1. The Cell
Concepts 6.2,6.3,&6.4

2. 6.2 Eukaryotic cells have internal membranes that compartmentalize their functions
Two types of cells- Prokaryotic and Eukaryotic
Prokaryotic : Bacteria and Archaea domains
Eukaryotic : Protists, Fungi, Animals, & Plants

3. Prokaryotic v. Eukaryotic
Both
Eukaryotic
DNA is in the nucleoid ( not enclosed)
Barrier- plasma membrane
DNA is in its nucleus
No nucleus
Chromosomes ( DNA )
Bigger than Prokaryotes
No organelles
ribosomes
Has organized structure of organelles
Jelly like substance- cytosol
Interior of cytoplasm

4. Prokaryotes v. eukaryotes cont.
The logistics of carrying out cellular metabolism sets limits on cell size.
Bacteria is the smallest cells known and they have been packed with enough DNA to program metabolism and enough enzymes to sustain itself and reproduce.
The plasma membrane only allows a specific amount of a particular substance to pass per second.
As a cell increases in size, the volume grows proportionally more than its surface area. Area increases = linear dimension is squared. Volume increases = linear dimension is cubed.
Large organisms have more cells not bigger ones.
Microvilli- increase surface area without an appreciable increase in volume.

5. Eukaryotic Cell
The biological membranes of the cell & organelles consist of a double layer of phospholipids and other lipids.
Different proteins are attached to its membranes and each type of membrane has a unique composition of lipids and proteins to help with its function.

6. 6.3 The Eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes
The Nucleus
Contains most of the genes ( some genes are in mitochondria and chloroplasts )
The contents is separated from the cytoplasm by the nuclear envelope ( double membrane ) – lipid bilayers with associated proteins
Pore complex lines each pore and regulate entry and exit of proteins, RNA, & large complexes of macromolecules.
nuclear lamina- a net like array of protein filaments that maintains the shape of the nucleus by mechanically supporting the nuclear envelope.
Chromosomes- structures that carry the genetic info.
Chromosomes are made of chromatin, a complex of proteins & DNA.
each Eukaryotic species has a characteristic number of chromosomes ( ex. Humans- 46 and the gametes- 23; fruit fly- 8 and gametes- 4)

7. The Nucleus cont.
Nucleolus- where RNA called ribosomal RNA ( rRNA ) is made from the instructions in the DNA.
In the nucleolus proteins from the cytoplasm are made with rRNA into large and small ribosomal subunits makes a ribosome.
Nucleus controls protein synthesis by making messenger RNA ( mRNA ).
When mRNA gets to cytoplasm ribosomes translate the message into the primary structure of a specific polypeptide.

8. Ribosomes: Protein Factory
Riosomes- complexes made of ribosomal RNA and protein; make proteins.
Build proteins in two cytoplasmic locales free ( suspended in cytosol ) & bound ( attached to ER or nuclear envelope ) ; same structure and can alternate locations.
Free- most protein synthesis in cytosol ( ex. Enzymes that catalyze the first steps of sugar breakdown ) .
Bound- make proteins that go into membranes for packaging within some organelles like lysosomes or secretion from cell.

9. Concept Check 6.3
What role do ribosomes play in carrying out genetic instructions?
They translate the genetic message into the primary structure of a specific polypeptide to make proteins.
2. Describe the molecular composition of nucleoli and explain their function?
Nucleoli consist of DNA & ribosomal RNA (rRNA) made according to its instructions,a s well as proteins imported from the cytoplasm. Together the rRNA & proteins are assembled into large & small ribosomal subunits.
3. What if? If the function of a particular protein in a eukaryotic cell is to make up part of the chromatin, describe the process of its synthesis. Include the cellular locations of all relevant molecules.
In the nucleolus rRNA is made from instructions by DNA then, rRNA + proteins from cytoplasm and form big and small ribosomal subunits then, they exit the nucleus to the cytoplasm to form a ribosome. mRNA is sent to cytoplasm to be translated into the primary structure of a protein’s polypeptide.

10. 6.4 The endomembrane system regulates protein traffic and performs metabolic functions in the cell
Endomembrane system- different membranes of the eukaryotic cell are part of the system. They carry out a variety of tasks in the cell.
Tasks like protein synthesis and their transport into membranes and organelles or out of the cell, metabolism and movement of lipids, and detoxification of poisons.
Membranes either directly relate physically or by transferring membrane segments as tiny vesicles ( sacs of membrane ).
Endomembrane system includes: nuclear envelope, ER, Golgi Apparatus, lysosomes, vacuoles, and the plasma membrane.

11. The Endoplasmic Reticulum: Biosynthetic Factory
ER- extensive network of membranes that it accounts for more than half the total membrane in many eukaryotic cells.
ER membrane is continuous with the nuclear envelope, the space between the two membranes of the envelope is continuous with the lumen of the ER.
Two types: smooth ER- without ribosomes and rough ER- with ribosomes

12. Endoplasmic Reticulum
Smooth ER : functions
Rough ER
Lipid synthesis: oils, phospholipids, and steroids
Metabolism of carbohydrates
Detoxification of drugs and poisons
Steroids produced in animal cells are sex hormones of vertebrates and the various steroid hormones secreted by the adrenal gland. ( cells in genitals)
Detoxification usually involves adding hydroxyl groups to drug molecules, making them more soluble and easier to flush from the body
Alcohol and other drugs use a lot of smooth ER enzymes to increase the rate of detoxification which increases the tolerance to drugs which in return requires a higher dosage.
Stores Ca+ ions
When a muscle cell is stimulated by a nerve impulse, Ca+ rush back across the ER membrane into the cytosol & trigger contraction of the muscle cell.
As a polypeptide chain grows from a bound ribosome, it is threaded into the ER lumen through a pore formed by a protein complex in the ER membrane.
Glycoproteins- proteins that have carbohydrates covalently bonded to them. The carbs are attached to proteins in the ER.
Secretory proteins depart from the ER wrapped in the membranes of vesicles that bud like bubbles from a specialized region called transitional ER.
Transport vesicles- vesicle in transit from one part of the cell to another.
Rough ER makes the membranes for the cell; it grows in place by adding membrane proteins and phospholipids to its own membrane.

13. Golgi Apparatus: Shipping and Receiving Center
Golgi Apparatus- products of the ER, like proteins, are modified, stored, and sent to other destinations.
Consists of flattened membranes sacs – cisternae- looking like a stack of pita bread.
Structural polarity, opposite sides of the stack ( cis face and trans face)
Cis face is near the ER and RECEIVES material, and a vesicle that buds from the ER can add its membrane and the contents of its lumen to the cis face by fusing with Golgi membrane.
Trans face gives rise to vesicles, which pinch off and travel to other sites; SENDS material.
ER products are modified while between the cis and trans regions
Manufactures certain macromolecules by itself. (polysaccharides secreted by cells)
Golgi manufactures and refines its products in stages, with different cisternae containing unique teams of enzymes.
Molecular identification tags, such as phosphate groups added to the Golgi products, aid in sorting b acting like ZIP codes on mailing labels.

14. Lysosomes: Digestive Compartments
Lysosome- a membranous sac of hydrolytic enzymes that an animal cell uses to digest macromolecules.
Their enzymes work best in acidic environments
Hydrolytic enzymes and lysosomal membrane are made by rough ER then transferred to the Golgi apparatus for more processing.
Proteins and digestive enzymes are spared from destruction because of their 3-D shape the protects vulnerable bonds from enzymatic attacks.
Lysosomes carry out intracellular digestion through Phagocytosis- indigestion of smaller organisms or particles.
food vacuoles fuse with lysosomes and its enzymes digest the food. From the digestion comes simple sugars, amino acids, and other monomers become the nutrients of the cell.
Lysosomes use their hydrolytic enzymes to recycle the cell’s own organic material called autophagy.
Lysosomes help the cell continually renew itself. Ex., human liver cells.
People with lysosomal storage disease have a lack of functioning hydrolytic enzymes in their lysosomes. The lysosomes become full of indigestible and it interferes with other cell activities.

15. Vacuoles: Diverse Maintenance Compartments
Membrane-bounded vesicles whose functions
contractile vacuoles- pump excess water out of the cell, thereby maintaining a suitable concentration of ions and molecules inside of the cell
Central vacuole- develops by the coalescence of smaller vacuoles, they come from the ER and Golgi apparatus.
The central vacuole’s membrane is selective in transporting solute ,so the cells sap ( the solution inside the central vacuole ) is different than the composition of the cytosol.
functions of vacuole include: holds reserves of organic compounds, main repository of inorganic ions, disposal sites for metabolic by-products that would endanger the cell if they accumulated in the cytosol, help protect plants against predators by containing compounds that are poisonous or unpalatable to animals, contribute to a cell’s growth when it absorbs water to become larger.

16. Concept Check
1. Describe the structural and functional distinctions between rough and smooth ER.
Rough ER has ribosomes on the outside ,and the smooth ER doesn’t. Both types of ER make phospholipids, but membrane proteins and secretory proteins are all the ribosomes of the rough ER. Smooth ER also functions in detoxification, carbohydrate metabolism, storage of calcium ions
2. Describe how transport vesicles integrate the endomembrane system.
Transport vesicles move membranes & substances they enclose between other components of the endomembrance system.
WHAT IF? Imagine a protein that functions in the ER but requires modification in the Golgi apparatus before it can achieve that function. Describe the protein’s path through the cell, starting with the mRNA molecule that specifies the protein.
The mRNA is synthesized in the nucleus and then passes out through a nuclear pore to be translated on a bound ribosome. The protein is synthesized into the lumen of the ER and could be modified there. A transport vesicle carries the protein to the Golgi apparatus. After more modification in the G. apparatus, another transport vesicle carries it back to the ER, where it will perform its cellular function.