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215 Cards in this Set
- Front
- Back
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Griffith
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experiment with Streptococcus pneumonia
(1928) transformation principle |
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Avery-MacLeod and McCarty’s experiment
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1944, proved that DNA was the heritable information, but the Streptococcus in all types of material
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Hershey Chase Experiment
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1952, proved that DNA was the genetic material once and for all, radioactive phosphate and Sulfur, proved protein did not have the genetic material using bacteriaphage
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1953
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Mechanism of DNA replication and how the
genetic instruction might work were proposed |
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minor and major groves
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spots for protein to bind
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mitotic spindles
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pull the chromosomes apart
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kinetochore
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is the protein structure on chromatids where the spindle fibers attach during cell division to pull sister chromatids apart.
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interphase chromosomes
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tend to occupy there own areas
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nucleosome
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dna rapped around a the histone proteins
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chromatid
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one portion of a chromosome
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heterochromatins perminantly
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does not contain genes, telemeres and centromeres
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nucleolus
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contains the genes for ribosomal RNA or rRNA, ribosome assembly takes place here
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Interphase Chromatin
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mainly Euchromatin
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Mitosis Chromatin
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Heterchromatin
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scaffold protein
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help compact DNA
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Nucleosome
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fundimental packing unit of DNA, about 200 pairs
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linker DNA
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between the two beaded strings
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145-147
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connect to histones
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Nuclease
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digests linker DNA
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procaryotes
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do not have histones
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Histones
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a family of small positively charged proteins
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H1
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linker histone helps pull nucleosome in a 30nm fiber, long tails at the C-terminus, acts as a clamp
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Histone core
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H1, H2A, H2B, H3, H4
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Chromatosome
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Nucleosome + Histone H1
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Chromosome remodeling complexes
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reposition the DNA wrapped around nucleosome, coupled by ATP hydrolysis
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Covalent modifications
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madifications that add groups, methylation, phosphorylation or acetylation
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white gene
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—required for normal pigment production for red eye color
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barrier sequence
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A special sequence to keep the
heterochromatin from spreading to neighboring areas on the chromosome |
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Genes that are accidently packaged into heterochromatin
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usually fail to be expressed
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X chromosome inactivation
in female mammals |
takes place during early embryo development
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An exmaple of Epigenetic inheritance
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—superimposed on
genetic inheritance based on DNA that influences gene expression |
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chromatatin is composed of
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DNA and proteins
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chromatin is
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loose
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chromosomes
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are condensed
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nucleic acid
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phosphate, pentose sugar, and nitrogenous base
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bonds
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phosphodiester
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proteins tend to bind
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on major and minor groves
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exons
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encode
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intron
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do not encode
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requirements for chromosomes
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telomere, replication origin, centromere
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G0
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cell is resting, in a cycle
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G1
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grows until it reaches the G1 checkpoint, checks to see if its ready for DNA synthesis
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S
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DNA synthesis
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G2
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grows until it reaches the G2 checkpoint, checks to see if its ready for cell division
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Mitosis
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cell division
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Prophase
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The two round objects above the nucleus are the centrosomes. The chromatin is condensing into chromosomes.
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prometaphase
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The nuclear membrane disintegrates, and microtubules have invaded the nuclear space. These microtubules can attach to kinetochores or they can interact with opposing microtubules.
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Metaphase
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The chromosomes align at the metaphase plate.
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Anaphase
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The chromosomes split and the kinetochore microtubules shorten.
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Telephase
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The decondensing chromosomes are surrounded by nuclear membranes. Cytokinesis has already begun; the pinched area is known as the cleavage furrow.
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DNA Polymerase
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is an essential enzyme for DNA replication
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DNA semi conservative
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• Each of the two strands of DNA is
used as a template for the formation of a complementary DNA strand |
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RO
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rich in AT, replication starts here
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Initiator proteins
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recruited to the replication orgin
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Semi conservative
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Meselson and Stahl, the expreriment showed that each strand of DNA was a template, 1958
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Requirements for DNA replication
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primer, Template, DNA polymerase
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Helicase
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unwinds
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Exonuclease
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Removes the RNA primers, hydrolysis of phosphodiester bonds
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DNA ligase
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fills in the gaps
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nuclease
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removes incorrect nucleotides
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Initiator protein
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recognizes the replication origin
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The problem at the replication fork
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DNA polymerase can
catalyze the growth of the DNA chain in only one direction |
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DNA polymerase
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can proofread as it's laying down a nucleotide
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RNA primer
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begins replication on the lagging strand
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RNA primase
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lays down RNA primer
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DNA repair polymerase
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later removes RNA primer
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•Replication Machinery
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- a group of proteins working together as a
large multienzyme complex • DNA helicase and single strand DNA binding protein • DNA primase and DNA polymerases • Sliding clamp and clamp loader |
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folding of lagging strand
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to bring the
lagging strand DNA polymerase in contact with leading-strand polymerase |
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DNA polymerase
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incapable of starting a new
DNA chain from scratch. |
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Telemerase
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allow the completion of DNA synthesis at the ends of
eucaryotic chromosomes, attracted my telemeric sequences |
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Telomere sequence at the end of chromosomes
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short sequence repeated thousands of times (does not encode proteins!)
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Telemerase adds
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additional repeats to the ends
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DNA polymerase at the telemeres
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completes the lagging strands
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Replicative cell senescence
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changes over time, cause the cell to die
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mutation
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any change in DNA
sequence or structure |
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DNA mismatch repair machinery
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detects errors and correct them
during DNA replication, cuts the newly synthesized strand out and is repaired by DNA ligase and Polymerase |
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depurination
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removal of a purine
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Deamination
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adding of U and replacing C
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UV radiation
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generates pyrimidine dimer, linking two pyrimidines
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framshift
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result from skipping a neuclotide
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DNA repair
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1) Excision via nucleases
2) Resynthesis via repair polymerases 3) Ligation via DNA ligase |
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Xeroderma pigmentosum
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autosomal recessive disease that arises from a defect in one of
several genes that encode DNA synthesis and repair enzy sensitive to UV radiation |
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breaks in DNA
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Ionizing radiation, mishaps at the
replication fork. strong oxidizing agents, and metabolites produced in the call can all cause breaks of this type |
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homologous recombination
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alternative strategy to repairing breaks
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Double strand breaks can be repaired
via nonhomologous end-joining |
but not perfect because it deletes nucleotides
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homologous recombination
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the exchange of genetic
information between a pair of homologous chromosome |
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homologous recombination occurs
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during crossing over in meiosis, provides variation in the gene pool
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Holiday junction
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the point where the strands cross
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DNA duplex
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hallmark structure in homologous recombination
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transposon
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jumping gene, mobile genetic element
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45%
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make up of transposons
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Prophase is when
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crossing over occurs
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flanking direct repeats
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on the outside of the element
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terminal inverted repeats
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ends of the transposon
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Barbara McClintock
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identified them in maize
recognized for her contribution in 1983 when she was 81 years old; awarded Nobel Prize in physiology or medicine |
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two different methods of transposition
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cut and paste, and replicative
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Retrotransposons
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requires RNA intermediate and requires an enzyme called
reverse transcriptase |
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Virus
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are infectious particles consisting of nucleic acidenclosed by coat proteins called capsid
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differences in RNA
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OH group that replaces the H, uricil, single stranded
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RNA tends
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to form a three D bond due to hydrogen bones
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RNA polymerase
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unwinds the DNA helix and adds nucleotides
complementary to the template one by one, DOES NOT REQUIRE A PRIMER |
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DNA rewinds
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directly after transcription is complete
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all polymerases
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are
large, multimeric enzymes with more than a dozen subunits; association of accessory proteins |
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transcription unit
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looks similar to a christmas tree due to all the RNA polymerases working at the same time
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ribosomal proteins
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found at the ends or rRNA
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mRNA
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codes for proteins
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rRNA
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form the core of ribosomes and catalyze the synthesis of proteins
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miRNA
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regulate gene expression
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tRNA
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serve as an adapter between mRNA and amino acids during protein synthesis
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initiation
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transcription apparatus assembles on the promoter;
RNA synthesis begins |
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elongation
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DNA unwinding; DNA is threaded through RNA
polymerase; addition of new rNTPs at the 3’ end of the growing RNA strand |
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Termination
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recognition of the terminator sequence;
the separation of the RNA molecule from the DNA template |
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Most important in initiation
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recognizing of the promoter sequence
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promotor region
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recognized by transcription apparatus to bind
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RNA coding region
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a sequence that gets copied into an RNA
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terminator sequence
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recognized by transcription apparatus to end
the transcription |
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In bacteria
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the sigma factor is required to recognized the promoter sequence, comes off after the first 10
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Pribnow box
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concensus sequence in bacteria
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the terminator
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gets coded, but the promoter sequence does not
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orientation of the promoter sequence determines
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the direction of transcription
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Eukaryotic transcription
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3 RNA polymerases, Eukaryotes require transcription factors,
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Assembly of transcription
factors at the promoter site allows... |
a) positioning the RNA polymerase
b) pulling the double helix apart to expose the template strand c) launching of RNA polymerase |
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RNA polymerase II
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synthesizes mRNA
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TATA Box
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important
sequence recognized by transcription factor TFIID within eucaryotic promoters(-25) |
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TBP
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is the subunit of the
general transcription factor TFIID that allows TFIID to bind to the TAA box sequence. binds to the minor grove |
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TFIIH
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opens the double helix by hydrolysis, phosphralates RNA polymerase II, and releases it
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When translation begins
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most of the general transcription factors are released
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Once translation is over
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RNA polymerase II is dephsphoralated to it can initiate again
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• Procaryotic mRNA
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get immediately processed, no extras done to it
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Eukaryotic mRNA
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A) Capping - Addition of Guanine that gets methylated at the 5’ end
B) Poly-Adenylation at the 3’ end splicing |
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exons are typically much...
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shorter than introns
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splicosomes are made of
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Five small ribonucleoprotein particles
(snRNPs) - U1, U2, U4, U5 and U6 |
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snRNPs
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Splicing is carried out by a large
complex |
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snRNAs
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carried out the catalytic portion of splicing by base pairing
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Lariet
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the loop formed during splicing
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importance of alternate slicing
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many variations from same copy
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exon junctional complex
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ensures that the Cap, poly A tail and splicing has been done before the mRNA exists the nucleus
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Rnase
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degrades RNA
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wobble
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refers to having the same first and second and variation at the third for the same codon
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stop codons
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UAA
UGA UAG |
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Start
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AUG
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tRNA
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adapter linking codon and amino acid sequence
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3'prime end on tRNA
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holds the codon
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anticodon
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most important end
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aminoacyl-tRNA synthetases
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recognition and attachment of the correct codon
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ribosomes
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translation of mRNA
e is a large complex of four rRNAs and more than 80 proteins |
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the three pockets of robosomes
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E-> P-> A
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Required for translation initiation
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mRNA, Ribosomal subunits, IF's 1,2,3, Initiator tRNA with Met, GTP
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polycistronic
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one mRNA molecule encodes several different protein, procaryotes
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tetracycline
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block aminoacylt tRNA from binding to the A site
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Streptomysin
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prevents the transition from intitation to elongation
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cholamphenicol
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prevents the peptidal transferase reaction
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chcloheximide
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bloacks the translocation reaction of ribosomes
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rifamyocin
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block intiation by binding to RNA polymerase
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ubiquitin
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makes for degrading
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Protosomes and Lysosomes
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degrade unwanted proteins
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26S
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refers to the particle size
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post translation modifications
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proteins may be cleaved, acetylated, or modified by
covalent attachment of carbohydrates (glycoproteins) - Specific amino acids within a protein may be modified (e.g. phosphorylation, methylation, carboxylation, etc.) |
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ribozymes
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is an RNA molecule
that possesses catalytic activity |
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DNA advantages
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Deoxyribose is much more chemically
stable than ribose; greater lengths of DNA can be maintained without breakage Figure 7-46 - The double helical structure of DNA and use of Thymine rather than Uracil allows easier repair of the molecule |
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gene expression
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The process by which a gene makes its effect on a cell or organism by directing the synthesis of a protein or an RNA molecule with a characteristic activity
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every cell
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contains the same genome
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differientiation
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achieved by gene expression, Process by which a cell undergoes a progressive change to a more specialized and usually easily recognized cell type
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cells make different sets of RNA and protein molecules
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cause differientiation
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sequence of DNA
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is not altered, we know this because if the chromosome were altered it could not produce the other cells in the organism
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housekeeping proteins
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all cells have these in common, These include the structural proteins of chromosomes, RNA polymerases, DNA repair enzymes, ribosomal proteins, enzymes involved in glycolysis and other basic metabolic processes and the proteins that make of the cytoskeleton.
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cell can control proteins made by
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by controlling how often a gene is transcribed, how RNA is processed, selecting mRNA to export from the nucleus , degrading certain mRNA molecules, selecting which mRNA are translated into ribosomes, and activating certain proteins after they’ve been made.
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transcription regulators
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proteins that control gene expression at the level of transcription along with regulator DNA sequences
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control of transcription
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is normally done at the step at which it is initiated.
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Regulator DNA sequences-
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used to switch the gene on and off. These can be as short at 10 nucleotide pairs. They tend to respond to a single signal.
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transcription regulator
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binds to the major grove of DNA.
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DNA binding motifs
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homeodomain, the zinc finger, and the leucine sipper.
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Dimerization
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roughly doubles the area of contact, it also makes it possible for many DNA sequences to be recognized by limited proteins.
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Bacteria regulate
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based on the food source that is available
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bacteria's genes can be encoded
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by a single promoter
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In E coli
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, five genes code for enzymes that that code for the amino acid trytophan.
Each of these five genes encodes a different enzyme, all of which are needed. The genes are transcribed as a single mRNA. |
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operon
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cluster of enzymes, controlled by a DNA sequence called the operator
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repressor protein
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switch genes on and off
Concentration of tryptophan is low, RNA polymerase binds to the promoter and transcribes the five genes. However if it is high, the repressor protein becomes active and binds to the operator which blocks the binding of RNA polymerase. |
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Activator proteins
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- able to bind and position RNA polymerase, allow poorly functioning promoters to become fully active.
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single promoter
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is normally controled by two transcription regulators
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the Lac operon in E coli
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is controlled by both Lac repressor and the activator protein CAP
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Lactose must be present and glucose must be absent
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in order for the Lac operon to be highly expressed, which allows the uptake of Lactose
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Enhancers
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increase the rate of transcription, from a distance of many nucleotides from the promoter
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mediator
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allows the Enhancer to interact with the promoter
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nucleosomes
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can inhibit the initiation of transcription if they are positioned over a promoter, which may have evolved to prevent to absence of proper activators
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transcription activators
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attract histone acetylases, which attach an acetyl group to lysines, which alters the structure allowing accessibility to promote transcription
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cell memory
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is a prerequisite of organized tissue, which is unique to eukaryotic organisms
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Combinatorial controls
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refers to the way that groups of regulatory proteins work together to determine the expression of a single gene.
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commitee
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many transcription factors working together to control a gene
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Eve
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a gene whose expression plays an important role in the development of the Drosophila embryo, if inactive flies die
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Fly experiment
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The findings of the antibody-staining showed that the cytoplasm of embryo contains a mixture of the transcription regulators that were each distributed in a unique pattern
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Reporter gene
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gene encoding a protein whose activity is easy to monitor experimentally
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Positive feedback loop-
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a key transcription regulator activates transcription of its own gene in addition to that of other cell-type-specific genes.
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DNA methylation
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blocks gene expression, the DNA methylation pattern is copied from parent to daughter
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Post-transcriptional controls-
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operate after RNA polymerase has bound to a gene’s promoter and started to synthesize RNA, and are crucial for the regulation of many genes.
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riboswitches
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Short sequences of RNA that change their conformation when bound to small molecules such as metabolites
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miRNA
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targets mRNA for destruction
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the precursor miRNA
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is processed to form mature miRNA, it then assembles with protein complex RISC.
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The target mRNA is either rapidly degraded
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within the RISC or transferred to and area in the cytoplasm where other cellular nucleases will destroy it.
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RNA interference
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targeted RNA degradation mechanism that helps to keep potentially dangerous invaders in check
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Dicer
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cleaves the RNA into small fragments called siRNA. Small interfering RNAs
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spatial and temperal
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regulation controls differentiation
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fully differentiated cells
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can still be used to drive the development of unfertilized eggs, Ex the frog experiment
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The expression pattern of gene can be altered
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in responds to extracellular cues and environmental change
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transcrption is controlled
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by proteins binding to regulatory
DNA sequences |
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Additional regulatory sequences
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exist upstream of promoter
sequence and transcription initiation site |
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Specific transcription regulator
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binding to certain regulatory DNA
sequences can switch the gene on or off. |
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transcription switches
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allow cells to respond to changes
in the environment |
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lactose
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glucose + galactose
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lactose is present and glucose is absent
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Presence of
lactose inside the cell --> allolactose increase --> allolactose binds to the repressor and make it fall off! Glucose absence -->cAMP produced and bind to CAP |
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glutocorticoid hormone
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- receptor complex can
influence transcription as a regulator |
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MyoD
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can induce fibroblasts to turn into “musclecell”
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Methylation pattern on the parental DNA strand gets copied
by |
methytransferase
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RISC
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RNA-induced
silencing complex |
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miRNA and siRNA
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work very similar, both target RNA for degrading, siRNA however has to be a perfect match, both are broken down in RISC
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