Cellular Processes

DNA Packaging

Think of "beads on a string"

Histone core: a protein that bind the DNA twice

Different types of Histones: H1, H2A, H2B, H3, H4

Only the H2A, H2B, H3, H4 form the histone core. The H1 is outside and not apart of the code.

Nuclesomes are formed when the DNA wraps around the histones twice.

Nuclesomes are strung together like beads on a string by linker DNA.

Interactions between nucleosomes cause the thin fiber to coil or fold into this thicker fiber.

The tight helical fiber needs help of the H1 which is outside the nucleosome.

The 30-nm fiber forms looped domains that attach to proteins.

The looped domains coil further.

The DNA is packaged with proteins in an elaborate complex known as chromatin (the basic unit of the nucleosome).

Prokaryotes

In prokaryotes, genes are organized as operons.

Multiple genes are controlled by the same promoter.

Operator is not in Eukaryotes it is in Prokarytoes

Lac Operon

Lactose operon is an operon required for the transport and metabolism of lactose in bacteria.

Lac Z is a gene that forms mRNA

Enzymes responsible is galactosidase

Lac Y takes in the lactose

Enzymes responsible is permase

Lac A adds an acidicyl group to lactose

Enzyme responsible is transacetylase

Lac I is the lac repressor (regulatory gene)

Can switch off the operon when binding to the operator and it is active by itself.

Operon is off!

Lactose is absent, repressor is on(repressor binds to the operator), opreron is off

Operon is on!

Lactose is present, repressor is inactive(allolactose inactive the repressor), operon on

cAMP Levels

Lactose is present, glucose is absent, cAMP levels are high and the CAP is activated

Lactose is present, glucose is present, cAMP levels are low and CAP is inactivated

Tryptophan

an amino acid

A negative regulator because it binds to a repressor

When tryptophan is absent, the repressor is inactivated which means it can't bind to the operator,operon is on

When tryptophan is present, the repressor is active which means it can bind to the operator, operon is off

Transcription Factors

General transcription factors leads to low(basal) levels of transcription

Repressor binds to the enhancer sequence and bends but prevents RNA poly II to bind

Proximal control elements are sequences in DNA close to promoter

allows RNA pol II to bind weakly

Transcription factors binds to the proximal elements and transcription is low level

Specific transcription ,like activators, lead to increased expression (high levels of transcription)

Activators bind to the enhancer sequence and bends the sequence

Distal control elements are enhancers that are located upstream or downstream of a gene

3 Stages of Cell Signaling

Reception: A signal molecule binds to a receptor protein located at the cell's surface.

Transduction: The receptor protein changes in some kind of way when the signaling molecule binds to it. The signal is conveyed to a form that can bring about a specific cellular response. Transduction usually occurs in a series of steps-signal transduction pathway.

AKA: Amplification (involves Second Messengers)

Cellular Response: The transduced signal triggers a cellular response

Types of Cell Signaling

Local Signaling

Paracrine Signaling

Involves direct signaling: affects nearby cells

Synaptic Signaling

Neurotransmitters released which diffuses across the synapse, stimulating the target cell.

Long-Distance Signaling

Exocrine/Hormonal Signaling

Hormone must travel through the blood stream

Types of Signal Molecules

Hydrophobic Signal Molecule

Receptor in Cell Cytoplasm

Receptor in Cell Nucleus

Hydrophobic Signal Molecule

Receptor on/in Cell (Plasma) Membrane

Membrane Receptors

G protein coupled receptor

A cell surface transmembrane receptor that works with the help of a G protein.

Tyrosine kinase receptor

Allows for the transfer of phosphate from ATP to the tyrosine kinase regions of a dimer, once a signal molecule binds to it.

Ion channel receptor

A membrane-bound receptor which undergoes a conformational change once the signal molecule attaches to the receptor. Allows for the passage of ions.

Phospholipid Bilayer

A membrane made up of two fatty acid
tails and a hydrophillic head.

Fatty Acids (Fats)

Triglycerides (Fats)

Saturated

Unsaturated

Oils

Present in plants, a layer of cellulose
and chitin which protects the cell.

Lipids

Glycerol

Mitochondria

Supplies energy to the cell through various cellular processes

Cell Wall

A protective wall that is made
from cellulose and chitin

Cytoplasm

An aqueous solution where the
cellular components reside in.

Vacuole

Contains water or
various liquids in the cell.

Central Vacuole

Food Vacuole

Nucleus

The component of a cell which
contains the genetic material of a cell.

Lysosome

A vesicle which breaks down
molecules and recycles them.

Endocytosis

Receptor Mediated

Phagocytosis

Pinocytosis

Ribosomes

Synthesizes proteins, made of RNA and proteins.

free or bound

proteins

Endoplasmic Reticulum

Focuses on synthesizing protein (rough) and lipids (smooth).

Smooth ER

Rough ER

Golgi Apparatus

Gives instructions to proteins and transports them

2. Elongation Cycle of Translation

1. Codon Recognition

Anticodon of aminoacyl tRNA base pairs with complementary mRNA codon in A site. Hydrolysis of GTP is present in this step. The aminoacyl tRNA with the appropriate anticodon binds and proceeds with the cycle.

2. Peptide Bond Formation

3. Translocation

Ribosome translocates tRNA in the A site to the P site. The empty tRNA in the P site is moved to the E site where it gets released. The mRNA moves with its bound tRNAs, which bring the next codon to the A site so it can be translated.

Translation

Molecule of mRNA is moved in a ribosome where codons are translates into amino acids. tRNA molecules interpret each type of nucleotide in sets of 3. A tRNA adds its amino acid to a growing polypeptide chain once the anticodon hydrogen bonds to the complementary codon on the mRNA.

1. The Initiation of Translation

1. A small ribosomal unit binds to an mRNA molecule. Then, an initiator tRNA, with anticodon UAC, pairs with the start codon, AUG, which carries the amino acid methionine (Met).

2. A large ribosomal subunit arrives to complete the initiation complex. The initiation factors are in charge of connection all the translation components. Hydrolysis of GTP gives off energy to the assembly. The initiator tRNA is in the P site while the A site is free for the tRNA who carries the next amino acid.

An rRNA molecule of a large ribosomal subunit catalyzes the formation of a peptide bond. This step removes the polypeptide from tRNA in the P site and attaches it to the amino acid on the tRNA in the A site.

1. A ribosome reached the stop codon and the A site of the ribosome accepts a "release factor".

3. Termination of Tranlastion

2. The release factor promotes hydrolysis of the bond between tRNA in P site and the last amino acid. Therefore, it frees the polypeptide from ribosome.

3.The two ribosomal subunits and the other parts dissociate.

3 Steps of Transcription

1. The initiation of Transcription

RNA polymerase binds to the promote, the DNA strands unwind, and the polymerase initiates RNA synthesis at the start point on the template strand

Eukaryotes

1. The eukaryotic promoter has a TATA box which is a nucleotide sequence containing TATA.

2. Transcription factors bind to the DNA before RNA polymerase II can bind to it.

3. Other transcription factors bind to the DNA along with RNA polymerase II, forming the transcription initiation complex.

Elongation

The polymerase moves downstream, unwinding the DNA and elongating the RNA transcript in 5' to 3' direction.

Termination

The RNA transcript is release and the polymerase detaches from the DNA

RNA Modifications after Transcription in Eukaryotic Cells

5' Cap and Poly A Tail

A 5' cap and a Poly A tail are added to the two ends of a eukaryotic pre-mRNA molecule in order to 1.) facilitate the export of mature RNA from the nucleus 2.) protect the mRNA from degrading 3.)help ribosomes attach to the 5' end of the mRNA when it is in the cytoplasm.

RNA Splicing

During RNA processing, the introns are cut out and the eons are spliced together.

Enzymes of DNA and their Functions

Helicase

Unwinds parental double helix at replication forks

Primase

Creates RNA primer and places one at 5' end of leading strand and several on lagging strand

DNA Pol III

Synthesizes new DNA strands by adding nucleotides to 3' end of RNA primer

DNA Pol I

Removes RNA primer and replaces it with DNA

Ligase

Connects fragments of DNA

Topoisomerase

Prevents DNA from "overwinding" by releasing tension ahead of the replication

Leading Strand

Synthesizes in a direction toward the replication fork

Lagging Strand

Synthesizes in a direction away from the fork

Replication Fork

point at which the two DNA strands begin to separate for replication

Origin of Replication

the point in the DNA at which replication begins

Cell Communication

Cells Signal one another frequently to tell other cells to begin replication, beginning at the phospholipid-bilayer.

This involves the Phospholipid-bilayer; where signal molecules activate cellular process, beginning with the attachment to a receptor.

Structure of DNA

Semi-Conservative Nature of DNA

DNA was discovered to be Semi-Conservative though the experiments by Messleson and Stahl. Both strands of parental molecule separate and each template synthesizes a new, complementary strand.

Complementary Bases

Adenine

Thymine

Guanine

Cytosine

Three Steps of DNA Replication

Initiation

Replication begins at the ORI, where helices begins to unwind the DNA. Topoisomerase releases tension ahead of the replication fork. The RNA primers are created to begin elongation.

Elongation

The primer begins the leading strand. The existing strand is now the template strand. DNA polymerase III begins putting down the new bases. The lagging strand is synthesized in okazaki fragments. DNA ligase puts together the okazaki fragments.

Termination

DNA polymerase I removes the RNA bases from the 5' end