Final Concept Map

Once the protein is made it needs o be folded correctly and transported to the correct location in the cell. If a cell doesn't need a functional protein, all possible steps must be viewed to see which can be blocked, thus the functional protein is not made or if it is made it doesn't reach its destination.

Most common step for this is the control at the level of transcription.

Transcription factors have t first bind the promoter then RNA pol II can bind. It's these transcription factors that help regulate/control transcription.

*In transcription we form pre-mRNA which is then processed to form mRNA* Associated with most eukaryotic genes are multiple control elements. These segments of noncoding DNA serve as binding sites for transcription factors that help regulate transcription. Control elements and the transcription factors they bind are critical for precise regulation of gene expression in different cell types.

Activators are created during transcription. They are specific transcription factors that turn on the cell when they enter it.

Activators can allow the transcription process to continue
or it can increase the level of transcription.

Activators are brought into contact with a group of mediator proteins through DNA bending. Then, the protein-protein interactions between the mediator and promoter proteins help to assemble and position the initiation complex on the promoter. This interaction helps RNA polymerase II to bind efficiently to the promoter increasing transcription rates to above basal levels.

Cells control which gene is expressed in a certain part of the body through combinatorial control of gene expression. An example is the liver cell, where activator proteins are present that bind to the enhancer sequences that increase expression of albumin gene. But no activator proteins are present that bind enhancer for crystallin gene (which can be found in the eye cells). In the liver cell, albumin gene has increased expression, while crystallin gene has basal (or background) expression.

Gene Regulation happens in the Transcription stage of gene expression

In prokaryotes genes are organized in gene groups called operons. Some operons preform specific tasks such as the operator(switch)

Activators or repressors( proteins that bond to the operator) control positive or negative regulation of genes

The LAC operon has positive and negative regulation such that all operons code for either positive regulation negative regulation or both such as LAC.

Repressors are created during transcription. They are specific transcription factors that turn off the cell when they enter it.

Repressors can stop the transcription process
or it can reduce the level of transcription if it is too high.

Repressor proteins help to cease the transcription process by binding to the enhancer. This causes RNA polymerase II to lose the ability to efficiently bind to the promoter, therefore, reducing transcription.

Initiation:
In order for initiation to begin,
eukaryotes require transcription factors.
The transcription factors will bind to the
promoter sequence in order to allow RNA
polymerase II to bind.

Elongation:
During elongation, RNA polymerase II
is attached to the +1 nucleotide. From
there, it will begin the synthesis of the
new RNA strand in the 5' to 3' direction.
The new nucleotides will be added to the
3' end of the growing RNA strand.

Termination:
The sequence AAUAAA signals the cell
to make a cut in the pre-mRNA and
release it from the DNA. Then, a modified
G nucleotide (CAP) is added to the 5' end
of the pre-mRNA. Meanwhile, a poly-a tail
is added o the 3' end of the pre-mRNA by
an enzyme called poly-A polymerase.

RNA Splicing:
During RNA splicing, the introns
in the pre-mRNA are removed so
that the exons can be joined
together. Spliceosomes are
responsible for the removal of
the introns. The ending result of
this process is mRNA.

Initiation: brings together mRNA, tRNA bering the first amino acid of the polypeptide and 2 subunits of ribosome (assembly of this complex needs GTP). The small ribosomal subunit along with the tRNA fist bind the 5' cap, scans mRNA to find the first AUG (Methionine). Then the large ribosomal subunit comes along to form a transition initiation complex. The first tRNA carrying Methionine is at the P-site.

Elongation: this stage begins when the next tRNA carrying the correct amino acid comes to the A-site. A peptide bond forms between the two amino acids. Thus, the enzyme that forms the peptide bonds is called, Peptidyl Transferase. The tRNA that is now empty in the P-site moves to the E-site to be released while the tRNA from site-A moves to site-P and a new tRNA comes to the A-site. The mRNA is read in 5' to 3' direction while the amino acids are added from N to C direction.

Termination: Once a STOP codon is reached in the A-site there is no tRNA that corresponds to a stop codon. Instead, a Release Factor sits in the A-site, dissociating the complex stopping translation (this is a GTP driven process).

At Initiation, small ribosome subunit initiator tRNA carrying Met of f-Met scan the mRNA to find the start codon. The large subunit then joins this complex to form a translation initiation complex

Proteins made on the free ribosomes can generally either enter the endomemebrane system by first going to the E.R. or they can go to other cell organelles (mitochondria, nucleus, peroxisomes, chloroplast - plant cell).

Secretory Pathway: path taken by a protein in a cell on synthesis to modification and then release out of the cell (secretion). There exist many pathways as well as exceptions.

Bacteria

Plasma Membrane: a thing lipid bilayer that surrounds the cell and separates the inside from the outside.

The cell membrane in bacteria is a lipid bilayer and they also contain fatty acids

Cell Wall: a protective layer that surrounds some cells and gives them shape and rigidity. It is located outside the cell membrane and prevents osmotic lysis.

Bacteria contain peptidoglycan in the cell wall, which are coposed of polysaccharide chains that are cross-linked by unusual peptides

Ribosomes: a complex of RNA and protein, they assemble amino acid to form proteins that are essential to carry out cellular functions. The DNA produces mRNA by the process of DNA transcription. (They are specialized cell organelles found in both prokaryotic and eukaryotic cells.)

Nucleoid: where genetic information is found, it has no membrane surrounding it. It attaches to the cell membrane and in immediate contact with the cytoplasm. It essentially controls the activity of the cell and reproduction.

Flagella: microscopic hair-like structures involved in the locomotion of a cell. They help to propel a cell through the liquid. Some can even sense changes in pH and temperature. They are coiled, thread-like type structure

Fimbriae and Pili: Fimbriae are short hair like projections located on the surface of bacteria, they are used to stick to the substrate or to each other (bacteria). Some bacteria also contain long projections called pili which are involved in forming a channel between 2 bacterial cells to transfer DNA from one cell to the other.

Cytoplasm: is a thick solution that fills each cell and is enclosed by the cell membrane. It is mainly composed of water, salts, and proteins.

Plasmid: a small, circular, double-stranded DNA molecule that is distinct from a cell's chromosomal DNA. They naturally exist in bacterial cells (some eukaryotes). They provide bacteria with genetic advantages.

Capsule: many bacterial cells secrete extracellular material in the form of a capsule or. slime layer. It is attached tightly to the bacterium and has definite boundaries.

capsules are usually polymers of simple sugars

Archaea

Plasma Membrane:

The cell membrane in archaea, it can be a lipid bilayer or a monolayer, they also contain phytanyl – archaeal phospholipids differ from those found in Bacteria and Eukaryotes, they have branches phytanyl side-chains instead of linear ones as well as an ether bond instead of an ester bond that connects the lipid to the glycerol.

Cell Wall:

Archaea do not contain peptidoglycan in their cell wall

Ribosomes: Protein synthesis

Flagella: Movement

these are nonhomologous

Cytoplasm:

Fimbriae and Phili: Attachment to surfaces and bacterial mating

Plasmid:

Membrane Lipids:

RNA polymerase:

Animal Cell

Cytoskeleton: Helps the cell keep shape and assists with movement

Intermediate Filaments

microfilaments:Proteins in the cytoskeleton

Microtubules: Proteins in the cytoskeleton

Microvilli: increase the surface area for diffusion and minimize any increase in volume, and are involved in a wide variety of functions, including absorption, secretion, cellular adhesion, and mechanotransduction.

Plasma Membrane

Receptors

Vessciles

Nucleus

Nuclear Envelope: A double membrane regulating what comes in and out the nucleus. This Envelope is lined with nuclear pore that are lined with proteins that allow transport in and out of the nuclease.

Nucleolus: Nonmembranous and helps produce ribosomes.

Chromatin: The DNA and proteins of chromosomes, helps in cell division.

Ribosomes: Made of ribosomal RNA and proteins in charge of making proteins and is located in 2 locations the cytosol (free ribosomes), and outside the ER (bound ribosomes)

Endoplasmic rectum: takes up almost more than half of the membrane attached to the nuclear envelope

Smooth ER :Lacks ribosomes,synthesizes lipids, metabolises carbohydrates, stores calcium ions and detoxifies poisons

Rough ER: bound ribosomes, secretes glycoproteins, distributes transport vesicles, MEMBRANE FACTORY

Peroxisomes: An oxygen rich membrane bound organelle

Mitochondria: Produces most energy needed to make the cell function and stores this energy in ATP

lysosomes: Membrane bound organelles filled with enzymes. These enzymes promote hydrolysis which is used to break covalent bonds

Golgi apparatus: Is made of different sacs one side receives material from the ER where the other side changes it and ships it off.Subtopic

Centrosome:Before cell division, the centrosome duplicates and then, as division begins, the two centrosomes move to opposite ends of the cell.

Flagellum:Helps with cell movement

Plant Cell

Nucleus

Chloroplast:converts energy from sunlight to chemical energy
stored in sugar molecules

Plasmodesmata:cytoplasmic channels through cell walls that
connect the cytoplasms of adjacent cells

Cell wall: outer layer of cell that protects cell from mechanical
damage; made of cellulose, other polysaccharides, and protein

Endoplasmic Reticulum

Ribosomes

Central vacuole: prominent in older plants; its functions include storage, breakdown of waste products, and hydrolysis of macromolecules; its enlargement is a major mechanism for plant growth

Cytoskeleton

Plasma membrane

Peroxisome

Golgi apparatus

Mitochondria

How does a cell make ATP?

1. Substrate-Level Phosphorylation
(can be attained through glycolysis
and the citric acid cycle)

A substrate that contains a phosphate group binds to the active site on an enzyme.This causes the phosphate group to bind to ADP (Adenosine diphosphate).

In the end,there will be a product and a
molecule of ATP (Adenosine triphosphate).

2. Oxidative Phosphorylation

Energy is used to add a Pi (inorganic
phosphate) to ADP to form ATP