Bittel and Ferguson Flashcards
Is DNA parallel or antiparallel
antiparallel
How often is there a turn in DNA
one turn every 10 bp
What digest linker DNA?
nuclease
What is a nucleosome core particle made up of?
8 histone proteins
- 2 molecules each of H2A, H2B, H3, H4
- 2x standee DNa that is 147 nucleotide pairs long
What are the universal features of cells on earth?
- all cells store their heredity info in the same linear chemical code: DNA
- all cells replicate their hereditary information by templated polymerization
- all cells translate RNA into protein in the same way
- each protein is encoded by a specific gene
- all cells function as biochemical factories dealing with the same basic molecular building blocks
- all cells are enclosed in a plasma membrane across which nutrients and waste materials pass
- life requires free energy
What does acetylation do for genes? methylation?
acetylation: activating
methylation: inhibiting
What is an Okazaki fragment?
chunk of DNA on lagging strand
look at DNA repair pathways
slide 12-13
What is homologous recombination
crossing over and gene conversion occurring in same chromosome, multiple opportunities for genetic reassortment
What is a DNA only transposon?
short invited repeats at each end
What enzyme is required for movement in DNA only transposon?
transposes
what is the mode of movement for DNA only transposon?
moves as DNA, either by cut and paste or replicative pathways
describe retroviral like retrotransposons
directly related long terminal repeats at each end
retroviral like retrotransposons enzyme
reverse transcriptase and integrase
retroviral like retrotransposons move of movement
moves via an RNA intermediate whose production is driven by a promoter in the LTR
describe nonretroviral retrotransposons
poly A at 3’ end of RNA transcript, 5’ end often truncates
nonretroviral retrotransposons enzyme
reverse transcriptase and endonuclease
nonretroviral retrotransposons move of movement
moves via an RNA intermediate that is often synthesized form a neighboring promotor
____ in somatic cells direct differentiation into Sertoli cells instead of follicle cells
Sry
What do Sertoli cells do?
secrete anti-mullerian hormone to suppress female development, causing mullerian duct to regress
What do leydig cells do?
secrete testosterone
In the absence of sry, what occurs?
genital ridge becomes ovary
PGC becomes egg
somatic cells differentiate into follicle cells (support cells) and theca cells (estrogen producing cells)
are gametes haploid or diploid?
haploid
What do capacitated sperm use to penetrate granulose cells?
hyaluronidase
What does the zona pellucida act as?
species barrier
The zona pellucida induces sperm to undergo ______ reaction, which does what?
acrosome, contents help sperm to tunnel through the zona pellucid and alters sperm so it can bind and fuse with plasma membrane of egg
what do membrane proteins ZP1, 2 and 3 do in binding of the sperm to the egg
ZP 2 and 3 form long filaments
ZP1 cross link the filaments
What is the central dogma of biology
DNA is transcribed to messenger RNAs which act as templates for protein synthesis in translation
What are the three phases of translation?
initiation
elongation
termination
describe initiation
ribosome assembles around the target mRNA. The first tRNA is attached at the start codon
describe elongation
tRNA transfers an amino acid corresponding to the next codon. The ribosome then moves to the next mRNA codon to continue the process, creating an amino acid chain
describe termination
when a stop codon is reached, the ribosome releases the polypeptide
What types of organs are commonly affected by short telomere syndrome?
organs with heigh cell turnover, such as bone marrow, liver, lungs and immune system
look at the two repair pathways
slide 35
How does radiation greatly increase mutation rates in all organisms?
ionizing radiation dislodges electrons in tissue causing free radicals which often damages DNA
UV light induces the formation of pyrimidine dimer: two thymine bases covalently bonded that blocks replication
SOS system in bacteria: SOS system allows bacteria cells to bypass the replication block with a mutation prone pathway
______ dimers result from ultraviolet light
pyrimidine
What is thymine dimer repair?
dimer is reputed by enzymes that cut out the surrounding nucleotides and fill the space back in
RNA sequence is the same as the ________ strand of DNA
nontemplate
DNA is transcribed by _______
RNA polymerase
function of mRNA
messenger RNA, code for proteins
function of rRNA
ribosomal RNA, form basic structure of the ribosome and catalyze protein synthesis
function of tRNA
transfer RNA, central to protein synthesis as adaptors between mRNA and amino acids
function of snRNA
small nuclear, function in a variety of nuclear processes, including the splicing of pre mRNA
snoRNA function
small nucleolar, help to process and chemically modify rRNAs and splicesomal RNAs/mRNAs
siRNA funciton
small interfering, turn off one expression by directing the degradation of selective mRNAs and the establishment of compact chromatin structures
piRNA function
piwi-interacting, bind to kiwi proteins and protect the germ line from transposable elements
lncRNA function
long noncoding RNA, may of which serve as scaffolds, they regulate diverse cell processes, including X-chromosome inactivation
What is the TATA box?
25 nucleotides from the transcription initiation site, protein TBP recognizes and binds to the TATA box providing the initial step to begin transcription
As soon as mRNA is ~ 25 nucleotides long it is capped, what do three enzymes work together to do?
- dephosphorylate the 1st nucleotide
- add GMP in reverse link (5’ to 5’ instead of 5’ to 3’)
- add methyl group to guanosine
_____ catalyzes one of the steps in clotting cascade. When mutated or deleted, it results in hemophilia.
Factor VIII
What is the exosome?
protein complex that cleans up damaged RNAs before they leave the nucleus
rich in RNAses and chops up RNAs for recycling
What are the functions of microRNAs?
regulate expression of more than 70% of all the protein coding genes
regulators of various biological processes including embryonic development, cellular proliferation, differentiation and apoptosis
microRNAs play a role in complicated diseases
What enzyme helps ensure that the correct amino acid is coupled to the tRNA?
aminoacyl-tRNA synthetase
What are the four steps in protein synthesis?
- new tRNA binds to A site pairing with codon
- carboxyl end of growing peptide is rebased from tRNA in P site. Peptide bond formation between the previous AA added and the new one. tRNAs in the P site and A site.
- Large subunit moves along mRNA held by small subunit, shifting tRNAs to P and E sites on small subunit
- small subunit moves 3 nucleotides along the mRNA and ejects the tRNA in the E site
What is the primary role of proteins in the ribosome?
stabilize the RNA core (2/3 of ribosome is RNA)
look at initiation of protein synthesis
slides 84-87
______ mediated decay eliminates mRNAs with premature stop codons
nonsense
How does a protein get sent to the proteasome
must be marked, protein E3 recognizes misfiled proteins and add multiple ubiquitin proteins to the misfolded peptide
the cap of the proteasome has what on it?
- ubiquitin receptor
- unfolds
- ubiquitin hydrolase
