formation of ribosomes.

3. Transfer RNA (tRNA) a single strand that folds itself into a cloverleaf. It is utilized to carry the activated amino acid to the ribosome where protein molecules are assembled. It has a specific region where the anticodon base sequence can combine with the codon base sequence on the mRNA.

Once the RNA molecules are formed, they diffuse out of the nucleus into all parts of the cytoplasm where they perform their functions termed translation.

DNA--------------------> RNA ---------------------> Protein synthesis

transcription translation

PROTEIN SYNTHESIS takes place in the ribosomes using the mRNA's strand of codons (nitrogen base triplets).

Three phases that occur during this process called TRANSLATION

1. INITIATION

a start signal on mRNA (UAC) causes the binding of the two ribosomal subunits and the matching of the first tRNA anticodon (AUG).

2. ELONGATION

The ribosome reads the code on the mRNA. A tRNA carrying an activated amino acid can bind to the mRNA codon if the tRNA has the COMPLIMENTARY anticodon. Peptide bonds are formed between the amino acids. The tRNA is released and the ribosome moves one codon down the mRNA, to continue the elongation cycle.

3. TERMINATION

Specific terminator codons (UAA, UGA, UAG) form the stop signals on the mRNA strand will end protein synthesis and release the polypeptide chain. The two ribosomal subunits will then dissociate.

Biochemical activates in the cell are controlled by two different methods :

Genetic regulation and Enzyme regulation

Genetic regulation

Gene function is controlled in several different ways. Some genes are normally dormant and can be activated by inducer substances. Other genes are naturally active and can be inhibited by repressor substances. Therefore, the amount of synthesized product can produce a negative feedback control. The gene can be stopped if the concentration of the product is high and the gene can be started if the product concentration drops.

Enzyme regulation

Also controlled by inhibitors and activators and many have negative feedback controls.

In addition to it's normal function, DNA must be able to repair itself because of damage. Chemicals such as dioxins, PCBs, PBBs, and radiation, both ionizing (X-Rays), and nonionzing (UV) can cause one or both strands to break.

Some damage may generate mutations. A frame-shift may occur with the deletion or addition of base pairs causing the information in the code to be out of phase. Point mutations involve changing of a single nucleotide. For instance, a replacement or substitution of a base can change the codon, thus affecting protein synthesis or even change the codon to a terminator codon, to stop protein synthesis and create an incomplete protein. Silent mutations occur when a codon specific for a particular amino acid is changed to another codon specific for the same amino acid.

The genetic regulation of the cells is a dynamic process and is used to preserve HOMEOSTASIS.