Messenger RNA -

Transcription -
Protein synthesis - translation -
tRNA, rRNA -
Synthesis of an RNA strand -
RNA polymerases are DNA dependent -
RNA polymerase binds to promoter site of the DNA - they need help from the transcription factors -
3' to 5' direction -
The polymerase creates a complementary RNA in 5' -> 3' -
Puzzle pieces: ribonucleoside triphosphates -
Transcription
Single type of polymerase with five subunits -
Sigma factor - added to the RNA polymerase before it attaches into the DNA - increase enzyme's
affinity - slides along the strand until it binds to a suitable promoter gene
-
The sigma factor is lost as the polymerase starts transcription -
Transcription elongation complex - conformation change -
TATABOX - consensus sequence - Pribnow box -
Rho factor - required for termination - ring that moves along the 3' direction -
Transcription in Bacteria
Three major types of RNA: mRNA, tRNA, and rRNA -
Primary transcript - pre-RNA - processed later by splicing -
rDNA - found in the nucleoli (humans) -
Transcription Factors -
-
Splicosomes -
Addition of 5' methylguanosine cap and polyAAA tail in the 3' -
-
Transcription in Eukaryotes
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Addition of 5' methylguanosine cap and polyAAA tail in the 3'
-
Double stranded RNA - siRNAs that leads to destruction -
Transcriptosome - RNA -
Other noncoding RNAs
Overlapping -
The Properties of the Genetic Code
Translation
Also known as transfer RNAs -
L-shaped, 3d structure + residues -
Aminoacyl tRNA synthases - enzyme that links the tRNA to the cognate amino acids -
tRNA
mRNA - ribosome moves along the strand - binds to the proper reading frame -
STEP 1: Bringing the Small Ribosomal Subunit to the Initiation Codon -
STEP 2: Bring the First aa-tRNA into the Ribosome -
STEP 3: Assembling the Complete Initiation Complex -
Triplet codon: 1 amino acid -
Initiation
12 initiation factors - eIF - eukaryotic initiation factor -
eIF4E - 5' of euk mRNA -
eIF4A - removes double stranded regions that might interfere the translation process -
eIF4G - linked bet the polyAAA tail and 5'MG cap of the mRNA - LINEAR TO CIRCULAR MESSAGE -
Initiaton in Eukaryotes
Aminoacyl tRNA enters the A site - binds completely to complementary DNA -
Nascent polypeptide attaches to tRNA on the P site -
The ribosome translocates the codon of the mRNA to the E site -
Both initiation and elongation require GTP hydrolysis -
Elongation
When the ribosomes reads a stop codon (UAG, UAA, UGA) -
Termination
Simultaneous translation in the mRNA by a lot of ribosomes -
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Simultaneous translation in the mRNA by a lot of ribosomes -
Polyribosomes - complex of ribosomes translating in an mRNA -
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Nucleus of a Eukaryotic Cell
Two cellular membranes arranged // to one another -
Keep from ions passing freely in between -
Encoded by LMNA genes
Polypeptides called LAMINS
Mutation in the gene - ex. Hutchinson-Gilford progeria syndrome (HGPS)
NUCLEAR LAMINA - meshwork of thin filaments - attachment of site of chromatin fibers -
Nuclear Envelope
Proteins called nucleoporins -
It is not a static structure -
The T Antigen (SV40)
Robert Laskey - nuclear localization signal (NLS) - allows proteins to enter the nucleus -
importin alpha/beta - resides in the cytoplasm -
Ran - GTP binding protein - regulation of transport - based on the concentration of RAN-GTP
concentration between the cytoplasm and the nucleus
-
Nuclear Pore Complex
Chromosomes and Chromatin
Human DNA: 6.4 billion base pairs - 2 m long -
The lowest level of chromosome organization
Chromatin binded on a histone
Highly conserved because of DNA which is common to all organisms
H1 - serves as a linker that binds to the linker DNA
Histones - high content of arginine and lysine
NUCLEOSOMES -
Dispersed state
Euchromatin
Telomeres and centromeres of chromosomes
Constitutive - always dormant
Barr bodies - activated during meiosis
Facultative - mostly dormant but are sometimes activated
During early embryonic development - equal amount of X chromosome with
males

Random process: 50/50 chance

Reactivation prior to meiosis
LYON HYPOTHESIS
Heterochromatization
Heterochromatin
HETEROCHROMATIN AND EUCHROMATIN -
Packaging the Genome
Breaking of the chromosome = resealed in inverse orientation
Usually nonviable
Inversion -
One piece of chromosome is attached to another
ABL gene that encodes protein kinase
Philadelphia chromosome - chromosome no. 9
Translocation -
Chromosomal Abberations and Human Disorders
12 The Cell Nucleus and the Control of Gene Expression
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ABL gene that encodes protein kinase
BCR gene from 22 is translocated to no 9
Results to chronic myelogenous leukemia
Portion of chromosome is missing
Down Syndrome - chromosome 5
Deletion -
Partial trisomy
Duplication -
Unusual stretch of repeated sequences - telomere -
End-replication problem - every replication the DNA becomes shorter -
Telomerase - add new repeat units to overhanging strand -
Telomeres
H3 histone variant - CENP-A -
Highly repeated DNA sequences (satellite DNA) -
Centromeres
Inheritance not encoded to DNA gene -
Epigenetics
Example of inducible operon -
In bacteria -
Absence of lactose - the lac operon binds to the DNA protein -
Increase of lactose - the translation stops - inhibitor binds to the DNA -
The Lac operon
An example of repressible operon -
Tryptophan - corepressor -
Absence of trp - operator site binds to - transcribes genes in the trp operon - synthesize proteins
to create trp
-
The trp operon
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DNA is semiconservative in fashion -
After replication: one old and one new strand -
DNA Replication
Replication forks -
Origin - oriC -
Replication in Bacterial Cells
Semidiscontinuous replication -
3' to 5' fashion -
Leading and lagging strand -
Okazaki fragments - joined by ligase -
Primase - puts a primer at the start of replication -
Synthesizes DNA -
DNA polymerase III - holoenzyme - subunits -
Beta clamp - holds the DNA template -
DNA polymerase I - only polymerase that synthesizes in 5' to 3' -
DNA Polymerase
Accurate copying of genetic sequence is crucial -
DNA repair - 3' to 5' exonuclease activity -
Bacteria - mismatch repair - repairs bases that is missed during the proofreading -
Ensuring High Fidelity in DNA Replication
Origin recognition complex - specific binding site -
Autonomous replicating sequencing - promote replication of DNA -
Vertebrate DNA does not contain -
Restricting One Replication per Cycle -
Origin of replication is bound by an ORC complex - "molecular landing pad" -
Proteins branded as "licensing factors" bind to ORC to form pre-RC -
Before S phase - Mcm2-Mcm7 activates -
Mcm proteins move with the replication fork - displaced after replication (in eukaryotes it remains
in the nucleus )
-
Replication in Eukaryotic Cells
Fix broken or wrong alterations of DNA segments - prevent mutation -
Transcription-coupled pathway - priority list
Global genomic pathway
Nucleotide excision repair - cut-and-patch mechanism -
Base Excision repair -
Mismatch repair -
Double-strand Breakage repair -
DNA Repair
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The Cell Cycle
Most of the parts of the cycle are part of the interphase stage -
M phase - mitosis phase
S phase - synthesis phase - DNA
Nerve cells, muscle cells and RBCs - highly specialized - does not divide 1.
Liver cells - upon surgical removal a.
Lymphocytes - proliferate to produce appropriate antigen b.
Does not divide unless given stimulus 2.
Cells that normally have mitotic activity 3.
Cell Cycles in vivo
Cdc2 - in yeasts -
Cyclin-dependent kinases = not only involved during the M phase
Role of protein kinases: -
Control of the Cell Cycle
Cyclin dependent kinases - checkpoint in between phases
Another subunit
Enters through a protein called MPF - two subunits -
Prophase, Metaphase, Anaphase, Telophase (PMAT)
Mitosis - nuclear division -
Cytokinesis - dividing cell splits into two -
Mitosis and Cytokinesis
Chromosome condensation -
Prophase
Attachment site to the mitotic spindle fiber -
Residence of several motor proteins -
Kinetochore - a button like structure - out the outer surface of the centromere - assembles during
prophase
Microtubules
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Formed by MAPs (microtubule-associating proteins) -
Aster - first stage - creates a star like shape -
Microtubules
Prometaphase - stage where the dissolution of the nuclear envelope starts
Greek word meaning "reduction" -
Leptonema - chromosomes become visible
Zygonema - synapsis occur
Bivalent - two chromatids
Pachynema - tetrad starts to form
Diplonema - chiasma - intersection between the two - crossing over of genetic information -
increases genetic variability

Diakinesis
Stages of Prophase I -
Haploidy - reducing number into half -
MEIOSIS
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Recognition of stimulus from outer surface of the plasma membrane -
Extracellular messenger molecules - help in cell-to-cell communication -
Translated into changes
Signal transduction - signals reach to target proteins -
Termination of message is important to halt the transfer of messages uncontrollably -
Protein tyrosine kinases -
Phosphorylate certain tyrosine residues -
Basic elements
Shrinkage in volume and cell nucleus
Billions of cells die from apoptosis everyday (i.e. RBC)
Programmed cell death -
Apoptosis
15 Cell Signaling and Signal Transduction: Communication Between
Cells
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Cancer cells ignore inhibitory signals -
Grow in the absence of stimulating hormone -
Can proliferate in the absence of a serum -
Protection from apoptosis -
Generate much of their ATP from glycolysis (anaerobic) --> lactic acid - promotes tumor growth -
Basic properties of a cancer cell
Carcinogenic chemicals - soot, cigarette smoke -
UV radiation -
Carry genes that interfere with the cell's processes
Lymphoma - Helicobacter plyori
DNA tumor viruses and RNA tumor viruses -
Diet -
NSAIDs - nonsteroidal inflammatory drugs - help in decreasing the risk of colon cancer -
Causes of Cancer
A very common disease - two leading causes of death in the West -
Cancer is said to be monoclonal -
Malignant transformation requires more than one genetic alteration -
Tumorgenesis - the development of a tumor - multistep process -
Breast, Colon, Prostate and Lung - common solid tumors - epithelial tissue -
* stem cells --> progenitor --> differentiated -
Tumor - expresses telomerase - enzyme that elongates telomeres - not the normal case -
The Genetics of Cancer
Suppresses the growth of tumors (correlation)
First identified: RB - responsible for retinoblasma
Inhibits cyclin-dependent kinases
Damage to DNA - stabilization of p53
APC: colon; BRCA1 and BRCA2 - breast cancer
Most often implicated with cancer cells - p53 gene
Tumor repressor gene - act as cell's brakes - restrain growth of the cell -
Prevent cell from apoptosis and promote metastasis
Src - avian sarcoma virus
PDGF - platelet derived growth factor
EGF - epidermal growth factor
Oncogenes - encode proteins - loss of growth control - normal to malignant state -
Alter the product
Duplication
Rearrangement
Can be converted into oncogenes
Proto-oncogenes - potential to subvert the cell's activities and push the cell towards the malignant
state
-
HNPCC - hereditary nonpolyposis colon cancer - satellite with sequences of abnormal
nucleotide number

Hereditary - genes that are involved in DNA repair -

Oncogenes and Tumor-Repressor Gene
16 Cancer
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nucleotide number
Common: surgery, chemotherapy, radiation -
Immunotherapy, inhibition process of oncogenes, inhibition of angiogenesis (blood vessels)
Development of an inhibitor called Abl kinase - chronic myelogenous leukemia
Humanized antibodies - that cling to malignant B - non-Hodgkin's lymphoma
Other several strategies: -
Best anticancer strategy - early detection (mammography, pap smear) -
Treatment of Cancer
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