Bio Concept Maps

Bio Concept Maps

Connections

Signal transduction pathways are required to create a response that could result In bulk transport.

Adenylyl cyclase is activated by g-proteins, which helps catalyze cAMP.

DNA Structure

In nucleic acid, they have phosphorus and in proteins, they can have sulfur; using that knowledge, we can connect the Hershey and chase experiment to using radioactive phosphorus and sulfur respectively to see what was concentrated within the bacterium.

Cell Resp/ Photosynth

Chemiosmosis connects to passive transport/osmosis because the movement of h+ down their concentration gradient.

Energy for active transport is required but it does not have to be ATP, it could be from electrons being sent down the electron transport chain through the different complexes.

The mitochondria and the chloroplast produce ATP similarly in which they both pump H+ against the conc. gradient. In both of these processes, the energy associated with this is used to add inorganic phosphate to ADP to form ATP.

Protein pumps are used in cellular respiration to transport protons into the inter-membrane space.

Photosynthesis and cellular respiration are reversed reactions to each other so knowing one, you essentially know the other.

Transcr/ Translat

Animal cell part with ER connect to translation using the ER.

A Common component of the cell is a ribosome, and they are known for making proteins, so how do they do that, through translation.

In prokaryotes, 5’cap and 3’ tail is not put on mRNA since translation happens simultaneously as DNA is transcribed into mRNA as opposed to the cap and tail being in eukaryotic mRNA to protect from the environmental dangers leaving the nucleus.

Glycoproteins

Protein, Lipids, and Carbs connect to Glycosylation. They are all used. Carbs are attached to proteins or lipids to create glycoproteins or glycolipids. 

Topic 2: Energy and Cell Communication

ATP Formation

Process in which energy is made for the use of the cells.

Photosynthesis

The process in which a plant uses sun energy to create their own energy within.

Citric Electron Flow

Electrons need to be transferred from the primary receptor to the p700 chlorophyll molecules to continue the process and create NADPH. Sometimes, there is too much NADPH present, so the electrons from the acceptor are transferred to FD. From there, they go to the cytochrome complex, the constant movement of the electron causes the formation of ATP.

Cell Respiration

The processed breakdown of glucose in order to create ATP.

Chemiosmosis

Part of Oxidation Phosphorylation

At first, complexes pump out H+ against their concentration gradient into the intermembrane space. (Occurring in electron transport chain)

After that occurs, the intermembrane space gets packed with H+ so they go back in. When this occurs, the H+ cross with the help of a ATP Synthase. The energy used to cross the protein is used to add a phosphate to ADP. When the phosphate attaches to ADP it creates ATP.

Succinyl CoA is turned into succinate which allows a phosphate to attach to GDP to turn it into GTP. When GTP is going to cycle back, ADP gets close and removes phosphate from GTP. This allows the phosphate to connect to ADP to create ATP.

Glycolosis

Step 7 of Glycolysis: 1-3 biphosphate glycerate needs a phosphate to be removed in order to become 3-phopshate glycerate. Phosphate is removed and it attaches to 2 ADP to form 2 ATP.

Step 10 of Glycolysis: Phosphoenol-pyruvate needs to have a phosphate removed to turn into pyruvate. So pyruvate can have a function later in pyruvate oxidation. The phosphate group leaves and it attaches to 2 ADP to form 2 ATP.

Anaerobic Fermentation

Fermentation occurs when there is no O2 present within the system. Glycolysis still occurs though.

Lactic Acid

Pyruvate is converted to lactate through NAD+ regeneration.

Alcohol

Pyruvate is converted to acetaldehyde and through NAD+ regeneration, ethanol is formed.

Aerobic Cell Respiration

Oxidative Phosphorylation

Oxidative Phosphorylation is broken up into two processes: The Electron Transport Chain (ETC) and Chemiosmosis

In the ETC:

• Electrons carried by NADH are sent to Complex I and e- carried by FADH2 is sent to Complex II
• e- from complex I and II are sent to Q then Complex III.
• Then to Complex IV then to be finally accepted by O2 to make water.
• Complexes I, III, and IV are H+ pumps and the energy released by sending e- down the ETC powers the proton pump to intuitively pump H+ out into the intermembrane space.
• As a result of this chemiosmosis is able to happen.
• Since there are a lot of protons in the intermembrane space, a proton gradient will form to go back inside the matrix and to do this, an enzyme called ATP Synthase will perform facilitated diffusions and the energy of the gradient will activate the enzyme and will add a phosphate ADP to make ATP.
• This is especially important since this is the point where the most ATP is made in cell respiration.

Citric Acid Cycle

Key Ideas are:

• Step 1: Acetyl CoA binds with oxaloacetate to make citrate
• Step 3: Isocitrate is converted to alpha-Ketoglutarate and CO2 and NADH
• Overall, a miniscule amount of ATP is made as well as FADH2 and NADH is made to be electron carriers for the ETC.

Pyruvate Oxidation

Pyruvate is oxidized to make Acetyl CoA.

Glycolysis

Key ideas are:

• Step 1: Hexokinase puts a phosphate on a glucose from ATP to make it Glucose 6-phosphate, making it more reactive.
• Step 3: Phosphofructokinase phosphorylates Fructose 6-phosphate to make it into Fructose 1, 6-bisphosphate.
• Glucose is oxidized to make pyruvate as the end product as well as NADH and a small amount of ATP.

Starts with:

Reception, then Transduction, and ends with a certain response.

Response

Based on the transduction pathway, different responses arise.

Let's take a look at the different responses to the epinephrine hormone...

Blood Vessel Constriction

• Epinephrine binds to an alpha receptor on a smooth muscle cell in the wall of a intestinal blood vessel.
• The cell contracts in order to allow less blood to flow with a constricted vessel to the intestines.

Blood Vessel Dilation

• Epinephrine binds to a beta receptor on a smooth muscle cell in the wall of a skeletal muscle blood vessel.
• The cell relaxes in order to allow more blood to flow with a dilated vessel to the skeletal muscle.

Blood Sugar Increase

• Epinephrine binds to a beta receptor on a liver cell.
• This results from glycogen breaking down in the reserves within the cell. Then to be released to effectually increase the blood sugar levels in the blood.

Transduction

Relay Molecules are converted to bring about a certain response through transduction.

2ndary Messenger cAMP

Cyclic AMP is a secondary messenger in transduction of the G Protein signaling pathway. Secondary messengers, mainly act to amplify the signal to render a greater response.

• When GTP/G Protein system binds to Adenylyl Cyclase, cAMP is made through phosphorylation of the enzyme with ATP coming from chemiosmosis in aerobic cell respiration.
• cAMP will then activate a Protein Kinase
• Depending on the process, there may be multiple protein kinases, the process may go through a phosphorylation cascade.

Phosphorylation Cascade

• Relay Molecule activates Protein Kinase (PK1)
• Then PK1 activated PK2 through the transfer of a phosphate from ATP, phosphorylation.
• This begins the cascade.
• PK2 activates an inactive protein through phosphorylation.
• In order to remove the phosphate off the protein kinase and active protein, a phosphatase is required and that is what PK2 and an active protein go through to convert them to their inactive forms.
• This process is necessary since the system does not need an excess amount of the response needed.

Reception

Reception can rely on different receptor-ligand systems.

Intracellular and Membrane Receptors

Receptors can be on the cell membrane or within the cell, intracellular.

• Membrane receptors bind to large and/or polar ligands since they cannot passively diffuse across the membrane.
• Usually transmembrane proteins
• Can be hormones, lipoproteins, extracellular matrix, neurotransmitters, and many other molecules bonded to it
• Intracellular receptors bind with small nonpolar ligands since they can diffuse past the membrane easily.
• A common example of this kind of reception deals with the steroid aldosterone.
• The hormone will bind to the intracellular receptor after diffusing across the membrane
• The hormone-receptor system enters the nucleus through the nuclear pore to bind to a certain gene to act as a transcription factor.
• DNA is transcribed to mRNA then translated to a protein

Intracellular Receptor

Membrane Receptor

Ion Channel Receptor

Ligand-gated ion channels require a specific ligand to bind to the receptor in order to open the channel protein to allow certain ions like Ca+ and Na+ though.

Tyrosine Kinase Receptor

Tyrosine Kinase Receptor:

• Made of two polypeptides, these polypeptides dimerize when a signal molecule is bound to each polypeptide
• Each polypeptide has the ability to function as a kinase (an enzyme that adds phosphate groups to something).
• Each polypeptide on dimerization functions as a kinase --> takes phosphate groups from ATP and adds it to other polypeptides (autophorylation)
• Activated receptor can now interact with other proteins to bring response from cell

*Phosphate groups are added to tyrosines --> referred to as Tyrosine Kinase Receptor)*

G-Protein Coupled Receptor (GPCR)

G-Protein Coupled Receptor (transmembrane protein):

• Types of Signal Molecules that use GPCR: Protein hormones, neurotransmitters, etc.
• GPCRs are all similar in structure; they typically bind to G Proteins
• G-Proteins are named this because they interacted with Guanosime Diphosphate (GDP) or Guanosine Triphosphate (GTP).

How GPCR Functions:

• Things Involved: GPCR, G-Protein, and an enzyme -- all inactive in the membrane
• G-Protein has the ability to bind both GDP and GTP, but when bound to GDP, it is in an inactive form.
• G-Protein is important because it needs to alter its shape to bind to GTP --> once GTP is bound, it can activate the enzyme

How Does the G-Protein Alter Its Shape to Bind to GTP:

• The signal molecule binds to GPCR.
• Once bound, there is a slight alteration in GPCR shape, this allows for G-Protein to bind to signal molecule
• This causes GDP (inactive when bound to G-Protein) to be replaced with GTP on G-Protein
• G-Protein is now bound to GTP, which makes it active
• Active G-Protein can now activate a nearby enzyme

*This all happens at Reception*

Topic 3: DNA structure, replication, expression and regulation:

Protein Modification

Folding

This is where the protein enters the ER and where a linear polypeptide folds into its characteristic and functional three dimensional structure. Amino acids in the ER react with each other to produce the three dimensional shape needed. This is now known as the native state. Failure to fold produces inactive proteins.

Glycosylation

Glycosylation is the process by which a carbohydrate is covalently attached to a target macromolecule, typically proteins and lipids. This modification serves various functions. Some proteins do not fold correctly unless they are glycosylated.

Multimeric Protein Assembly

Proteolytic Cleavage

Proteolytic cleavage is the process of breaking the peptide bonds between amino acids in proteins. This process is carried out by enzymes called peptidases, proteases or proteolytic cleavage enzymes.

Translation

Translation in Prokaryotes

Translation in prokaryotes is relatively the same as in eukaryotes.

However, the start amino acid for them is f-met.

The small subunit is connected to a section called Shine-Dalgarno.

Translation in Eukaryotic

This occurs in the cytoplasm of the cell.

Uses mRNA and tRNA to connect amino acids so protein can be made.

This protein is later used in different parts of the cell or throughout the body.

tRNA is made.

TRNA- a single R N A strand, this anticodon binds the codon (5’ to 3’) bring the correct amino acid to be added during translation. Amino acid and the appropriate tRNA enter the active site of the specific synthetase, Tyrosyl-tRNA synthetase. Uses ATP to create covalent bonding between both. Finally is released to work in eleongation

mRNA is decoded to produce the specific sequence of amino acids in a polypeptide chain.

TRNA binds with the small subunit, which is connected to the mRNA. It binds to the start codon AUG. Then, the large ribosomal subunit come along to form a translation initiation complex. 

Elongation

Large subunit is composed of 3 sites E, P, and A. The P site holds the tRNA that carries the growing polypeptide chain. The A site holds the tRNA that carries the next amino acid to be added to the chain. The E site is the exit site, where discharged tRNA’s leave the ribosome. Amino acids are added from N to C direction. This is repetitive until there is a stop codon. The amino acids are connected by peptide bonds.

Termination

When amino acid reaches a stop codon (UAA, UAG, or UGA) translation is stopped. This causes the protein to be released. This allows the protein to take its own path based on what kind of protein was made.

Protein with ER signal

Contain a signal peptide that allows the ribosome to go towards the endoplasmic reticulum. The signal peptide is connected to the signal recognition particle. This brings the protein closer to the ER membrane. When it reaches the membrane, the ribosome is released, and the protein goes into the ER membrane. After this, it travels to the Golgi apparatus where it receives the information to go to the plasma membrane and complete its task. 

Regular protein

The protein is released and it goes and works for either nucleus, peroxisomes, or the mitochondria. 

Transcription and Gene Regulation

Gene Regulation in Prokaryotes

A prime example of gene regulation in prokaryotes is with the lac operon.

• This regulation occurs in transcription.
• There are two types of regulation
• Positive which uses activator proteins to bind to the operator which allows for transcription to happen.
• And Negative which uses repressor proteins to bind to the operator which does not allow for transcription to occur.
• The operator is the on/off switch for expression and control operons which are clusters of genes.

In the lac operon...

• lac, meaning lactose, will suggest that lactose is needed for this operon to work.
• It uses both positive and negative responses meaning both activators and repressor are used.
• Regulatory gene I is always active which codes for the repressor protein and is upstream from the promoter.
• The constitutive genes are lac Z which codes for beta galactosidase which breaks down lactose into glucose and galactose, lac Y which codes for permease to allow lactose into the cell, and beta galactoside-transacetylase.
• Repressors are always active so if glucose is not present, the repressor will bind to the promoter and expression be at the basal level.
• If lactose is present and glucose is not as present, the repressor will bind to allolactose and cAMP will bind to CAP and then bind to the promoter and the operon will be on, meaning there will be high expression.
• If glucose and lactose are highly present, glucose will block the production of cAMP through blocking adenylyl cyclase and through the transitive property, cAMP will not bind to CAP and thus not bind the promoter. This will ultimately lead to basal expression.

Transcription in Prokaryotes

The process of transcription in prokaryotes is the same as eukaryotes except some unique features

• The location of transcription for prokaryotes is in the cytoplasm of the cell since there is no nucleus in prokaryotic cells.
• They use RNAP which is RNA polymerase.
• No 5' cap nor poly A tail is necessary.

Additionally, there is no RNA processing in prokaryotes since translation occurs simultaneously as DNA is transcribed.

Gene Regulation in Eukaryotes

Regulation can occur at any point of the process from making DNA into pre-mRNA in transcription or by making proteins in translation.

There are two types of expression of a gene in regulation:

• Basal: Low-level expression which results in low level DNA transcription, this results in the mRNA made leaving the nucleus and instantaneously being degraded.
• High Level: High level expression which allow the mRNA made to be used to make a protein through translation.

To allow for these types of expression, there are transcription factors that have different types of expression...

• General leads to basal transcription of DNA
• Specific leads to changing the level of transcription from low to high.
• Needs activators to bind the distal control elements, enhancers, to increase the transcription level.
• A DNA bending protein will then bend the DNA strand to make the activator closer to the promoter where mediators and specific transcription factors are bound to it.
• The activators are then bound to the mediator
• RNA polymerase II is then recruited to transcribe the DNA.

Transcription in Eukaryotes

• Transcription in Eukaryotes requires RNA Polymerase to make RNA nucleotides for pre-mRNA.
• The RNA Polymerase II transcribes the DNA from 3' to 5' to make the antiparallel pre-mRNA strand from 5' to 3'.

Transcription in eukaryotes occurs in the nucleus of the cell.

RNA Processing

The reason transcription in eukaryotes makes pre-mRNA instead of regular mRNA like prokaryotes, they have introns that do not express any genes and they need to be removed. Additionally, the newly formed pre-mRNA needs to exit the nucleus to be translated by free ribosomes and it needs to be protected from degradation in the environment so...

Then spliceosomes come in to remove the introns and connect the exons, at this point, the pre-mRNA is then matured in to mature mRNA and is ready to exit the nucleus.

Initiation

• A Eukaryote has a promoter usually consisting of As and Ts called the TATA box upstream of the start point of transcription.
• Transcription factors bind to the DNA strand so RNA polymerase binds to the promoter.
• RNA Polymerase unwinds the DNA and transcribes the DNA from 3' to 5' to make the pre-mRNA 5' to 3'.

Elongation

• This is where RNA polymerase II adds the complementary RNA nucleotide to the correct nucleotide base in the 5' to 3' direction.
• This processes downstream from the start point of transcription.

Termination and RNA Processing

Termination

• This process occur within the nucleus still and adds the 5' G cap on the 5' end of the pre-mRNA and a poly A tail to the 3' end.
• The poly A tail needs a sequence , AAUAAA, to add the tail with the help of poly A polymerase.

RNA Processing

The reason transcription in eukaryotes makes pre-mRNA instead of regular mRNA like prokaryotes, they have introns that do not express any genes and they need to be removed. Additionally, the newly formed pre-mRNA needs to exit the nucleus to be translated by free ribosomes and it needs to be protected from degradation in the environment.

Then spliceosomes come in to remove the introns and connect the exons, at this point, the pre-mRNA is then matured in to mature mRNA and is ready to exit the nucleus.

DNA Structure and Replication

Replication

We first start off with double stranded DNA (dsDNA) and create a replication bubble. This replication bubble happens at the origin of replication (sequence of nucleotides, aka ORI). The replication bubble creates two forks at each end of the bubble, and now each separated stand has to be used as a parent strand to form complementary daughter stands at thee ORI, suggested by the semiconservative model.

DNA is separated at the ORI with the help of helicase, which separates the two strands to form the replication bubble. SSB's (single stranded proteins) keep the DNA single stranded. Topoisomerase helps relieve any strain caused by the unwinding of DNA.

DNA Polymerase III: enzyme that adds nucleotides only to the 3' end, adds complementary base to daughter strand, needs RNA primer to add nucleotides, needs help of another protein called sliding clamp, contains two DNA polymerases in bacterial replication (DNA poly III and DNA poly I)

Synthesis of Leading Strand: Uses Primase and DNA Polymerase III

DNA Polymerase synthesizes leading strand towards replication fork and only one primer is required to synthesize the leading strand, created in the 5' to 3' direction

Lagging Strand Synthesis:

Multiple RNA primers have to be laid down and then extended by DNA poly III to form short Okazaki fragments. These RNA Primers are removed by DNA poly I and are replaced with DNA nucleotides. Enzyme Ligase seals any gaps by connecting nucleotides by phosphodiester linkages

Structure

Hershey and Chase

In 1953, Hershey and Chase used bacteriophages (these transfer their genetic material into bacteria cells and reprogram the cells to make more bacteriophages, made of two components: proteins and DNA) to determine what was injected into bacterial cells.

Using two tubes, they labeled one tube with 32P (radioactive phosphorus) and 35S (radioactive sulfur). They infected bacteria with 35S and another set of bacteria with bacteriophages with 32P. These two were mixed into a tube and later shaken to release bacteriophages from the bacterial surface.

They then centrifuged the bacterial cells and looked for radioactivity in the supernatant and pellet. They found that radioactivity was only present inside the bacteria cells when they only used 32P (DNA). This indicated that DNA was injected inside bacteria and not protein.

Messleson and Stahl

Used to find model of DNA replication:

Bacterial cultures are grown in regular 14N and 15N (controls).

After growing 15N in several rounds of bacteria, they were transferred to medium containing 14N.

They were grown for 20 mins -> bacteria is removed -> DNA is extracted from these bacteria and subjected to centrifugation with CsCl -> DNA is combined with CsCl and spun at high speeds -> resulted in a gradient of CsCl concentrations.

The density of CsCl was highest at the bottom of the tube and the lowest at the top.

DNA in this solution formed a band at the point in the tube where the density of CsCl corresponded with its density.

Three bands of distribution are possible

• High density (top of tube)
• Intermediate density (middle of tube)
• Low Density (top of tube)

Messleson and Stahl Conclusion

Chargaff's Rule

Amount of Adenine = Amount of Thymine

Amount of Guanine = Amount of Cytosine

Possible Base Pairings in DNA Double Helix

Purine + Purine: Too wide

Pyrimidine + Pyrimidine: Too narrow

Purine + Pyrimidine: width is consistent with X-ray data

Nitrogenous Base Pairs are held together by hydrogen bonds

Structure of DNA Strand

Watson and Crick

They came up with the double helix model of DNA; this structure satisfies the x-ray image if the two strands were antiparallel.

They used the semi-conservative model to represent DNA, but there were other DNA models that competed.

A) Conservative Model: Two parent strands reassociate after acting as templates for new strands, thus restoring the parental double helix

B) Semi-conservative: Two stands of the parental molecule separate, and each function as a template for the synthesis of a new complementary strand

C) Dispersive: Each strand of both daughter molecules contains a mixture of old and newly synthesized DNA.

Fredrick Griffith (1928)

In 1928, Fredrick Griffith tried developing a vaccine against pneumonia. He injected mice with these cells using two strains of the bacteria, a pathogenic (disease-causing, S-Strain) and a nonpathogenic one (R-Strain).

S-Strain: smooth presence due to the presence of capsule outside the cell wall

R-Strain: lacked the capsule

*capsule made the cell pathogenic*

Mouse Injected with S-Strain (Pathogenic Control): Mouse Dies

Mose Injected with R-Strain (Nonpathogenic Control): Mouse is Healthy

Mouse Injected with Heat-Killed S Cells (Nonpathogenic Control): Mouse is Healthy

Mixture of Heat-Killed S Cells and Living R Cells: Mouse Dies

• Griffith found that the R-Strain has changed to S-Killing
• Something from S-Strain entered living R-Strain and altered the genetic makeup (no one knew that DNA was what transferred)

Topic 1: Cell Structures and Functions

Macro Chemistry

Nucleic Acids

Responsible for Proteins Synthesis

Through Transcription of DNA to mRNA

Then translates mRNA to a functional protein

Carries genetic material of the cell

Like DNA

And RNA

Forms Hydrogen bonds

Between Nitrogenous Bases

Which Consist of Purines and Pyrimidines

Pyrimidines: U/T/C

Purines: A/G

Forms Phosphodiester Linkages

Between C3 and C5

Proteins

Responsible for Functions in the Cell

Cell-Cell recognition

Signal Transduction

Explains how a signal (ligand) leads to a response

Enzymatic Activity

Builds up molecules to more complex structure

This is Anabolic

Which breaks down molecules

This is Catabolic

Transport

Form Disulfide Bonds Ionic Bonds Ion-Dipole Interactions Hydrophobic Interactions Hydrogen Bonds

In Tertiary and Quaternary

Form Hydrogen Bonds

In Secondary Structure

Form Peptide Bond

In Primary Structure

Lipids

Can come in two forms

Unsaturated

Not easily superimposable

If superimposed, the membrane will be more fluid.

Which makes diffusion easier

Double Bonded Carbons

Saturated

No Double bonded Carbons

Superimposes into a unit structure

If superimposed, the membrane will be less fluid.

Which make diffusion harder

Crucial to Phospholipid bilayers in the cell

Membrane bound organelles

Cell Exterior Membrane

Forms Ester Linkages

Between Glycerol and Fatty Acid

Carbs

Provides ENERGY for the cell

Forms Glycosidic Linkages

Polymerizes through dehydration

Common Components of Cells

Mitochondrion

Cytoplasm

Ribosome

DNA

The Three Domains of Life:

Eukarya

Eukaryotic Cells

The cell membrane separates the inside of the cell from what is outside. It controls what can go inside and outside the cell. It also helps with the transportation for the molecules.

Passive Transport

Transportation across the membrane with no use of energy.

Facilitated Diffusion

This is a mode of passive transport. This is used when certain molecules can't pass the membrane. When this happens proteins can be used. The protein will have a channel that will allow certain solutes to cross the membrane.

Requires a PROTEIN

To move large/polar molecules

Osmosis

This is a mode of passive transport. The movement of water molecules from a low concentration to a low concentration. For example sugar cant cross the membrane so it needs water to dissolve and cross correctly.

Which move water

From Low Concentration To High Concentration

Diffusion

This is a mode of passive transport. The molecules cross the membrane from a high concentration to low concentration to create a equilibrium.

Movement of small nonpolar substance

From High Concentration To Low Concentration

Active Transport

Active transport is a mode of transportation across the membrane that uses energy. The molecules go from a low concentration to a high concentration. They move across against the concentration gradient.

Moving substance against concentration gradient

Required ATP

Bulk Transport

Mode of transport across the membrane. This occurs when there are small particles crossing across the cell without using the membrane.

Exocytosis

Occurs when small particles exit the cell as bulk transport.

Excrement of substance

Endocytosis

Occurs when small particles enter the cell. Using the transportation bulk transport.

Engulfing of substances

Receptor-Mediated Endocytosis

This occurs when the receptor proteins in the surface see a molecule they want from the outside. They create a coated vesicle to keep the molecule inside.

Ligand required to to bind to receptor

Molecules are places in a COATED vesicle

Pinocytosis

This occurs when liquids and small particles go into the cell. They create vacuoles to stay in the cell.

"Drinking"

By placing molecules into a vesicle

Phagocytosis

Small food or large particles go into the cell and create a vacuole to stay in there.

"Eating"

By putting food in a vacuole

Organelles of Eurkaryotic Cells:

Extra:

Subtopic

Plant Cells:

1. Nucleus: includes nuclear envelope, nucleolus, chromatin
2. Cytoskeleton: includes microfilaments
3. Golgi Apparatus
4. Mitochondria
5. Ribosomes
6. Smooth and Rough Endoplasmic Reticulum
7. Peroxisome
8. Cell wall: outer layer that maintains cell’s shape and protects cell from mechanical damage; made of cellulose, other polysaccharides, and protein
9. Plasmodesmata: cytoplasmic channels through cell walls that connect the cytoplasms of adjacent cells
10. Chloroplast: photosynthetic organelle; converts energy of sunlight to chemical energy stored in sugar molecules
11. Central vacuole: prominent organelle in older plant cells; functions include storage, breakdown of waste products, and hydrolysis of macromolecules; enlargement of the vacuole is a major mechanism of plant growth

*Italicized is specific to Plant Cells

Animal Cells:

1. Flagellum: motility structure present in some animal cells, composed of a cluster of microtubles within an extension of the plasma membrane
2. Centrosome: region where the cell's microtubules are initiated; contains a pair of centrioles
3. Perixisome: organelle with various specialized metabolic functions, produces hydrogen peroxide as a by-product and then converts it to water
4. Mitochondrion: organelle where cellular respiration occurs and most ATP is generated
5. Lysosome: digestive organelle where macromolecules are hydrolyzed
6. Golgi apparatus: organelle active in synthesis, modification, sorting, and secretion of cell products
7. Ribosomes: complexes that make proteins; free in cytosol or bound to rough ER or nuclear envelope
8. Plasma membrane: membrane enclosing the cell
9. Cytoskeleton: reinforces cell’s shape; functions in cell movement; components are made of protein (includes: microfilaments, intermediate filaments, and microtubules)
10. Endoplasmic Reticulum (ER): network of membranous sacs and tubes; active in membrane synthesis and other synthetic and metabolic processes; has rough (ribosome-studded) and smooth regions (includes rough ER and smooth ER)
11. Nucleus:

• Nuclear envelope: double membrane enclosing the nucleus; perforated by pores; continuous with ER
• Nucleolus: nonmembranous structure involved in production of ribosomes; a nucleus has one or more nucleoli
• Chromatin: material consisting of DNA and proteins; visible in a dividing cell as individual condensed chromosomes

Prokarya

Prokaryotic Cells

Cell Membrane

All prokaryotic cells are surrounded by a plasma membrane, but they do lack membrane-bound organelles.

Bacteria cells contain a fatty acid

Archaea cells contain a Hydrocarbon

Structure of Cell

Major Nutritional Modes of Prokaryotes:

Autotroph:

Photoautotroph:

• Energy Source: Light
• Carbon Source: CO2, HCO3^-, or related compounds
• Types of Organisms: Photosynthetic prokaryotes (ex: cyanobacteria), plants, certain protists (ex: algae)

Chemoautotroph:

• Energy Source: Inorganic chemicals (ex: H2S, NH3, or Fe^2+)
• Carbon Source: CO2, HCO3^-, or related compounds
• Types of Organisms: Unique to certain prokaryotes (ex: sulfolobus)

Heterotroph:

Photoheterotroph:

• Energy Source: Light
• Carbon Source: Organic Compounds
• Types of Organisms: Unique to certain aquatic and salt-loving prokaryotes (ex: Rhodobacter, Chloroflexus)

Chemoheterotroph:

• Energy Source: Organic Compounds
• Carbon Source: Organic Compounds
• Types of Organisms: Many prokaryotes (ex: Clostridium), protists, fungi, animals, and some plants

Organelles of a Prokaryotic Cell:

Archaea

Components of an Archaea Cell

• Lack a defined nucleus which puts them into the prokaryotic category
• Unicellular
• Reproduce Asexually
• Plasmids
• Inclusions
• Flagella
• Pili
• Sometimes may contain Capsules and Slime Layers but can be very rare
• Known for being extremophiles living in areas of extreme conditions such as high in acid, salt, or heat
• Linkage between Phospholipid head and side chain is in the form of L-isomeric form
• Plasma Membrane is found in the form of monolayers
• Cell wall in archaea made to fit the environment of the organism. In some cases may be no cell wall
• Flagella is different from bacteria in that it is powered by ATP
• Includes Cell Wall but is lacking peptidoglycan which is a distinguishing feature between bacteria and archaea. Instead, they contain pseudomurein
• Hamus- long helical tube with three hooks that allow the cell to attach to other cells and to surfaces which encourages the formation of a community
• Cannulae- hollow tube structures that connect cells after division
• Archaeal ribosomes are different in shape from any other ribosome and contain proteins unique to archaea
• Contain ether bonds linking fatty acids to molecules of glycerol
• RNA polymerase of archaea contain more than eight polypeptides
• tRNA has unmodified methionine
• Metabolism differs from bacteria in that there are various types such as dentrification, nitrogen fixation, hyperthermophilic growth, and chemolithotrophy.

Bacteria

KEY:

Bold - Bacterial Chromosome

Underline - Found in both bacterial chromosomes and 'a thin section through the bacterium Corynebacterium Diphtheriae'

1. Fimbrae: attactment structures on the surface of some prokaryotes (not visible on TEM) *TEM is transmission electron microscope
2. Nucleotide: region where the cell's DNA is located (not enclosed by a membrane)
3. Ribosomes: complexes that synthesize proteins
4. Plasma Membrane: membrane enclosing the cytoplasm
5. Cell Wall: rigid structure outside the plasma membrane
6. Glycocalyx: outer coating of many prokaryotes, consisting of a capsule or a slime layer
7. Flagella: locomotion organelles of some prokaryotes

Components of a Typical Bacterial Cell:

• Plasma Membrane: selectively permeable barrier, mechanical boundary of cell, nutrient and waste transport, location of many metabolic processes (respiration, photosynthesis) detection of environmental cues for chemtaxis
• Gas Vacuole: Buyancy for floating in aquatic environments
• Ribosomes: protein synthesis
• Inclusion bodies: storage of carbon, phosphate, and other substances
• Nucleoid: localization of genetic material (DNA)
• Periplasmic Space: Contains hydrolytic enzymes and binding proteins for nutrient processing and uptake
• Cell Wall: gives bacteria shape and protection from lysis in dilute solutions
• Capsules and Slime Layers: resistance to phagocytosis, adherence to surfaces
• Fimbriae and Pili: attachment to surfaces, bacterial mating
• Flagella: movement
• Endospore: Survival under harsh environmental conditions

*Not present in all prokaryotes