The A&P of the Cell

The cellThe smallest living unit.Your body consists of billions and billions of cell that are all working together to keep you alive.

*The cell theory*1. A cell is the simplest living unit.2. The activity of an organism depends on both the individual and collective activities of its cell.3. The biochemical activities of cells are dictated by the relative number of their specific subcellular structures.4. Continuity of life from one generation to another has a cellular basis.

The composite/generalized cellAll cells in the body have generally three main structures:CytoplasmA plasma membraneA nucleusThe exception to this rule is the fully matured red blood cell, which lacks a nucleus.

Cell Structures: The plasma membraneThe plasma membrane is the defining point of a cell. It separates the inside of the cell from the outside.Another name for the plasma membrane is the phospholipid bilayer.

The phosopholipid bilayerLets break down the phrase phospholipid bilayer.Bilayer= Bi=twoBilayer= two layersPhospho=phosphateLipid=fat

Has a head that contains the choline, a nutrient necessary for building a cell membrane, and phosphate that causes a change in polarity on the cell surface. The head is called hydrophyllic because it is designed to touch water.

Has a tail that is a chain of fatty acids that are insoluble in water. They are called hydrophobic because the fatty acids avoid water at all costs.

Phospholipid bilayer- a two layer lining of phospholipids that have hydrophyllic heads that touch the inside and outside of the cell, and a hydrophobic tail that creates a barrier that defines what stays inside and what stays outside the cell.

Fluid Mosaic modelFluid- movableMosaic- Structure made up of many different parts.Fluid Mosaic Model- a multitude of different proteins float in the fluid bilayer.

Membrane lipidsGlycolipids-lipids with carbohydrate sugars attached. Also act as a cell surface marker.

Transmembrane proteins: Proteins that are in or on the lipid bilayer. Allows the transport of substances and information across the membrane.Interior protein network: provides structural support and helps give membrane its shape.Cell surface marker: self-recognition. Creates glycoproteins and glycolipids that give the cell its own identity.

Transporters: selective; only lets certain substances through.Enzymes: carries out chemical reactions inside the cell membrane.Cell surface receptors: Picks up chemical messages outside of the cell. Glycocalyx: Gives the cell its own ID tag.Cell adhesion proteins: allows cells to stick togetherliterally.Cytoskeletal attachments: surface proteins that interact with other cells are often anchored by the cytoskeleton by linking proteins.

CholesterolCholesterol is a steroid found in the cell membrane of all animal cells. Cholesterol is needed to maintain the cell membrane, and can be produced in our bodies, and retrieved in the food we eat.

No need to copy this downLong hand:(10R,13R)-10,13-dimethyl-17-(6-methylheptan-2-yl)-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-olIUPAC NAME: (3)-cholest-5-en-3-ol

Membrane junctionsAlthough some cells are considered free-floaters inside the body (i.e. rbcs) most cells have some anchoring mechanism to bind themselves together and to other surfaces.

Three factors that can bind cells together.1. Glycoproteins in the glycocalyx act as an adhesive. (tight junctions)2. Wavy contours of the membranes of adjacent cells fit together in a tongue-and-groove fashion. (Desmosomes)3. Special membrane junctions are formed. (Gap junctions)

Membrane TransportOutside of each cell, there is a fluid that is called interstitial fluid. This fluid, derived from blood, acts as a nutrient rich soup.

Membrane Transport continuedAlthough there is constantly information and materials moving back and forth to and from the cell by the access of a transmembrane protein, there are certain selective means by which these materials can enter the cell.

Methods of getting material through a membranePassive ProcessesDiffusionFiltrationActive ProcessesActiveVesicular traffickingEndocytosisTranscytosisPhagocytosis

Passive Processes Diffusion- the tendency of molecules and ions to move from areas of high concentration to areas of low concentration.

Simple diffusionNonpolar and lipid soluble substances diffuse directly through the lipid bilayer. Includes oxygen, carbon dioxide, and fat soluble vitamins. Example: oxygen in blood cells

Facilitated diffusionSome molecules are way too large to fit through a membrane. These molecules, like glucose, need to either be ferried across by a carrier molecule, or it needs to be dissolved in a solution, like water and brought through a channel.

Facilitated diffusion

OsmosisThe diffusion of water through a semipermeable membrane is called osmosis. Water can freely move in and out of the cell through specialized channels called aquaporins.

It is all about homeostasisIf two solutions have different concentrations of solutes, then the one with the higher concentration of solutes is called hypertonic.The solution with the lower amount of solutes is called hypotonic.If the two solutions are equal in solutes, it is called isotonic.

Active TransportPrimary Active Transport- Sometimes, when we must maintain a certain concentration gradient of solutes regardless of the outside environment, we can expend ATP and use solute pumps to push a certain amount of solutes against a concentration gradient to maintain a particular level.Example: sodium-potassium pumps

Primary active transport

Secondary active transportAs ions are built up inside a cell membrane, the ions that will eventually leak out can be used to facilitate transport. As these ions are leaking back down a concentration gradient, they can do work by taking other solutes with them.

Vesicular traffickingMovement of large particles through the cell membrane through sacs called vesicles.Exocytosis-shipping materials out of the cell.Endocytosis- bringing materials from outside of the cell to inside the cell.

phagocytosisAlso known as cell eating Phagocytosis is a type of endocytosis that brings in a large particle for digestion. These vesicles are usually brought to and combined with a lysosome that will release enzyme to break down the larger particle into smaller particles. Indigestible materials are then kicked out of the cell through exocytosis.

PinocytosisPinocytosis is a process by which certain cells can engulf and incorporate droplets of fluid. This is a nonselective process.i.e.- Cells of the small intestines

The plasma membrane: resting potentialMembrane potential= voltageAll body cells generate at least some resting potential inside the body. All cells are said to be polarized because of the -50 to -100 mV resting potential they have innately.The negative sign means the voltage occurs inside the cell.

Resting potentialDiffusion causes ionic imbalances that polarize the membrane, and active transport maintains that membrane potential.Typical ions that are associated with resting potential: Na+, K++

If you recallEarlier we made mention in diffusion that solutes move down a concentration gradient. This is true for unpolarized particles and some ions, but not all ions.Some ions can hinder diffusion due to the electrical differences in the potential of the ions and the membrane of the cell.They can also move not only through a chemcial concentration gradient, but an electrical concentration gradient.In conculsion, some ions are driven not only by chemical differences, but electrical differences in the membrane of the cell from which they diffused.

The plasma membranes interaction with the environmentThe glycocalyx is a major player in the cells interaction with the outside.Cell membrane can react with biochemicals and other hormones outside of the cell that may cause the cell to act or react to the outside environment differently.

Cell environment interactions Cell adhesion molecules- also called CAMs. Allows cells to anchor themselves to other cells. (i.e. desmosones) CAMs act as:Velcro like molecules that allow attachment to other cellsAct as an arm for migrating cells to cling to when moving through the body.

SOS signals that rally leukocytes when blood vessels are damaged.Sensors that respond to cell tension synthesis or degradation of adhesive membrane junctions.Intracellular signals that direct cell migration, proliferation (making others of its kind), and specialization.

Membrane receptorsMembrane receptors are integral proteins and glycoproteins that create binding sites on the cells surface.Contact signaling- the actual touching of two cells. The signals given off by the cell tell the cells how to react with each other. *Vital for the immune system*

Chemical signaling- using the membrane receptors to pick up chemicals that bind specifically to said membrane receptor. These chemicals are called ligands.NeurotransmittersHormonesParacrines

G-protein linked receptorsExert effects through a G-protein that usually acts as a middle man to signal the activation or deactivation of ion channels or enzymes. This usually causes a secondary messenger to activate to communicate with the cells metabolic machinery. Secondary messengersCyclic AMPIonic calciumBoth are designed to transfer the phosphate groups of ATP to other molecules.

NO- Nitric oxideChemical that can cause an array of cell activities to occur.Very tiny and thus can slip in and out of the cell very easily.

CytoplasmCellular material between the plasma membrane and the nucleus. Contains three major pieces:CytosolCytoplasmic organellesInclusions

CytosolA viscous semitransparent fluid that suspends other cytoplasmic elements. (i.e. organelles, solutes, etc.)

InclusionsChemicals that may or may not be present depending on cell type. (Melanin, glycogen granules)

Cytoplasmic organellesMetabolic machinery of the cell. Each organelle has its own function.

MitochondriaStructure:Rodlike, double-membrane structures; inner membrane folded into projections called cristae.Function:Site of ATP synthesis; powerhouse of the cell.

RibosomeStructure:Dense particles consisting of two subunits, each comprised of rRNA and protein. Free or attached to rough endoplasmic reticulum.Function:The site of protein synthesis

Rough Endoplasmic reticulumStructure:Membrane system enclosing a cavity, the cisterna, and coiling through the cytoplasm. Externally studded with ribosomes.Function:Sugar groups are attached to proteins within the cisternae. Proteins are bound in vesicles for transport to the Golgi apparatus and other sites. External face synthesizes phospholipids.

Smooth ERStructure:Membranous system of sacs and tubules; free of ribosomes.Function:Site of lipid and steroids (cholesterol) synthesis, lipid metabolism, and drug detoxification.

Golgi bodyStructure:A sack of smooth membrane sacs and associated vesicle close to the nucleus.Function:Packages, modifies and segregates proteins for secretions from the cell, inclusion in lysosomes, and incorporation into the plasma membrane.

LysosomesStructure:Membranous sac containing acid hydrolases.Function:Site of intracellular digestion.

PeroxisomesMembranous sacs of oxidase enzymes.The enzymes detoxify a number of toxic substances. The most important enzyme catalase, breaks down hydrogen peroxide.

CiliaStructure:Short cell-surface projections; each cilium is composed of nine pairs of microtubules surrounding a central pair.Function:Coordinated movement creates a unidirectional current that propels substances across cell surfaces.

FlagellaStructure:Like cilium. But longer. Only found in sperm cells in humans.Function:Propels the cell.

MicrovilliStructure:Tubular extensions of the plasma membrane; a bundle of actin filaments.Function:Increase surface area for absorption.

NucleusStructure:Largest organelle. Surrounded by the nuclear envelope; contains fluid nucleoplasm, nucleoli, and chromatin.Function:Control center of the cell; responsible for transmitting genetic information and providing the instructions for protein synthesis.

Nuclear EnvelopeStructure:Double membrane structure pierced by pores, outer membrane continuous with ER, and is studded with ribosomes on its surface.Function:Separates the nucleoplasm from the cytoplasm and regulates passage of substances to and from the nucleus.

Nuclear envelope

NucleoliStructure:Dense spherical nonmembrane bound bodies that are composed of ribosomal RNA and proteins. When you look at a stain of a nucleus, the dark spot in its center is the nucleoli.Function:Site of ribosome subunit manufacture.

ChromatinStructure:Granular. Thread-like material composed of DNA and histone proteins.Function:DNA constitutes the genes. Often combine with histones to form chromosomes.

The cell cycleIncludes the growth, reproduction and cell death.

InterphaseThe period in the cell cycle where the cell grows, replicates its DNA and prepares for mitosis, this takes up most of the cell cycle.SubphasesG1 phase= 1st subphase, cell growthS phase= 2nd subphase, DNA replicationG2 phase= 3rd subphase, cell prepares for division.

DNA ReplicationDNA helix is unwound and broken by the enzyme DNA helicase. The site where the DNA is being split in two is referred to as the replication fork.Each nucleotide strand serves as a template for building a new complimentary strand of DNA. At the site where new nucleotides attach to the newly forming strand, an amassing of proteins and enzymes called a replisome forms.

At sites where DNA synthesis occurs, there will be RNA primers that actually start the synthesis. When the primer is in place DNA polymerase starts attaching nucleotides to the old strands, the leading strand will be continually synthesized. (3 prime to 5 prime end)the lagging strand will need to be put together in pieces. (5 prime to 3 prime end)

DNA ligase then fixes any breaks in the sugar backbone of the new DNA molecule. Any errors will then be removed by base excision repair (BER) and repaired by DNA polymerase and DNA ligase.

ProphaseNucleoli disappears. Centrosomes begin to move to opposite ends of the cell.Spindle fibers are beginning to form.

metaphaseChromosomes are aligned down the center of the cell.Spindle fibers attach to the centromere located on each of the chromosomes.

anaphaseSpindle fibers pull on the chromosomes at the centromeres.Centromeres on each chromosome split simultaneously.The daughter chromosomes are pulled to opposite ends of the cell.

TelophaseChromosomes are covered by a newly forming nuclear envelope.The chromosomes are then unwound back into chromatin.The cell membrane begins to pinch into two pieces.

cytokinesisThe cell membrane completely seals off and two entirely separate cells are formed.The ring where cytokinesis forms is called the contractile ring and it is composed mostly of actin microfilaments.

Protein synthesisThe creation of a protein. Directed by the genetic code, which occurs by translation of mRNA into protein via tRNA.

genesGenes are segments of DNA that carry instructions for creating polypeptide chains.Polypeptides- a chain of linked amino acids. Proteins are created by linking polypeptides together.All proteins are polypeptides. Not all polypeptides are proteins. Meaning that sometimes more than one polypeptide needs to be added together to form a functional unit.

When a strand of DNA is readThe four nucleotide bases A, T, G, and C form the words that create amino acids. Amino acids are read in groups of threes (3). This is called a triplet and each triplet forms an amino acid.The three nucleotides that are being read are called a reading frame. If the reading frame is adjusted, the resulting amino acids being created may change.

In human DNAThere areas of non-encoding regions called introns, filled with junk DNA that does not contain genetic information.The regions that contain the encoding regions of DNA are called exons.

RNAIt is important to realize that in interphase, DNA never leaves the nucleus. It is because of this that a message needs to be sent to the ribosomes so that they know what proteins to create.

TranscriptionInvolves the transfer of information from a DNAs base sequence to a complimentary base molecule.Each gene has three regions that are important in transcription: The promoter region, the coding region, and the termination sequence.

RNA polymeraseAn enzyme that is present in the nucleus of the cell.RNA Polymerase reads the DNA and is responsible for creating the appropriate mRNA strand.

Promoter regionRegion where the gene acts as a light switch. RNA polymerase recognizes that promoter region and knows to begin transcription there.RNA polymerase binds to the promoter region and the DNA double helix unwinds.

As RNA polymerase runs down the unzipped portions of the DNA, it reads one side of the DNA and creates a complimentary mRNA.

After the complimentary mRNA is produced, it breaks free of the DNA and the DNA is folded back into its helix.

When RNA polymerase runs into the terminator sequence, the RNA folds over on itself and the mRNA stops being produced.After that the mRNA and RNA polymerase break off of the DNA strand.

SpliceosomesRemember that our mRNA still has those junky introns in it, so in order to get rid of them, we have a special RNA protein complex called spliceosomes that enter the mRNA and snip out the introns.

TranslationIn protein synthesis, we take the nucleic acid sequences we have from mRNA and translate them into tRNA.Each triplet in the mRNA base sequence is called a codon. Since there are four nitrogenous bases, and three bases per amino acid, you have 64 possible combinations, and only 20 amino acids. This means multiple sequences must code for one amino acid.

Amino Acid Chart

Once the mRNA is carried out of the nucleusIt is bound to a small ribosomal subunit that is in the cytoplasm.Then tRNA comes into play and starts to bring the appropriate amino acids to the ribosome.tRNA binds the amino acid to the mRNA through hydrogen bonds and the complimentary bases that are attached to the mRNA form the anticodons.

As each new amino acid is brought to the ribosome and bound to the mRNA, the old tRNA is broken off without its amino acid (which is no attached other amino acids) and is sent back into the cytoplasm to get more amino acids.

Once the stop codon on the mRNA sequence has been reached, the synthesis of the amino acid sequence halts and the resulting chain of amino acids is your protein.

Other Roles of DNAAntisense RNAs: A piece of a DNA strand that can intercept the mRNA and bind to it causing the prevention of protein translation.microRNAs: Can silence other parts of RNAs preventing translation.Riboswitches: Acts a switch to turn on/off protein synthesis in response to certain environmental conditions.

Transcription and TranslationAnimationsTranscription:http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.html

Translation:http://vcell.ndsu.edu/animations/translation/movie-flash.htm