Macromolecules

Lipids

Lipids are a type of fat molecule and is also referred to as triacylglycerol or triglyceride. Main function of lipids is energy storage

Two fats Lipids are made out of:

Prokaryotes

Bacteria^

Bacteria contains peptidoglycan

Protects bacterial cells from environmental stress. Also helps give the cell wall structural strength, protecting the cell wall. ^

Flagella

Allows cell movement

Pili

Is adhesive and allows itself to attach to surfaces.

plasmid

Separated from chromosomal
DNA so it can replicate independently.

Nucleoid (DNA)

Regulates growth and replication. It also controls bacterias activity and reproduction.

Cell wall

Helps maintain cell shape. It also prevents the cell from bursting when theres too much water.

Capsule

Helps cell attach to surfaces in its own environment

Eukaryotes

Endoplasmic Reticulum

Rough endoplasmic reticulum

Produces proteins for the rest of the cell to function. This process is called protein synthesis. Rough ER is also studded with ribosomes.

Smooth Endoplasmic

Synthesis lipids and metabolizes carbohydrates. It also detoxifies drugs and poisons, and stores calcium ions. Smooth ER also lacks ribosomes attached to it.

Lysosome

Lysosomes are membrane-bound organelles packed with enzymes. They also use their hydrolysis enzymes to recycle the cell's own organic material.

Microtubule

Helps cell maintain shape. Involves chromosome segregation and mechanical support, organization of the cytoplasm.

Vacuoles

Food vacuoles:
Are formed when cells take food or other particles

Contractile Vacuoles:
Are formed when many freshwater protist and pump excess water out of cells.

Central Vacuoles:
Are found in many plant cells. And they serve as a repository for inorganic ions, like potassium and chloride.

Microfilament

It is made of a protein called Actin. Microfilaments also assist with cell movement. Microfilaments have other functions which include cell motility, changes in cell structure etc.

Cytoskeleton

Also assist in cells shape, and cell movement.

Peroxisome

Contain digestive enzymes to break down toxic materials in the cell.

Mitochondria

Produces ATP for cell survival and functioning . The mitochondria is known as the powerhouse of the cell.

Golgi apparatus

A process or factory in which they receive proteins from ER

Intermediate filaments

Creates cell cohesion and acute fraction of tissue cell sheets under tension.

Proteins

Protein Structure

Primary Structure:

Amino acids are linked together through dehydration/condensation reactions

Polypeptide Chains

Secondary Structure:

Main chain interactions among different amino acids, amino acids present determine secondary structure.

Alpha Helices

Beta Pleated Sheets

Tertiary Structure:

Polypeptide will fold through the interactions among R-groups

Folds into 3D shape

Quaternary

Polypeptides come together to form a functional protein. R-groups of both polypeptides interact.^

Forms a Functional Protein

Amino Acids

Amino acids include a central carbon (alpha carbon) connected to an amino group, a carboxyl group, a hydrogen (main chain), and a R-group (side chain)

Polar R-groups

Side chain contains a H, CH, or a carbon ring. NH can be classified as non-polar or polar. All non-polar R-groups are hydrophobic.

Non-polar R-groups

Side chain contains a OH, SH, or NH group. NH can be classified as polar or non-polar. All polar R-groups are hydrophillic

Charged R- groups

Acidic R-groups

Side chain contains a complete negative charge and is Acidic. All acidic R- groups are hydrophilic.

Basic R-groups

Side chain contains a complete positive charge and is Basic. All basic R-groups are hydrophilic.

Functions

Receptor Proteins

Cell's response to chemical stimuli

Contractile and Motor Proteins

Movement

Hormonal Proteins

Coordinates an Organisms activities

Structural proteins

Support

Enzymatic Proteins

Accelerates chemical reactions

Defensive Proteins

Protection against disease

Storage Proteins

Storage of Amino Acids

Transport Proteins

Transport of Substances

Nucleic Acids^

When the CO group is in the middle of the chain

When the CO group is at the end of the chain

Alpha Glucose

Beta Glucose

Similarities between eukaryotic and prokaryotic

Both have cytoplasem

Both have cell membrane

Have ribosomes

Both have DNA

DNA

Double Stranded Helix

Deoxyribose Pentose

Polynucleotide

RNA

Ribose Pentose

Ribose Pentose

Includes rRNA, mRNA, tRNA

Nucleotides

5 carbon sugar (pentose)

phosphate

nitrogenous base

Purine

A and G

Pyrimidine

C and T

Phosphodiester Linkage

Lipids

Proteins

Phospholipid Bilayer

Consists of hydrophobic fatty acid tails and a hydrophilic head that can also be unsaturated or saturated

Apart of temperature, presence of cholesterol also affects membrane fluidity

When subject to low temperature, this results in reduced movement of phospholipids causing the membrane to be more gel like and rigid. When subject to high temperatures, the membrane becomes more crystalline and fluid.

Presence of cholesterol regulates the movement of phospholipids in membranes.

The cell membrane is made up of two major components

Types of transport

Passive transport

Substance moves from high-low concentration

Osmosis

diffuses across a membrane from the region of lower solute concentration to the region of higher solute concentration until the solute concentration is equal on both sides

Facilitated diffusion

Use proteins to speed up transport of a solute by providing efficient passage through the membrane

Channel proteins

provide corridors or channels that allow a specific molecule or ion to cross the membrane.

Voltage gated ion channel

Change in membrane potential allows ions to flow across the membrane through a channel

Carrier proteins

Carrier proteins undergo a subtle change in shape that translocates the solute-binding site across the membrane

Electrogenic pumps

transport protein that generates voltage across a membrane

Active transport

Substance moves from low to high concentration

Na+ and K+ pump

Foe every 3 Na+ transported outside the cell, 2 K+ ions are transported inside the cell. This type of uneven charge distribution creates a voltage difference across membranes.

Proton pump

positive charge leaves the cell, we can see a slight negative charge develop inside the cell and positive charge outside just across the membrane.

Cotransport

G- Protein Coupled Receptor (Reception)

Signal molecule binds to receptor, receptor activates and changes shape

G-Protein binds to GPCR and activates by replacing attached GDP to GTP

Activated G-Protien will activate a nearby enzyme

Enzyme removes a phosphate group from G-Protein (Phosphatase)

GTP converts back to GDP, G-Protein is no longer active

Reception

Transduction

Cyclic AMP

GTP G-Protein Binds to Adenylyl cyclase, GTP is then hydrolyzed activating adenylyl cyclase

cAMP activates a protein kinase, cAMP is converted to AMP by the enzyme phosphodiesterase

The activated protein Kinase will then activate another protein kinase with a phosphate group taken from ATP

Protein phosphatase catalyze the removal of phosphate groups from the proteins, protein is inactive again

Last kinase in the signal transduction cascade enters the nucleus and activates a transcription factor

Response

Active transcription factor binds with DNA

Transcription factor stimulates transcription of a specific gene

Resulting mRNAs direct the synthesis of a particular protein

Cell responses can vary due to receptor types or intracellular proteins present

Eeleases glucose from cell: blood glucose level increases

Cell may relax: increase blood flow to muscles

Cell may contract: decrease blood flow to digestive system

Types of reception

Intracellular receptors

Used by small non polar signals because they can diffuse across the membrane

A hormone (aldosterone) passes through the plasma membrane

Aldosterone binds to a receptor protein in the cytoplasm activating it

The hormone receptor complex enters the nucleus and binds to specific genes

The bound protein acts as a transcription facto, stimulating the transcription of the gene into mRNA

The mRNA is translated into a specific protein

Membrane receptors

Used by polar hydrophilic signals (1st messenger) because they cannot diffuse across the membrane alone

G protein linked recept

Ion channel receptor

Tyrosine kinase receptor

Tyrosine Kinase Receptor

Signal Molecules attach to each polypeptide (2) and both polypeptides dimerize

Activated Tyrosine Kinase regions takes phosphate group from ATP (kinase) and adds to tyrosine polypeptides (Autophosphorylation)

Now the fully activated receptor activates relay proteins to carry out cellular responses

aerobic cell respiration

Krebs cycle/ Citric cycle

Located: Mitochondria matrix

Input: 2 Acetyl CoA, 6 NAD+, 2FAD

Output: 6 NADH, 2FADH2, 2 ATP

Net: 6 NADH, 2 FADH2, 2 ATP

The process to produce ATP was at substrate level, phosphorylation

Key steps: Acetyl CoA+ forms citrate. And Isocitrate forms alpha ketoglutarate

Glycolysis

Located: in the cytosol

Inputs: 1 glucose, 2 NAD+, and 2 ATP

Output: 2 pyruvate, 2NADH, 4ATP

Net: 2 pyruvate, 2 NADH, 2 ATP

The process to produce ATP is substrate level phosphorylation

Key steps: Used enzyme hexokinase to convert glucose to G6P which made phosphofructokinase.

Oxidative phosphorylation

located: Proteins in inner membrane (H+ pumped to intermembrane space)

Input: O2, 10 NADH, 2FADH2

Output: H2O, 26-28 ATP

Net: H2O and 26-28 ATP

The process to produce ATP was the coupling od chemiosmosis with the electron transport chain.

Key steps: ATP synthase the formation of ATP which is the endogenic process). ADP + Pi

Pyruvate Oxidation

Located: started in cytosol, finally in mitochondria ira matrix

Input: 2 pyruvate, 2 COA, 2 NAD+

Output: 2 Acetyl CoA and 2 NADH

Net: 2 Acetyl CoA and 2 NADH

No ATP was made

Cell Respiration

An enzyme interacts with a substrate that has a phosphate group.

The reaction leads to formation of a product and transfer of the phosphate group from the substrate to ADP to form ATP.

Another way is through a process called oxidative phosphorylation where energy is used to add a Pi to ADP to form ATP.

How cells make ENERGY

Photosynthesis

Within PS2, photon of light is absorbed by chlorophyll which causes electrons to jump to excited state, then they go back down to the ground state releasing the absorbed energy.

This energy is then absorbed by another neighboring pigment molecule and its electrons jump to an excited state and then go back to ground state releasing the absorbed energy, eventually reaching the main reaction center pair of chlorophyll a molecules.

From here electrons are grabbed by an electron acceptor molecule. Electrons from the primary electron acceptor then go down an electron transport chain eventually reaching chlorophyll a molecules of photosystem 1.

In PS1, photon of light absorbed by one of the pigment molecules causes electrons to be excited, as they go back to the ground state energy is released which eventually reaches the main chlorophyll a molecules.

Electrons of these chlorophyll a molecules jump to the excited state and are grabbed by a primary electron acceptor.

From there electrons go to Ferridoxin then on to NADP+ to form NADPH. The electron hole chlorophyll molecules is supplied from electrons coming down the electron transport chain. This flow of electron transfer is called – non cyclic or linear flow of electrons.

This transfer of electrons down the electron transport chain lead to formation of ATP by photophosphorylation.

Stages of Signaling

Archaea

Extremophile s ^

Extremophiles have two types. One being extreme halophiles which live in highly saline environments. While extreme thermophiles live in very hot environments

provides more chemical stability to the membrane.

Transcription and DNA/RNA processing:

Stages of transcription:

1) Initiation: After RNA polymerase binds to the promoter, this makes the DNA strand unwind and the polymerase initiates the RNA synthesis at the start point of the template strand.

2) Elongation: The RNA polymerase makes its way along the gene, unwinding the DNA and elongating the RNA transcript 5----3. In the make of transcription the DNA strands reform a double helix. Elongation continues until it reaches the terminator.

3) Termination: Once the polymerase reaches the terminator which is the sequence of DNA nucleotides that marks the end of the gene, it detaches from the DNA

Eukaryotic

Transcription occurs in the nucleus and forms pre-mRNA

Contain different promoter elements: For example the TATA box and the initiator elements

Eukaryotes have three types of RNA polymerases, I, II, and III, unlike prokaryotes

Eukaryotes form and initiation complex with the various transcription factors that dissociate after initiation is completed.

RNAs from eukaryotes undergo post-transcriptional modifications including: capping, polyadenylation, and splicing.

Prokaryotic

Transcription occurs in the cytoplasm. It forms mRNA from DNA

Prokaryotes have only one type of polymerase

There is no such structure seen in prokaryotes

Post transcriptional modifications dont occur in prokaryotes

Translation

Stages of Translation

A small ribosomal subunit along with the tRNA bind to the mRNA, scans mRNA to recognize the start codon, then large ribosomal subunit comes to form initiation complex. aminoacyl tRNA synthase corrects the match between tRNA and a amino acid.

Anti-codon on aminoacyl tRNA base pairs with mRNA codon on A site. Peptide bond forms among amino group on the A site and amino group on the P site, removes polypeptide from P site to A site. tRNA translocates and empty tRNA is moves to the E site and is released.

Once stop codon is reached in the A site, a release factor sits in the A site. The complex then disassociates and stops translation.

Prokaryotic

tRNA carries first amino acid, formyl-methionine (f-MET) to the P site

Enzyme that forms peptide bond among amino acids in A and P sites is Peptidyl Transferase^

Eukaryotic

tRNA carries first amino acid, Methionine (MET) to the P site

Peptidyl Transferase is also used to form peptide bonds among amino acids in A and P sites.

same stop codon and is also a GTP driven process.

Protein transport

To the ER

An SRP binds to the signal peptide, halting synthesis momentarily

The SRP binds to a receptor protein in the ER membrane, part of a protein complex that forms a pore

The SRP leaves, and polypeptide synthesis resumes, with simultaneous translocation across the membrane

The signal peptide is removed by signal peptidase (an enzyme in the receptor protein complex)

The rest of the completed polypeptide leaves the ribosome and folds into its final conformation through the addition of carbohydrate groups

A glycoprotein is formed

From the ER, the protein id shipped through a vesicle to the Golgi

The Golgi pitches off transport vesicles to transport the proteins to various locations

Lysosomes, other type of specialized vesicle is available for fusion with another vesicle for digestion

A transport vesicle can carry proteins to the plasma membrane for secretion

Examples of secreted proteins

Digestive enzymes: Amylase

Peptide hormones: Insulin

Milk proteins: Casein

Serum proteins: Albumin

ECM proteins: Collagen

Polypeptide synthesis begins on a free ribosome in the cytosol

To cytoplasm

To organelles

Nucleus

Mitochondria

Peroxisomes

Chlorplasts

Gene Expression

Replication

Prokaryotes

Takes place in the Cytoplasm

Consists of 1 ORI sequence

Carried out by DNA polymerase 1 and 3

Eukaryotes

Takes place in the Nucleus

Consists of multiple ORI bubbles that are fused together to speed up the process

Carried out by DNA polymerase alpha and beta

Transcription

Prokaryotes

Occurs in the Cytoplasm

Done by RNA Polymerase

No additional proteins are needed

Eukaryotes

Occurs in the Nucleus

Done by RNA Polymerase 2

Proteins known as Transcription Factors are needed

Translation

Formation of proteins from mRNA

Prokaryotes

Prokaryotic mRNA's occur in the cytoplasm (Transcription and Translation are coupled)

Eukaryotes

Eukaryotic mRNA's occur in the nucleus