Coolie Mae's Cell Biology Notes

Cell Biology

I. Discovery of cells
- -Robert Hooke
  - -first described the chambers in cork (1665)
  - -named the chambers: cells (dead cells)
- -Anton van Leewenhoek (1665-1675)
  - -looke at pond scum
  - -saw "animals in the water
  - -described the living single celled organisms
- -Mathas Schleidein (1838)
  - -plant biologist
  - -plant tissue composed of cells
  - -plant embryo arise from single cell
- -Theodor Schwann (1839)
  - -all plants and animals composed of cells
  - -cells are the structure unit of life
- -Rudolf Virchow (1855)
  - -cells can arise only by divding from preexisting cells
II. Basic properties of cells
- -life
  - -growth
  - -reproduction
  - -can be cultured in a lab
  - -HeLa cell - human with tumor (Henrietta Larks)
- -highly complex
  - -very well organized
- -genetic program
- -acquire and utilize energy
- -metabolism
- -mechanical activity
- -sensitivity
- -self-regulation
Cell size : surface area / volume (ratio)
Prokaryotic:
- no nucleus
- no nuclear membrane
- smaller
- less complex
- nucleoid
- no membrane bound organelles
- binary fission
- no cytoskeleton
- smaller ribosomes
- little DNA coding for fewer proteins
Eukaryotic:
- nucleus
- nuclear membrane
- larger
- nucleus
- membrane bound
- mitosis and meiosis
- cytoskeleton
- big ribosomes
- much more DNA/ proteins
Plant:
- cell wall
- chloroplasts
Animal:
- no cell wall
- no chloroplasts
Types of Prokaryotes
- -Archaebacteria
  - -Methanogen: convert CO2 + H2 >> CH4
  - -Halophiles: live in salty environments
  - -Thermoacidophiles: live in acidic hot springs
- -Eubacteria
  - -Mycoplasma:
    - -smallest living cells (.02 microns in diameter)
    - -only prokaryote that lacks a cell wall
  - -Cyanobacteria
    - -photosynthetic
    - -release O2
    - -N2 fixation
- Types of Eukaryotes
  - -unicellularity
    - -protozoans
      - -most complex
      - -do everything as an organism
Viruses: DNA and RNA +protein; not living (intracellular parasite)
Viroids: RNA only (no protein)
92 elements naturally occur in the envrionment
15 very common in human system
96.6% H,C,N,O in living systems
3.4% made up of other 11 elements
atoms:
- nucleus: protons (+) and neutrons (+/-)
- electron cloud: electrons (-)
atomic #: number of protons
atomic mass: protons + neutrons
chemical bonds:
- -covalent:
  - -nonpolar bond: equal sharing of electrons (O2)
  - -polar bond: unequal sharing of electrons (H2O)
- -Non-covalent:
  - -ionic bond: total loss or gain of electrons (NaCl)
    - -results from transfer of electron from on atom to another leading to atoms with positive or negative charges which attract each other
  - -hydrogen bond: weak bond; partial sharing of electrons
    - -weak electrostatic interaction with single hydrogen shared between two electronegative atoms
  - -hydrophobic interactions: H2O fearing;
    - -between groups insoluble in water such groups tend to clump together to minimize exposure to water
  - -van der Waals interaction: very weak interactions
    - -occur between electricaly neutral molecules that are very close together due tooslight perttubations of electron distrubution
Water:
- -70% of the cell's weight is water
- -high heat capacity
- -cohesion: surface tenstion (H2O to H2O)
- -adhesion: capillary action (H2O to substance(glass tube))
- -good solvent
- -ice floats for aquatic animals
Acid, Base, Buffers:
- -Acid: chemicals which can realease H+ (HCl)
- -Base: chemicals which can accept H+ (NaOH)
- -Buffer: can accept or realease H+ when needed to minimize pH flucutations
The nature of biological molecules
I. organic chemistry
- -center around the chemistry of C
- -Carbon
  - -binds upto 4 other atoms
  - -C-containing chains can be linear, cyclic, or branched
  - -stable compound
II. Hydrocarbon
- -contains hydrogen and carbon
- -saturated or unsaturated
  - saturated: fats singlge bond
  - unsaturated: liquid oils double bonds
III. Functional groups
- -OH: hydroxides
- -SH
- -COOH
- -NH2 amino
IV. Classification of Biological Molecules
- -Monomer: Glucose: single sugar
  - -building block for macromolecules
- -Macromolecules
- -Vitamins
- -Steroids
V. Four Basic families of biological molecules
- -Carbohydrates
  - -glycogen
  - -starch
  - -cellulose
  - -chitin
- -Lipids
  - -fat, oil
  - -triglycerides
  - -sterol, steriods
  - -phospholipids
    - -phosphate head (hydrophilic)
    - -Fatty acid tails (hydrophobic)
- -Nucleic Acids
  - -DNA
    - -Phosphate, sugar(-H), Bases(ATGC)
    - -T and C: pyrimidines
    - -A and G: purines
  - -RNA
    - -Phophate, sugar (-OH), Bases (AUGC)
- -Proteins
  - -amino acids
  - -single chain
  - -double or mutiple chains (protien complex)
  - -proteins can help other structures supporting it
  - -protein plus lipid / protein plus carbohydrates
    - -glycoportien
  - -nucleicprotein: nucleic acid plus protein
  - -Protein structure
    - -primary structure(1st Degree)
      - -NH2- aminal end
      - -COOH- carboxyl end
    - -Secondary structure (2nd Degree)
      - -Beta-sheet
        
        90 degree
      - -Alpha helix
        
        180 degree
    - -Tertieary structure (3rd Degree)
      - -Globular protein
    - -Quarterary structure (4th Degree)
      - -serveral polypeptide chains
      - -can associate together
      - -structure form related to function
cell membrane
review organelles and their functions
plant cells and animal cells
structure and function of the plasma membrane
- I. Functions
  - -compartmentalization
    - -nucleus, mitochondria, chloroplasts, etc
  - -selectively permeable barrier
  - -transporting solutes
  - -response to external signals
    - -protein hormones
  - -Intercellular interactions
  - -Locus of biochemical reactions
  - -energy transduction
- II. Membrane Structure
  - -phospholipids
  - -cholesterol abundantly found in animal cell, not yet detected in plant cell
  - -fluid mosaic model
    - -developed in 1972 by Jonathan Singer and Garth Nicolson
    - -def.: fluid lipid bilayer core with mosaic of proteins penetrating deeply into or through bilayer (dynamic structure)
  - -membrane composition
    - -lipid/protein ratio
      - -varies greatly depending on cell type
    - -phosolipids
      - -amphipathic
    - -cholesterol
      - -animal cells
  - -the lipid bylayer
    - -1925: Gorter and Grendel
      - -used red blood cells to study membrane
      - -used hypotonic solution to explode RBC to extract membrane
      - -placed in container of water so that hydrophobic tails would stand up in the water
      - -determined surface area of now defunk membranes and determined surface area of regular cell
      - -ratio turned out to be 2:1 and scientist determined that the membrane must be a bilayer
    - -Artificial lipid vesicle
      - -liposome: lipid bilayer with antibody and drug in core targets cancer cells
    - -Membrane carbohydrates
      - -2-10% of membrane weight is made up of carbohydrates
      - -asymmetric localization
        
        -blood types (A, B, AB, O)
      - -Glycoprotiens
      - -Glycolipids
    - -proteins
      - -12-50 different proteins
      - -integral proteins: span across the plasma membrane
      - -peripheral proteins: totally outside or inside the membrane
        
        -loosely attached
      - -lipid anchored proteins: form covalent bonds with lipids
    - -lipids and membrane fluidity
      - -importance of membrane fluidity
        
        -exocytosis and endocytosis
        -change in shape to fit spaces
      - -transition temperature
        
        -more energy(heat) to change ordered phospholipids
        
        -more rigid
        
        -less energy needed to changed disordered phospholipids
        
        -less rigid
The asymmetry of membrane lipids
- -lipids
  - -highly asymmetriclly distrubted
  - -distrubution of lipids on either side of the membrane is very different
  - -lipids move freely in lateral direction, but do not flip/flop often, however there are enzymes(flippases) that move certain lipids between the leaflets
Cell membrane
- -selective permeability
  - -Diffusion
    - -gases (O2, CO2, CO, NO)
    - -water(osmosis)
    - -hypertonic, isotonic, hypotonic, plasmolysis, turgur pressure
    - -no extra energy needed
  - -Ion channels
    - -Ca
    - -no energy needed is called passive transport
  - -Facilitated transport
    - -glucose
    - -Fig. 4.31
  - -Active transport
    - -concentration is higher at the destination of item
    - -requires ATP
    - -Na+ - K+ ATPase pump ATP > > > ADP = energy - -P\
    - -cotransport
      - -symport
      - -antiport
- Mitochondria: P 182-185 (structure and function) P208-212 (Importing mitochondria proteins and peroxisomes)
- I. Mitochondria:
  - -Known for >100 years
  - -Morphology
    - -sausage-shaped can sometimes be spherical or elongated
    - -size is 1 to 4 micrometers in length
    - -shape can change within cell(two mito. can fuse or a single mito. can divide)
    - -arise from preexisting mito.
  - -Number in cells
    - -liver cells have approx. 1500 mito.(15-20% of cell volume)
    - -muscle cells have numerous mito.
    - -prominent in plant cells and sperm midpiece
  - -Possess two kinds of membranes
    - -Outer mito. membrane
    - -Inner mito. membrane
  - -Membrane divide into two compartments
    - -Matrix: in the center of the mito.
      - -gell like structure due to high protein concentration
    - -Intermembrane space
      - -between the outer and inner membrane
  - -Traits of two mito. membrane
    - -Outer membrane contains 50% lipids by weight
      - -many enzymes are present as well
      - -derived from certain bacterial walls since both contain porins(protein)
        
        -porins form protein channels and allow < 10,000 daltons to pass freely
    - -Inner membrane
      - -high protein/lipid ratio (3:1 by weight)
      - -at least 60 different proteins
      - -derived from bacterial membrane
  - -Matrix
    - -contains many proteins
    - -smaller ribosome
    - -contains circular DNA which can code a few protiens
      - -these proteins are vital to the mitochondria
    - -most proteins however are produced from nuclear DNA and imported
Article: Cellular respiration
billions of mitochondria
energy is required by life for movement, reproduction, thought
metabolism:
p223-228
p245-246
in mitochondria: (CH2O)+O2 --> CO2 + H2O + energy(ATP/heat)
in choroplasts: CO2 + H2O + light > > > CH2O + O2
Chloroplasts
chemosythetic organisms (aerchabacteria) except to the rule
6CO2 + 12H2O + energy >>> C6H12O6 + 6O2 + 6H2O
glucose becomes starch and sugar
starch is stored in potatoes and rice etc
opposite of respiration
chloroplasts found in cells found in mesophyll
stroma: enzymes for chemical produciton of glucose
- within are grama and then thylakoid then lumen then chlorophyll is seen
light reactions and dark reactions(light independent reactions)
light reactions(grama)
light causes electrons to increase in energy
ADP then converted to ATP by the high energy electrons
the light also causes water to be split
NADP binds to H ions and forms NADPH
dark reactions (stroma)
Calvin cycle: CO2 >> RuBP (5 carbon molecule) >>unstable 6 carbon molecule >>> forms 2 3carbon molecules >> ATP gives up energy(forms ADP) >>.NADPH gives up energy (froms NADP) >>> PGAL forms some leaves and forms glucose the rest continues on the cycle and forms RuBP so that cycle can began again
Inner region of mitochondria is negative charged so protien is positive and is attraced to the mitochondria
Hsp70: heat shock protein chaperone70
receptor unwinds protein to allow through mitochondria membrane and Hsp70 aids in the unwinding
once inside the mitochondria the protein is refolded by mHsp70
after being refolded the protein loses its targeting sequence with the use of protease and then can be associated with the inner membrane wall of the mitochondria
http://www.symbiosinc.com
Chapter 7: Interactions between cells and their environment
-Introduction
- -cells interact with each other to form tissues
- -cell migration, growth, differentiation, tissue, organization during embryogenesis
-The extracellular space
- -glycocalyx
  - -carbohydrates
  - -provide protection for microvillia
- -extracellular matrix (ECM)
- -components of ECM
-Interactions of cells with noncellular substrate
- -integrin
- -focal contact
- -hemidesmosomes
-Interactions of cells with other cells
- -selectin
- -immunoglobulins
-Other structures
- -tight junctions
- -gap junctions
- -plasmadesmota
Chapter 8 Endomembranes
- -Introduction
  - -Endomembrane compartmenlize cells
  - -many organelles formed with endomembrane
- -Dynamic natures of the endomembrane systems
  - -vesicles form and destroy
  - -secretory pathways
    - -constitutive
    - -regulated
  - -endocytic pathway
- -techniques used in endomembrane research
  - -autoradiography
  - -pulse-chase
  - -subcellular fractionation
    - -homoginzation/centrifugation
  - -genetic mutants
- -Endoplasmic Reticulum
  - -sER (smooth ER)
    - -functions
      - -synthesis of steroids in endocrine cells
      - -detoxification of organic compounds in liver cells
      - -storage of Ca+
  - -rEF (rough ER)
    - -protien synthesis
    - -protein glycocylation(can happen in golgi appratus*)
    - -protein translocation by vesicles
      - *sorting of proteins occurs
ER >>> Golgi >>> other organelles (lysosomes/endosomes/plasma membrane)
- -golgi complex
  - -processing plant
  - -glycosylation
- -vesicle transport
  - -COP II
  - -COP I
  - -Clathrin-coated
- -lysosome
- -phagocytosis
  - -endocytosis
  - -pinocytosis
  - -receptor mediated
cytoskeleton
- -structure and support
- -molecular transport
- -contractabliity and motility
- -spatial organiazation
- -three major types
  - -intermediate filament(10nm)
    - -spread out throughout cell
  - -actin filament (microfilament)(smallest)(7nm)
    - -distributd close to plasma membrane
  - -microtubules(largest)(25nm)
    - -associated with nucleus
microtubules
- -made from tubulin(alpha and beta types)
- -13 protofilaments for one microtubule
- -the use of two differnet molomors allows for flexiblity in the tubule as far as length and rigidity
- -GTP >>> GDP provides energy
- grow shrink
intermediate filament
- -solid structure comprised of individual strands of filament
- - I.e. bridge cable
actin filament
- -monomer
- -two strands of monomers forming a helix
- -requires ATP for dissassocaition of monomers
- - ATP grows and ADP shrinks
Second exam covers
- -chapter 5
- -chapter 6
- -chapter 7
- -chapter 8
- -chapter 9
I. Types of cytoskeletons
- -microtubules
- -intermediate filaments
- -actin filaments
II. Characteristics of cytoskeletons
- -size
- -distribution
- -monomers and filament polarity
- -polymerization and depolmerization
- -energy input, ATP or GTP
III. Molecular motors
- -kinesin (work with microtubules)
- -dynein ("")
- -myosin - works with actin filaments
IV. Muscle contractility
- -sacromere
- -mechanisms of muscle contraction
Gene: segment of DNA that codes for a specific characteristic in the human body
- -example: eye color
Chromosomes: 23 pair (46 total) half from each parent
Phenotype: physical characteristic
Genotype: genetic characteristic
- heterozygous: Tt
- homozygous: TT or tt
allele: the individual genetic parts: example T is allele and t is an allele
linkage group:
genetic map:
crossing over:
nucleotides:
chargoff:the quantity of A=T and the quantity G=C but A+T not equal to G+C
hybridization: two strands of DNA can associate with one another even if they come from elsewhere
denaturation: the disassociation of the double helix
renaturation: reassociation of two strands of DNA to form a double helix
Tm: Melting temp. of DNA 85-90 degrees C
FISH: Fluoresence In Situ Hybridization
- -biotinylated probe
- -avidin
- -fluorescent dye
- -combine DNA strand from two different organisms to determine whether they are related
autosomes: 22 sequenced + 2 sex
highly repeated sequence
satallite DNA: DNA found away from main strains
mini-satallite DNA: 12-100 base pairs for each repeat and can reach a 3000 repeat number
micro-satallite DNA: 1-5 base pair for each repeat and form 50-100 base pair clusters
- sometimes can reach 30000 clusters in a human genome
DNA Fingerprinting
- -isolate mini-satallite DNA and ampphifiy it through PCR
melting temp (Tm): temp. at which DNA seperates
- -varies because of different concentrations of (G+C) which have three hydrogen bonds
- -temp. can vary between 80 degrees and 90 degrees C
moderately repeated sequence
- -can occupy 20-80% of DNA
- -histones(postive charged) organizes DNA(negative charged)
- -rRNA is important for protein synthesis and translocation
no repeated sequences
- -functional protiens can be found in nonrepeated sequences
- -only one sequence of DNA is found for individual protiens
synapsis: the pairing of homologous chromosomes pairing together
restricition Digestion of DNA
- -restriction enzyme or restriction endonuclease
- -can destroy foreign DNA
- -over 100 different enzymes have been isolated and identified
- -range in size 4-8 nucleotides CTTAAG is recongized by EcoR I
  - -stagger cut DNA
- -Sma I creates blunt end when it cuts DNA
DNA >>>>>>> RNA >>>>>>>>> Protein
- transciption translation
- transcriptional translationa
- control control
prokaryotes:transcription and translation are simultaneous processes
- only one type of RNA polymerase
- noninterruption in bacterial genes (exceptions do exist)
eukaryotes: transcription and translation are separate processes
- three types of RNA polymerases
  - polymer I >>> rRNA
  - polymer II >>> mRNA
  - polymer III >>> tRNA
- post transcriptional modification>>> RNA processing
  - splicing intron
  - 5' methylguanosine cap
  - 3' poly(A) tail
Early studies said
- One Gene >>>> One Enzyme
modified later
- One Gene >>>> One Protein
recently modified again
- One Gene >>>> One Polypeptide
Important concepts
- -promoter
- -core enzyme & sigma factor
- -transcription unit
- -primary transcript
- -5' cap
- -3' poly(A) tail
- -intron
- -exon
- -ribozyme
- -antisense strand
- -sense strand
- -codon
- -wobble hypothesis
- -aminoacyl-tRNA synthetase
- -shine-Dalgarno sequence
- -stop codon
promoter (prokaryotes)
5'--------TTGACA------------TATAAT---------A------3'
3'--------AACTGT------------ATATTA---------T-------5'
-----------(-35)-------------(-10)----start site-----
---------(--------consenus sequence--------------)
Large amounts of T/A found on end because of smaller number of hydrogen bonds
- <----------upstream--------|-----------downstream--------> +
sigma factor: helps RNA poly to bind and establish specifity
P475 don't worry about eukarytoic
-CH3 : methyl
ribosomes:
- two different units
  - -big unit
  - -small unit
EXAM III Chapter 10,11,13 Nine questions from EXAM II Nine questions from Study Guide
P413 first few pages history concepts mutations crossing over
420 chemical nature of the gene**************
genome structure Tm
repeated sequence trans
gene duplication p424 supercoil,
p441
p444 restriction enzymes endonuclueses
homework 449
rna transcritpin
structure of promoter
- -bacterial systems
translation
structure: ribosomes tRNA anticodon
poly(A) tails
mguanosine
primary transcript
mRNA half-life
rRNA half-life much longer than mRNA
ribozymes
P504 polysomes
Chapter 10
1. Why were the traits that mendel chose to study in the pea plant considered lucky choices?
- -they were the only traits governed by genes
- -none of the traits he chose acted as if they were part of the smae linkage group
- -all the traits he chose could be found on the same pea plant
- -they all obeyed the law of segregation
2. Alleles are?
- -different forms of the gene for the same trait
- -genes for different traits
- -always identical
- -inherited in pairs, both members of which come from the same parent
3. a brown eyed man has one allele for brown eyes and one for blue eyes. Half his sperm carry the allele for brown eyes, and half carry the allele for blue eyes. This is an illustration of
- -mendel's law of independent segregation
- -mendel's law of independent assortment
- -mendel's law of segregation
- -none of the above
4. Which of the following observations provided evidence that Mende's "units" were located on the chromosomes?
- -chromosomes occur as homologous pairs
- -the number of linkage groups and chromosomes is always equal
- -one member of each homologous pair goes to each gameete during meiosis
- -all of the above
5. Given that alleles are laocated on chromosomes, and whole chromosomes are passed on to gametes, why don't offspring get all the alleles on a parental chromsome?
- -genetic recombination is a result of gene dupoliation during evolution
- -genetic recombination is a result of mutation
- -genetic recombination is a result of crossover between member of homologous pairs.
- -all traits on a given chromosome are always found together in offspring
6. Watson and Crick used all of the following information in deducing the structure of the genetic material except
- -Avery, MacLeod, and McCarty's indentification of DNA as the "Transforming principle."
- -x-ray diffraction studies by Astbury, Franklin, Pauling and Wilkins
- -Chargaff's rules of DNA base composition
- -microscopic examination of DNA structure
7. Given the structure of DNA as described by Watson and Crick, all of the following must be true of DNA except
- -the 3' end of one of the strands must be aligned with the 5' end of the other strand
- -the total number of purine bases must equal the total number of pyrimidine bases
- -the sequence of bases on one strand must be identical to those on the other strand
- -the sequence of bases in the genome of one organism must be different from the sequence of bases in the genome of a different organism
8. The structure of different DNAs can vary in all of the following ways except
- -the helix may be right-handed or left-handed
- -the sequence of nucleotide bases can be different
- -the molecule canb e fully hdrated as in the B form, or drier as in the A form
- -the bases can be attached to the sugars or the phospates of the backbone
9. Which portion of the curve represent renaturation of the nonhistone coding sequences of the DNA
- -A
- -B
- -C
- -cannot determine from this curve
10. Which portion of the curve represents renaturatiuon of the most repetitive DNA
- -A
- -B
- -C
- -cannot determine from this curve
11. What is probably the source of the DNA used in this curve?
- -virus
- -bacterium
- -eukaryote
- -none of the above
12. In situ hybridization is used to
- -locate sequences of DNA on the chromosome
- -identify mini- and microsatillite DNAs
- -identify homologous pairs of chromosomes
- -identify the centromere portion of chromosomes
13. Which of the following statements is true of repeated DNA sequences
- -all repeated sequences have coding functions, but not all coding sequences are repeated
- -all nonrepeatd sequences have coding functions, and all coding sequences are nonrepeated
- -all repeated sequences lack coding functions, but not all coding sequences are nonrepeating
- -some coding sequences are repeated; others are nonrepeating
14. Human cells contian several different proteins that bind calcium. They share similar amino acid sequences but are found in different cell types. What can you infer about the genes for these proteins
- -they are all part of the family of globin genes
- -they probably arose in evolution by gene duplication
- -they are part of a family of pseudogenes
- -they must all reside on different chromosomes
15. Cultured hamster cells treated with methotrexate become resistant to the drug by amplifying the gene for DHFR. This is an example of
- -selective gene amplification
- -random gene duplication and selective survival
- -evolution
- -all of the above
16. In eukaryotes, transposable elements arise by
- -reverse transcription of RNA, followed by insertion into the genome
- -excision of a portion of the chromosome, followed by insertion at a new place in the gemone
- -both A and B
- -Neither A nor B
17. Which of the following is not a role that has been suggested for transposable elements in the process of evolution
- -Mutational effects of transposable elements accumulate in a suppressed form, then are suddenly expressed, resulting in new species
- -Insertion of transposable elements into the genome results in gene duplication and the evolution of multigene families
- -Transposable elements have no role n evolution; they are genetic parasites
- -Natural selection always favors species with many transpoable elements
18. Which of the following kinds of "maps" of genomes rely on the frequency of crossover events
- -genetic maps
- -physical maps
- -nucleotide sequence groups
- -restriction fragment maps
19. Restriction endonucleases have become essential tools in the study of molecular biology. Which of the following true statements sums up the significance of these enzymes from the point of view of the bacteria that make them
- -restriction endonucleases cut DNA into fragments that can be easily sequenced
- -restriction endonucleases cut DNA in precisely defined sets of fragments
- -Restriction endonucleases cut any type of DNA, as long as it has not been methylated at the cutting sites
- -restriction endonucleases can elave either blunt or sticky ends
20. Under which of the following conditions would the restriction fragment lengths be identical (i.e., lack polymorphisms?
- -when DNA from homologous chromosomes of the same individual is cut with the same restriction endonuclease
- -when DNA from the same chromosome derived from identical twins is cut with the same endonuclease
- -when DNA from the same chromosome derived from nonidentical siblings is cut with the same endonuclease
- -all of the above
Chapter 10: Answers
I. DNA the most susceptible molecule to environmental damage
- - Ionizing radiation, break DNA backbone
- -chemicals, alter bases structurally
- -ultraviolet radiation, form thymine dimers
II. Nucleotide Excision Repqr
- -remove part of strand containing certain types of bulky lesions
- -steps in repair process
  - -pair of endonucleases make incisions in backbone of altered strand on each side of lesion
  - -damaged oligonucleotide now held in only by hydrogen bonds
  - -helicase thought to strip damaged oligonucleotide away from intact strand
  - -once exercised, gap filled by DNA polymerase and strand sealed by DNA ligase
III. Base Excision Repair
- -remove altered nucleotides that distort helix
- -DNA glycosylases
  - -recognize alteration
  - -break glycosidic bond connecting base to sugar
  - -remove base
- -Different types of DNA glycosylases
  - -each more or less specific for particular altered base
  - -types of damage recognized by DNA glycosylases
    - -Uracil: forms by hydrolytic removal of cytosine amino group
    - -8-hydroxyguanine: results from damage by free oxygen radicals
    - -3-methyladenine: caused by alkylating agents
- -Steps in repair process
  - -DNA glycosylase recognizes altered base and remove
  - -Once base removed "debased deoxyribophospate" in site removed by endonuclease
  - -Gap enlarged by phophodiesterase
    - -filled by DNA polymerase
    - -sealed by DNA ligase
IV. Mismatch repair
- -enzyme removes mismatched nucleotide how does an enzyme know which is the mismatched?
- -in bacteria parental strand has methyl groups on certain adenosine residues; newly syntheized daughter strand is not methylated right away
- -repair system patrols DNA looking for mismatch before methylation of the daughter strand
  - -if mismatch found, enzyme removes and replaces nucleotides from nonmethylated strand
  - -returns base pair to original status
P 413:
Chapter 14 Cellular Reproduction
- mportant
  - -pay particular attention on the morphology and behavior of chromosomes, mitotic spindle, nuclear membrane during cell divsion.
  - -compare and contrast mitosis and meiosis
Cell Cycle: Interphase (G1, S, G2 [DNA replication])
- M-phase (Mitosis, Cytokinesis)
Cell Cycle Control: (Cyclin-dependant kinase, cyclin [MPF maturation-promotion factor])
- (phosphorylation, dephosphorylation)
Cell Division: (mitosis[prophase, prometaphase, metaphase, anaphase, telophase], meiosis [spermatogenesis, oogenesis])
mitosis: somatic cells
germ cell: sperm/oocyte
reproductive cells
synapsis: pairing of homologous chromosomes

Review of Cell Cycle

-the phases of the cell cycle
- -Interphase
  - -G1: cell growth, Gap 1
  - -S: DNA replication
  - -G2: cell growth, Gap2
  - -90% of cell cycle
  - -exception: G1 and G2 absent during early embryonic cleavage
  - -exception: G0- if a cell does not divide and stays in an inactive state permanently, G1 should be considered as G0
- -M phase
  - -mitosis: nuclear division
  - -cytokinesis: cytoplasmic division
  - -10%
-control mechanisms for cell cycle progress
- -the cell cycle control system
  - -checkpoint: molecular brakes for cell-cycle control
    - -G1: checkpoint
      - -cell size
      - -environmental conditions
      - -DNA quality
    - -G2: checkpoint
      - -cell size
      - -DNA replication (Quality and Quantity)
- -the cell-cycle control system is based on cyclically activated PROTIEN KINASES
- -some terms related to cell-cycle control system
  - -phosphorylation: normally protein is substrate of protein kinase use of ATP to ADP and addition of phosphate to substrate
  - -diphosphorylation: phosphate is released from substrate
    - -many cellular proteins can be either activated or inactivated by phosphorylation or diphosphylation
cyclin-cdk complex
- -cyclin: a protein involved in cell-cycle control its conc. varies in a cyclical fashion
- -cdk: cycling-dependant kinase activity is regulated by the accumulation and destruction of cyclin
- -MPF: maturation-promoting factor (mitosis)
  - -a cyclin-cdk complex regulating entry into M-phase
  - -phosphorylates nuclear lamina for nuclear membrane breakdown
  - -phosphorylates microtubule-associated protien to allow microtubles to form mitotic spindle
Cell cycle-control proteins and processes are very conserved
- -yeast >>>> animals and plants
How does a cell stop its progress from one stage to the next?
- -if there is damage to the DNA in the G1 phase this damage will led to the synthesis of some proteins and those proteins are inhibitors which inhibit the cyclin-cdk complex activity
- -P53, P16, P21, P27
DNA Damage: + inactive p53 (low level) >>> active p53 (high level) + >>>> transcritption and translation of p21 >>>>->>>> cyclin-cdk complex is arrested in G1 phase
The cycle in vivo:
- -three major categories of cells
  - -cells with extrreme structural specialization e.g. nerve cells, muscle cells
  - -cells that normally don't divide, but with right stimuli, make DNA and divide
    - e.g. liver cells
- -length of cell cycles are hightly variable
Mitosis
- -greek "mitos" threadlike chromosomes
  - -daughter cells identical to each other and motehr cell
  - -maintian the same number of chromosomes
  - -rapidly increase cell number
  - -found in somatic cells
- -usually and arbitrarily divided in 5 stages
  - - Prophase
    - -nuclear evelope breaks down
    - -formation of mitotic spindle
    - -chromosomes compacted into 2 rod-shaped chromatids
    - -2 chromatids connected at centromeres
      - -centromere
        
        -primary constriction on chromosome contain hightly repeated sequences for protien binding
      - -kinetchore
        
        -outer centromere surface platelike structure attachment site for mitotic spindle MT's
  - -Prometaphase
    - -definitive mitotic spindle forms
    - -chromosomes start to move to center
  - -Metaphase
    - -chromosomes aligned at spindle center
    - -both chromatids attached to spindle
  - -Anaphase:
    - -sister chromatids split synchrnously and move towards opposite sides
  - -Telophase
    - -each chromati (daughter chromosomes) arrives at the poles of the spindle
    - -nuclear envelope starts to reesemble
    - -division of cytoplasm begins
  - -Cytokinesis
    - -cell surface indentation
    - -place of furrow same as plane of metaphase plate
    - -contractile ring theory
      - -action filaments aligned parallel to cleavage furrow
      - -myosin filaments are involved
      - -mitotic spindle determines the plane of cytoplasmic cleavage
      - -cell wall formation in plant cells
Meiosis
- -process during which number of chromosomes reduced to half of the parentals
- -two sequential divisions follow distributing chromsomes to 4 nuclei
- -ensure production of haploid gametes
- -during chromsome pairing genetic recombination occurs to increase variablity
- -variablity provieds raw materials for natural selection
- -species w/ variation may respond better to adverse environmental changes
- -stages of meiosis
  - -prophase
    - -typically lengthened extraordinarily compared to mitosis:
    - -e.g. human females
      - -oocytes enter prophase I about time of birth can stay there for decades
    - -Leptotene:
      - -chromosomes become gradually visible in light microscope
    - -Zygotene:
      - -synapsis: process by which homologoues joined
      - -synapsis occurs by formation of synaptonemal complex (SC)
      - -bivalent (2 homologues) or tetrad (4 chromatis) is formed
    - -Pachytene:
      - -homologues held very close together
    - -Diplotene
      - -crossing-over occurs
      - -chiasmata can be seen
    - -Diakinesis
      - -prepare chromosomes for attachment to spindle
      - -nucleur envelope breaks down
      - -tetrads start to move to metaphase plate
  - -Metaphase I:
    - -homologous chromosomes aligned at the equator of cell
  - -Anaphase I
    - -homologous chromosomes pairs separate and migrate toward opposite poles
    - -each chromosome still consists of 2 chromatids connected at centromere
  - -Telophase I
    - -chromosomes (each w/ 2 chromatids) complete migration
    - -new nuclear membrane forms
  - -Cytokinesis:
    - -in most species, cytokinessi produces 2 daughter cells ( female, polar body, secondary oocyte)
    - -haploid number of chromosomes
    - -diploid amount of DNA
  - -Prophase II
    - -chromosomes recondense and starts to line up at metaphase plate (equator
  - -Metaphase II
    - - spindle fibers attach to kinetochore
    - -chromosomes line up on the metaphase plate
    - ***oocytes of many vertebrates halt here and wait for fertilzation;
      - Meiosis can be completed if egg is fertilized
  - -Anaphase II
    - -sister chromatids separated and move to opposite poles
  - -Telophase II
    - -chromosomes again enclosed by nuclear membrane
    - -half the chromsomes number and DNA amount
    - -4 cells form

-Major differences between

Mitosis	Meiosis
chromosomes replicates once cell divides once	chromosomes replicates once cell divides twice
no change in number of chromosomes or DNA	half reduction of chromosomes and DNA
two daughter cells	four daughter cells
occurs in somatic cells	occurs in germ cells
no genetic recombination	genetic recombination
no synapsis	synapsis

Cancer
what is cancer
what are the characterisitics of cancer cells
what causes the transformation of normal cells into cancer cells
what genes are involved in the formation of cancer cells
what are the major differences between tumor-suppressing genes and onco genes
fig. 16.3 p712
retinoblastoma
RB gene product is an inhibitor of transcription
recessive gene