DNA

Class notes

• helicase: unwinds parental double helix

• binding proteins: stabilize separate strands

• primase: add s short primer to template stand

• DNA polymerase 3: read parent strand and synthesize

• DNA polymerase1: remove RNA primer and insert DNA nucleotides

• ligase: create bonds between the okazai fragments so the back bone is complete

• steps to replication:

  1. DNA unwinds at the origin of replication.

  2. Helicase opens up the DNA-forming replication forks; these are extended bidirectionally.

  3. Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA.

  4. Topoisomerase binds at the region ahead of the replication fork to prevent supercoiling.

  5. Primase synthesizes RNA primers complementary to the DNA strand.

  6. DNA polymerase starts adding nucleotides to the 3'-OH end of the primer.

  7. Elongation of both the lagging and the leading strand continues.

  8. RNA primers are removed by exonuclease activity.

  9. Gaps are filled by DNA pol by adding dNTPs.

  10. The gap between the two DNA fragments is sealed by DNA ligase, which helps in the formation of phosphodiester bonds.

• 5’ → 3’ - new strand being synthesized

• need primers

  The Cell Cycle

  • basic function of the cell cycle

    • accurately duplicate DNA

    • split the DNA copies into genetically identical daughter cells

  • chromosomes

    • tightly coiled pieces of DNA that condense before cell division

    • most eukaryotic cells have 2 copies of every chromosome

    • they form in attached identical pairs

  • our somatic cells are diploid (two copies of each chromosome. we have 46, 23 from each parent

  • euchromatic - less dense & more spread out

  • heterochromatic - more dense, a lot more histones

  • purpose of mitosis?

    1. organisms can grow larger

  • replace old, worn-out, injured cells with new, identical ones

    Prokaryote Cell Division

  • binary fission

    • how bacteria reproduce (asexual)

    • increase population #’s

  • Regulation of the Cell Cycle

    • controlled by the interaction of proteins called cyclins and cyclin dependent kinase enxymes (cdks

Cyclins

• APC/C:

  • add a ubiquitin that activates the securin and causes separse to seperate

  • once the ubiquitin is attached to the securin, it goes through the protesome to be broken down

  • this activates the separese to break down cohesion the connects the sister chromatids

External Factors

PDGF

Positional Inhibition

Cancer

• Proto-oncogen

CH. 12 - THE CELL CYCLE

• cell division plays several important roles in life

  • as prokaryotes divide, it’s actually reproducing b/c the process gives rise to another organism

  • for multicellular eukaryotes, cell division enables each organism to develop from a single cell— the fertilized egg

  • cell division continues to function in renewal and repair in fully grown multicellular eukaryotes, replacing cells that die from accidents or normal wear and tear

Cellular Organization of the Genetic Material

• cell’s DNA is called a genome

  • prokaryotes often have a single DNA molecule

  • eukaryotes usually consist of a number of DNA molecules

• before the cell can divide, all of this DNA must be copied, and then two copies must be separated so that each daughter cell ends up with a complete genome

• replication and distribution of so much DNA is manageable because it is packed into structures called chromosomes

  • DNA molecule carries several hundred to a few thousands genes filled with units of information

  • associated proteins maintain the structure of the chromosome & help control activity

• entire complex of DNA and proteins that this the building material of chromosomes is referred to as chromatic

• 236

CH. 15 - THE CHROMOSOMAL BASIS OF INHERITANCE

New Combinations of Alleles: Variation for Natural Selection

• chromosomes lines up independently of other pairs during metaphase I, crossing over prior to that during prophase I, and can mix and match parts of maternal and paternal homologs

  • recombinant chromosomes resulting from crossing over may bring alleles together in new combinations

• gene variation provides raw material for natural selsction

  • traits conferred y particular combination of alleles best suited for environment, that species will thrive and produce more offspings

• discovery of linked genes and recombination due to crossing motivated Stertevant to construct a genetic map

  • hypothesized % of recombinant offspring, recombination frequency, calculated from experiments depends on the distance between genes on a chromosome

  • further apart genes are, the higher the probability that a crossover will occur between them and higher recombination frequency

• linkage map: genetic map based on recombination frequencines

  • shows three genes, body color, wing size, an cinnabar

  • based strictly on recombination feqruencines, only an approx, pic of a chromosome

  • portray order of enes along a chromosome, not precise locations

• cytogenic map: locate genes with respect to chromosomal features, such as strained bands

• map units: distance between genes

• genes that are too far apart that a crossover is virtually certain

  • recombination in crosses involving two such genes can have a max value of 50%

Abnormal Chromosome Number

• Nondisjunction: members of a pair of homologous chromosomes do not move apart properly during meiosis I or sister chromatids fail to separate during meiosis II

  • one gamete receives two of the same type of chromosome while another receives no copy

• if either of aberrant gametes unite with a normal one, the zygote will also have an abnormal # of a particular chromosome, known as aneuploidy

• fertilization involving gamete w/ no copy of a particular chromosome will lead to missing chromosomes in zygote

  • aneuploid zygote is said to be monosomic for that chromosome

  • if chromosome is present in triplicate in the zygote, the aneuploid cell is trisomic for that chromosome

• nondisjunction can also occur during mitosis

  • if occurred in early embryonic development, the aneuploid condition is passed along by mitosis to a large # of cells and is likely to have a substantial effect on the organism

• polyploidy: more than two complete chromosome sets in all somatic cells (general term)

  • more nearly normal in appearance than aneuploids

    • 3 for triploid and 4 for tetraploidy

    • triploid cell may arise by the fertilization of an abnormal diploid egg produced by nondisjuction of all its chromosomes

    • tetraploidy could result from the failure of a 2n zygote to divide after replicating its chromosomes

    • common in plant kingdom & plays important role in plant evolution

      • bananas are triploid

      • wheat hexaploid

      • strawberries octoploid

Alterations of CHromosome Structure

• error in meissis or damaging agents such as radiation can cause breakage of a chromosome, leading to four types of changes

  • deletion: occurs when a chromosome fragment is lost

    • it will miss certain genes,

    • broken fragment may become reattached as an extra segment to a sister or nonsister chromatid, leading to duplication

  • duplication: an alteration in chromosome structure due to fusion with a fragment from a homologous chromosome, such that a portion of a chromosome is puplicatied

    • fragment may also reattach to the original chromosome, but in the reverse orientation, producing inversion

  • inversion: an alteration in chromosome structure resulting from reattachment of a chromosomal fragment in a reverse orientation to the chromosome from which it originated

  • translocation: fragment join a nonhomologous chromosome

• deletions and duplications especially likey to occur during meiosis

  • in crossing over, nonsiting chromatics sometimes exhcnage unequal-sizd segments of DNA. practices of such an unequal crossover are one chromosome with a deletion and one with a duplication

• diploid embryo homologous for a large deletion or, if a male, has a single X chromosome w/ a large selection is usually missing a number of essential genes, lethal

• duplications and translocations tend to be harmful

  • reciprocal translocations, which segments are exchanged between nonhomologous chromosomes, and in inversions, balance of genes is not abnormal

  • cal alter phenotypes

Human Conditions Due to Chromosomal Alterations

• most chromosomal alterations are so disastrous to development that the affected embryos are spontaneously aborted long before birth, some times of aneuploidy appear to upset genetic balance less than others, allowed them to survive birth and beyond

Down Syndrome (Trisomy 21)

• affects 1 out of 830 children in U.S>

• results in an extra chromosome 21, so that total is 47 chromosomes

• characteristics include; facial features, short statue, correctable heart defects, and developmental delays

  • increased chance of getting leukemia and alzhermer’s disease but have lower rate of high b/p, atherosclerosis, stroke, and many types of solid tumors

• life span little lower than average

Aneuploidy of Sex Chromosomes

• upset balance less than those involving autosomes

  • y chromosome carries relatively few genes

• extra x chromosome in male (XXY) have Kinefelter syndrome

  • occurs one ever 650 live male birhts

  • have male sex orangs, but testes are small and produce little or no sperm

  • taller than average height, less muscle mass, enlarged breast tissue

• females with trisomy X (XXX)

  • one in 1000 live female birhts

  • generally healthy w/ slightly taller than avg.

  • risk for learning disabilities

• monosomy x, also called Turner syndrome

  • one in 2500 live female birhts

  • lack ability to reproduce

  • typical intelligence

Disorders Caused by Structually Altered CHromosomes

• many deletions cause severe problems

  • cri du cbat, deletion in chromosome 5

  • child born with this deletion has a small head w/ unusual facial features, severe intellectual disabilities, and a cry that sounds like a mewing of a distressed cat

• chromosomal translocations can also occur during mitosis; implicated in certain cancers, including chronic myelogenous leukemia (CML)

  • happens during mitosis of cells that are precursors of white blood cells

  • exchange of a large portion of chromosome 22 w/ a small fragment of chromosome 9 produces a much shortened, easily recognized chromosome 22, called the Philadelphia chromosome

    • leads to uncontrolled cell cycle progression

Genomic Imprinting

• phenomenon in which expression of an allele in offspring depends on whether an allele is inherited from the male or female parent

• occurs during gamete formation and results in the silencing

• of a particular allele of certain genes

• offspring will express only one allele of an imprinted gene, the one inherited from a specific parent, either female or male

• imprinting can involve either silencing an allele in one type of gamete or activating it in the other

  • consists of methyl groups that are added to cytosine nucleotides of one of the alleles

  • such methylation may silence the allele, an effect consistent with evidence that heavily methylated genes are usually inactive, in some cases shown to activate expression of allele

    • in case of Igf2 gene: methylation of certain cytosines on the paternal chromosome leaders to expression for eh paternal Igf2 allele

CH. 16 - THE MOLECULE BASIS OF INHERITANCE

Evidence That DNA Can Transform Bacteria

• 1928, Federick Griffith was trying to develop a vaccine against pneumonia

  • studied two strains, one pathogenic (disease causing) and one nonpathogenic (harmless)

    • surprise to find that when he killed bacteria with heat and then mixed the cell remains w/ living bacteria of nonpathogenic strain, some of the living cells became pathogenic

    • newly acquired trait was inherited by all descendants of the transformed bacteria

    • some chemical components of dead pathogenic cells caused this heritable change, called this phenomenon transformation

Evidence That Viral DNA Can Program Cells

• additional evidence came from studies of viruses that infect bacteria

• 1952 Hershey and Chase performed experiments showing that DNA is the genetic material of a phage known as T2

  • knew that T2 was composed almost entirely of DNA and proteins

  • could reprogram its host cell to produce viruses

• devised an experiment showing that one of the two components of T2 actually enters the E.coli vell during infection

  • used radioisotope of phosphorus to tag DNA in a second batch

  • bc proteins contain sulfur, radioactive sulfur atoms were incorporated only into the proteins of the phage

  • radioactive phosphorus labeled on the DNA, not the protein

  • tested to see which type of radioactively labeled molecule had entered the bacterial cells

• found the phage DNA entered the host cells, but the phage protein did not

• when bacteria were returned to a culture medium and infection ran its course, E.coli released phages containing some radioactive phosphorus, further showed DNA inside the cell played an ongoing role during the infection process

• hershey-chase provided powerful evidence that nucleic acids, rather than proteins, are the hereditary material

Additional Evidence That DNA is the Genetic Material

• Erwin Chargaff (1950) - reported that the base composition of DNA varies from on species to another

  • 32.8% of sea urchin DNA nucleotides have the base A, whereas only 24.7% of those from the bacterium E. coli have an A

  • number of adenines approximately equaled the number of thymines, and the number of guanines approximately equaled the number of cytosines

• Chargaff’s rules

  1. DNA base composition varies between species

  2. for each species, the percentage of A and T bases are roughly equal, as are those of G and C bases

Building a Structural Model of DNA

• 1950s, the arrangement of covalent bonds in a nucleic acid polymer was well established; researchers focused on discovering the three-dimensional structure of DNA

  • watson saw an X-ray diffraction image of DNA produced by Wilkin’s accomplished colleague Rosalind Franklin

  • spots in the image were produced by x-rays that were diffracted as they passed through alinged fibers of purified DNA

  • confirmed that DNA was helical in shape, also added to earlier data suggesting the width of the helix and the spacing of the nitrogenous bases

  • presence of two strans accounts for double-hekix

• watson & crick began building models of a double helix

  • franklin knew the sugar-phosphate backbones were on the outside of the DNA molecule, she put negatively charges phosphate groups facing the aqueous surroundings while hydrophobic nitrogenous bases in the interior

  • watson constructed the sugar-phosphate backbones to be antiparallel