Cell: small membrane bound units filled with a concentrated aqueous solution of chemicals and endowed with the extraordinary ability to create copies of themselves by growing and dividing in two

Similarity of all Cells

-DNA

-same components required for DNA synthesis

-D sugars and L amino acids

-ATP for energy

-phospholipid membrane

2 Categories

Prokaryote vs. Eukaryote

I. Prokaryote

-no nucleus

-no cytoskeleton

-no RNA processing

-no internal membranes

-no compartments

II. Eukaryote

-more complex

-10x size of Prokaryote

Main Compartments of Eukaryote

1. Nucleus

-enclosed by nuclear membrane

- holes = nuclear pores lets protein in and RNA out

-contains chromatin

- contains RNA

-contains nuclear matrix = lamenae

-chromatin bound to nuclear matrix

-nucleolus makes ribosomes

2. Cytoplasm

I. Cytosol = liquid

II. Free floating structures (3)

1. Free ribosomes - not bound to anything, make proteins (3 kinds)

-make proteins that stay in cytoplasm

-make proteins that go into nucleus

-make proteins that go in to mitochondria or chloroplasts

2. Cytoskeleton (3 types)

-made of long filaments

Three functions

1. Framework

2. Motility

3. Movement of cargo in the cell

3. Proteasome

-garbage can of the cell

-degrading cytoplasm proteins old proteins and misfolded proteins

-present of self antigens

III.Membrane bound organelles (7)

Exocytosis - vesicle fuses with membrane and components all dumped out of the cell

Vesicles can fuse with membrane bound organelles as well

end membrane system = series of membrane organelles connected by membrane fusion over time.

- inside the membrane bound organelle is equivalent to outside the cell

Endomembrane system drove the evolution of prokaryotic cell to eukaryotic

Evidence

-bacteria and mitochondria are similar size

-mitochondria and their own DNA and divide independent of the cell

-they have their own protein synthesis machinery

-have two membranes

There are 7 membrane bound organelles - most are glycosylated which means they have sugars bound to them on the extra cellular side

1. Rough ER -

3 types of proteins made by rough ER

1. Secreted proteins - proteins get secreted into to the lumen

3. Intralumenal proteins - proteins stay in the ER

4. Membrane bound proteins - proteins that stay in the membrane

2. Smooth ER

-site of phospholipid synthesis

Smooth ER continuous with rough ER continuous with nuclear envelope

3. Transition vesicles

-transport between organelles

-buds off ER and forms golgi apparatus.

-joins with -sis face

4. Golgi apparatus-sorts proteins

-has 2 sides sis and trans

-post office of cell - sorts proteins

-glycosylations process gets modified….vesicles bring back enzymes.

-transition vesicles fuse to form first cisternae of sis face

-cisternae progress though medial to trans while vesicles bud off and bring back enzymes to previous cisternae

5. Secretory vesicles

-secretes to plasma membrane

-comes of trans golgi and fuse with plasma membrane to secret

1. Constitutive secretion - all the time secretion

2. Regulated secretion in response to something. Vesicles line up at plasma membrane and await the signal

Proteins get secreted unless otherwise told

6. Lysosome

-disposal of cell

-proteosome

-disposes of stuff that endocytosed from the cell

-degrades with hydrolytic enzymes that break down macromolecules

Major enzymes

1. Protease - breaks down protein

2. Nuclease - breaks down nucleic acid

3. Lipease - breaks down lipids

- low pH helps to denature proteins

-provides a unique environment in which enzymes can be active (protects the cell)

7. Perioxisome -protects the cell from hydrogen peroxide

Macromolecules (4 Classes)

Types of Bonds (4)

1. Covalent - sharing of electrons, strong

2. Ionic e- donated from one atom to another, dissociated in water weaker than covalent

3 Hydrogen Bond (between molecules)

- partial + partial -

-created by polar molecules

-one atom ahs greater electro negativity and attracts the e- more

-weaker than ionic

4. Hydrophilic bonds (not real bonds)

-all carbons and hydrogens

- groups stick together by the repulsive force of water

I. Carbohydrates

-one sugar = mono

-two sugars = di

Bound to something glyco-

Sugars are hydrophilic

Uses

1. Energy

2. Structure (cellulose)

3. Information - protein sorting

A. Monosaccharides (adloses and ketoses)

-building blocks

-hydrocarbon chain with hydroxyls on almost every chain

-double bonded O is carbonyl carbon.

-long chains for rings

-alcohol = hydroxyl

B. Disaccharides

- one carbohydrate is always links to carbonyl carbon (carbon that is double bonded with O)

-if the hydroxly group on the carbon that carries the aldehyde or ketone is drawn down its alpha and up its beta

II Lipids

-hydrophobic, water soluble, mostly carbon and hydrogen

1. Fatty Acids (3)

-amphipathic

-has hydrophilic and hydrophobic regions

- fatty = hydrocarbon tail, acid = -COOH so one end is polar

A. triglycerides

Glycerol + 3 fatty acids

Hydrophilic head and hydrophobic tail

Condensation rxn gives off water

B. Phospholipids

-2 hydrocarbon chain + PO4- (phosphate group)

-PO4 is very hydrophilic

C. Glycolipids

2 hydrocarbon chains + carbohydrate

-protect the cells from mechanical damage

-lubricate the cells

-cell to cell recognition

How do fatty acids behave in water?

2. form a micelle (glob) in water, hydrophobic tail stick together and hydrophilic heads face out

3. Form a bilayer- hydrophobic tails stay together while hydrophilic tails face out

-has and inner leaflet and outer leaflet

2. Fluidity

More fluid = move easily

Less fluid = move less easy

Lipids do not often change leaflets (flip-flop) when the do there is an enzyme that helps them called flip ease

(lipids are produced in smooth ER and added to only one side of membrane)

A. Purpose of fluidity

1. allows membrane proteins to diffuse and interact

2. Aids membranes in fusion

3. Insures membrane molecules are evenly divided between daughter cells

B. Regulation of Fluidity

Regulated by saturation of lipids

- they are able to pack in tighter

-Double bonds put at kink in the hydrocarbon

3. Cholesterol

-found in many membranes and is amphitheatric

-has a polar head (OH) , rigid planar steroid ring structure and nonpolar hydrocarbon tail

-the oxygen reacts with the head of phospholipids and the nonpolar tail reacts with the phospholipids tail

Reaction with unsaturated phospholipids in a membrane

-cholesterol is smaller than most phospholipids

-fills the gaps created by unsaturated tail (fills in the kinks)

-decreases fluidity of unsaturated membranes

Reaction with saturated phospholipids in a membrane

-cholesterol fits between phospholipids and creates a space

- increases the fluidity of saturated membranes

4. Other lipids (sex steroids and stress steroids which are built from cholesterol)

-steroids usually have hydrophilic groups on both ends of molecule

-This helps the steroid move through the membrane

III Proteins (doers of the cell)

Functions

1. Catalyze

2. Form structure

3. Receptors

A. Protein Structure

- polymers of amino acids also called a polypeptide

1. Amino Acids

-general formula

H

H2N-C-COOH

R (20 possible R groups

4. Classes based on R group

1. Acidic (hydrophilic)

-have one addition carboxyl group in R group

- negatively charged at physiological pH

2. Basic (hydrophilic)

- positively charged at physiological pH

3. Uncharged polar (hydrophilic)

-serine, threonine, tyrosine have on OH group and can be phophorylated

-tyrosine has a ring structure that can change secondary structure

- not charged at physiological pH, but is polar

4. Nonpolar (hydrophobic)

-lipid soluble

-proline, phenylalanine, tryptophan- ring structures

2. Disulfide Bonds

-work like staples to hold the protein together

2 types

1. Intra disulfide bonds = between two cysteine in same polypeptide

2. Inter disulfide bonds = between two cyteines in different polypeptides

3. Peptide Bonds

-amino + carboxyl group = water and peptide bond

-peptide bond is very strong

-one end always has an amino group - N

-other end has carboxyl or C terminal N ---------- C

- backbone (part that doesn’t contain R groups) is amino, alpha ,carboxyl

- backbone repeats and is always the same it’s the side chains that differ

- proteins can go up to 10,000 amino acids -very large

- there is not rotation about the peptide bond, but lots of rotation about single bonds that allow proteins to fold into lots of shapes

- most proteins usually on have one confirmation

-usually form the most thermodynamically favorable confirmation which can be hard to predict

4. Levels of Protein Structure (4)

1. Primary - the amino acid sequence

2. Secondary alpha helix and beta sheet

3. Tertiary - folding of secondary structures

4. Quaternary - subunit structures

Primary - The amino acid sequence

- the final structure of a protein is determined by the sequence of amino acids which is specified by DNA

Secondary

-short portions of a protein fold into a conformation that allows maximum hydrogen bonding

2 Basic patterns

1. Alpha helix

2. Beta sheet

-These are the most common because they involve hydrogen bonding only between the backbone not the R groups

-many primary structures can form these secondary structures

Alpha Helix

- four hydrogen bonds per twist

- only occurs in right handed confirmation

-each oxygen is H bonded that why it’s so stable

- hole down the middle of helix, but not big enough for transport

- R groups are sticking out to the side

A. Hydrophobic Alpha Helix

- An alpha helix with all hydrophobic R groups can pass through membranes

- this is the most common way in which proteins pas through membranes

B. Amphipathic Alpha Helix

-An amphipathic alpha helix aligns with hydrophilic amino acids on side and hydrophobic amino acids on the other

-hydrophilic sides go in , hydrophobic sides go out

-they arrange themselves in the membrane

-can arrange to form an aqueous pore

-makes a hydrophilic hole in the membrane

- H bonding only in the backbone of the chain

B-Sheet