MCAT Biology

Classifications:

Eukaryotes

Prokaryotes

Eukaryotes:

Protists, Fungi, Plants, Animals

Cell wall present in fungi and plants

Nucleus

Multiple linear chromosomes

Ribosomal subunits 40S and 60S

Membrane-bound organelles

Steroids in plasma membrane

Mitosis/meiosis

Prokaryotes:

Bacteria, Archaea

Cell wall present

No nucleus; nucleoid

Predominately circular DNA (plasmid)

Ribosomal subunits 30S and 50S

No membrane-bound organelles

No steroids in membranes

Binary fission

Endosymbiotic Theory

The organelles of eukaryotic cells evolved through symbiosis or prokaryotes

There are similarities between mitochondria, chloroplasts, and prokaryotic cells:

• Multiply through binary fission

• Contain circular DNA

• Have transport proteins called “porins”

Approximate Size and Density of Macromolecules

Nucleus: Diameter (5-10 um) ; Density (1.4-1.7 g/cm³)

Mitochondria: Diameter (1-2 um) ; Density (1.1 g/cm³)

Ribosome: Diameter (0.02 um) ; Density (1.6 g/cm³)

Chloroplasts: Diameter (5-10 um) ; Density (1.6 g/cm³)

Archaea and Bacteria Similar Traits

• Similar shape

• Same ribosomal density

• Multiply through binary fission

• Phospholipids

• Most have cell walls but some do not

• Found in animals, soil, oceans

Archaea Only

• Genetically more similar to eukaryotes than bacteria are

• Some varieties can survive very high temperatures

• Membrane lipids have ether bonds (more resistant than ester)

• Example: methanogens are archaeal cells that produce methane

Bacteria Only

• Membrane lipids have ester bonds

• Some varieties are pathogenic

• Cell walls contain peptidoglycan

• Example: cholera, E.coli

B. The ribosomes would be further from the surface than the mitochondria

Smaller and denser items will get pushed further down

Ribosomes are smaller and denser than mitochondria

Remember: ribosomes are not organelles

Fluid Mosaic Model

Phospholipid Bilayer

Amphipathic

Something that possess both hydrophilic (water-dissolving, polar) regions and hydrophobic (water resistant, nonpolar) regions

Structure of Phospholipid

Types of Proteins in Membrane

Peripheral

• Surface proteins

• Some glycoproteins

Integral

• Completely embedded

• Transmembrane

  • Transport proteins (i.e., channel proteins)

  • Some glycoproteins

  • Membrane receptors

Peripheral vs Integral Abundance

• Many more peripheral proteins than integral proteins

Embedded within the Lipid Bilayer

• Integral proteins can either be partly or fully embedded within the lipid bilayer

• Proteins that are entirely embedded in the lipid layers are hydrophobic

Transmembrane proteins

• A type of integral protein that can cross the membrane

• Some act as transport proteins for ions and molecules

When an integral protein crosses the lipid bilayer, it…

Becomes shaped like an alpha-helix

Glycoproteins and Glycolipids

• On the extracellular surface of membranes, proteins and lipids often have short carbohydrate chains extending out

  • Form hydrogen bonds with the water surrounding the cells which reinforce the cell’s structure

• Glycoproteins can be integral or peripheral

Membrane Receptors

Type of integral protein that binds to molecules outside of the cell and transfer messages from outside the cell to inside the cell

Can be:

• Ligand-gated ion channel receptors

• Enzyme-coupled

• G-protein coupled

Lipid Raft Theory

• Lipid rafts are dense regions of the plasma membrane that are heavy in cholesterols and serve as protein signaling platforms

• They can move across regions of the cell membrane as a unit

• They can also be broken down into smaller rafts

Controversy of Lipid Rafts

They can only be observed indirectly, so the existence of lipid rafts is controversial

Passive Transport Types

Simple Diffusion

Facilitated Diffusion

Osmosis

Filtration

Active Transport Types

Primary vs Secondary

Exocytosis

Endocytosis

• Pinocytosis (cell-drinking)

• Receptor-Mediated

• Phagocytosis

Passive Transport Definition

• Molecules move in and out of the cell according to the concentration gradient

• Relies on KINETIC energy

• No ATP is needed

Simple Diffusion

• Something small

• Going towards gradient

• Gases

Facilitated Diffusion

• Requires transport proteins

• Polar, hydrophilic molecules

• Larger molecules (glucose)

Carrier Proteins: molecules bind to proteins

Osmosis

• Involving a solvent

• Water across a semi-permeable membrane

• Direction of flow depends on the concentration of solute within cell vs external solute

Filtration

• Water molecules and small solutes are pushed through a selectivity permeable membrane due to hydrostatic pressure

• Usually a consequence of cardiovascular activity

Osmolarity

Solute concentration per volume solvent

Osmolality

Solute concentration per mass solvent

• Too high → ADH

Tonicity

Measure of osmotic pressure gradient between two solutions

It is only influenced by solutes that can’t cross the membrane

Isotonicity

Concentration is the same in and out of cell

Hypertonicity

Greater concentration outside the cell

Shrivel = Crenation

Hypotonicity

Greater concentration inside cell

Bloat

Passive Transport Summary:

A. Lyse

The cell will bloat since it is in a hypotonic solution

No change in volume and dividing does not cause bloating

Active Transport Definition

Molecules move against the concentration gradient

Cellular energy (ATP)

Primary Active Transport

Makes DIRECT use of ATP to push molecules against the concentration gradient

Sodium-potassium pump

Secondary Active Transport

Uses INDIRECT forms of ATP to push molecules against the concentration gradient

Electrochemical Potential Driven

Sodium-Potassium Pump

3 Na⁺ OUT

2 K⁺ IN

ATP → ADP

Energy from conversion drives the pump

Electrochemical Potential Driven

• Coupling of power from the primary active transport

• Countertransporter: Na⁺ H⁺

  • More sodium than usual

  • Makes extracellular Na⁺ more driven to go back in (more stronger with pump)

    • Indirectly driven by Na⁺/K⁺ pump

  • Na⁺ coming in causes H⁺ to go out

Countertransporter (aka Antiport)

2 molecules are transported in opposite directions at the same time

Ex. Na⁺/H⁺ and Na⁺/Ca²⁺

Co-transporters (aka Symport)

2 or more molecules transported in same direction at the same time

Ex. Na⁺/glucose and SGLT: sodium-dependent glucose transporters

• SGLT body absorbs filtered glucose

• SGLT 2 inhibitor for diabetes 2

Exocytosis

Ways in which larger molecules are transported from the cell to the extracellular environment

• Proteins, hormones, antibodies, glycogen

Happens via vesicles, which allow watery substances across fatty bilayer

Endocytosis

Bringing large molecules into the cell

Uses a vesicle

Pinocytosis

• Cell takes in molecules across the water in big quantities from the extracellular environment

• Membrane invaginates, then pinches off and brings in particles through the newly formed vesicles

• Lysosomes come and bind to vesicles

  • Produce hydrolytic enzyme mixtures, so they can cut through water

  • Also break down whatever is floating in water

• Efficient way to grab a lot of things all at once and haul them into the cell

• Non-specific

Receptor-Mediated

• Clathrin-dependent endocytosis

• Extremely selective

• Works through receptors clathrin and adaptor proteins

  • Adaptor proteins: govern communication and signaling

    • By linking up in certain configurations

    • Form coordinated communication across the cell

    • Some carry material between organelles within the cell

• AP-2: bind with clathrin

Clathrin Triskelion

One leg binds to adaptor protein, the other 2 bind to more clathrin

Ligand

Phagocytosis

• Cell-eating

• Cell is moving around to find targets to eat

  • cell = phagocyte

• Target large items they want to ingest

• Frequently carried out by immune cells, which detect foreign pathogens

1. Where binding is occurring

2. Shape changes and target is internalized

Process of Phagocytosis

1. Binding and absorption

2. Phagosome formation

3. Phagosome and lysosome to form a phagolysosome

4. Digestion

5. Release of microbial products

   1. Exocytosis

Viruses

Comprised of:

• Protein Coat = capsid protein

• Single or double strand DNA or RNA

Bacteriophages

Viruses that exclusively infect bacteria via lytic or lysogenic processes

Lytic Cycle

1. Virus Enters Cell

2. Virus Replicates

3. Host Cell Lyses (destructs)

4. Release of Viruses

5. New Viruses Infect Other Cells

Lysogenic Cycle

1. Viral Nucleic Acid Incorporated into Host Cell Chromosome

2. Nucleic Acid is Replicated along with DNA

3. No Lysis. Host Cell Survives

4. If DNA Exits Cell, it can Enter Lytic Pathways and Infect

Retrovirus

Single-stranded RNA uses reverse transcriptase to make DNA

DNA-Containing Viruses

1. DNA viruses that replicate in host cell nucleus use host cell’s DNA polymerase

2. DNA viruses that replicate in cytoplasm need their own DNA and RNA polymerases

RNA-containing viruses

Replicate in host cell’s cytoplasm

Central Dogma

DNA → (transcription) mRNA → (translation) Protein

DNA Replication

DNA needs to make more of itself

Pyrimidine

CUT the pie

C: Cytosine

U: Uracil

T: Thymine

Purines

Pure as Gold (AG)

A: Adenine

G: Guanine

Nucleobase Bonding

G - C

A - T in DNA

A - U in RNA

G-C and H-bonds

The more G-C content, the more H-Bonds

Thus, higher melting or annealing temperatures

Nucleotide:

Sugar, Base, and Phosphate Group

Nucleoside:

Sugar and Base only

Sugar and Base Bond

N-Glycosidic Bond

Phosphate and Free 3’-OH bond

Phosphodiester bonds

Reverse Compliment / Complementary Strand

Complementary strand will be in 3’ to 5’ so make sure to make it 5’ to 3’ for final answer

C complements G

A complements T (in DNA) and U (in RNA)

Structure of ATP

DNA is Semiconservative

Two strands running antiparallel

Half old and half new DNA once replicated

Helicase

Helps to unwind the DNA

Primase

A type of RNA polymerase

Polymerases

Enzymes that synthesis chains of nucleic acids

Polymerase III

Haloenzyme

Ligase

Enzyme that fuses Okazaki fragments

Okazaki Fragments

Each individual 3’ → 5’ sections

Single-Stranded Binding Proteins

To stabilize single-stranded DNA (ssDNA) during DNA replication and other cellular processes

Transcription

DNA → RNA

Direction: 5’ → 3’

RNA polymerase; sense vs anti-sense

Stopping

Post-transcriptional modifications (hnRNA → mRNA)

RNA Polymerases

rRNA → RNA pol I

mRNA → RNA pol II

tRNA → RNA pol III

RNA Processing Steps

1. Capping: Methyl G to 5’ end

2. Polyadenylation; adenosines to tail (3’ tail)

3. Editing: bases changed or deleted

4. Splicing: Intron removed, exons expressed in the final RNA

Translation

Codon: 3 letters; each codon stands for an amino acid

64 different combinations

• Degeneracy, tRNA wobble

• tRNA, rRNA, and protein synthesis

• Direction of synthesis termination

• Point mutation, frame shift mutation, nonsense mutation, missense mutation

Where is the information for eukaryotic cell survival and function stored?

In the nucleus as DNA

Transcription and translation allow the cell to…

Communicate general information as mRNA

used as a blueprint to build proteins

Transcription Steps

1. Initiation: RNA polymerase binds at the promoter region of a specific gene to open the DNA double helix

2. Elongation: Base-pairs are added in the 5’ to 3’ direction (U replaces T in RNA)

3. Termination: mRNA is released

4. Processing: prevent degradation: add 5’ cap and poly-A tail ; splicing: remove introns and join exons

Translation Sites:

Ribosomes are composed of a large and small subunit that come together to form 3 sites:

• A: a tRNA molecule carrying a specific amino acid binds to the corresponding mRNA codon

• P: an amino acid is added to the growing polypeptide chain

• E: tRNA is released from the ribosome

Catalysts

Increase rate of rxn (forward and reverse)

Enzymes and Activation Energy

Lowers activation energy

Enzymes do NOT change:

• Equilibrium constant

• Free energy (delta G)

• Enthalpy (delta H)

Enzymes are ___ in reaction

Recycled

Appear in products + reactants

Enzymes are sensitive to…

pH and temperature

Purpose of Cofactors and Coenzymes

To improve enzymatic function

• Apoenzymes

• Holoenzymes

• Prosthetic Groups

Cofactors:

In organic molecules, metal ions (Zn⁺², Cu⁺², Fe³⁺)

Coenzymes

Small, organic, vitamin derivatives (NAD⁺, FAD, coenzyme A)

Six Classification for Main Enzymes: LIL’ HOT

Ligase

Isomerase

Lyase

Hydrolase

Oxidoreductase

Transferase

Ligase

Join, use ATP

Isomerase

Rearrangement, isomers (constitutional and stereoisomers)

Lyase

Cleavage without H₂O

Hydrolase

Cleavage with H₂O