IR WEEK 2 Flashcards by Jackie Marquez

what is the spontaneous loss of ~500 purine (A,G) bases lost per cell per day because of hydrolysis of the glycosal linkage to deoxyribose

depurination

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when does depurination occur?

when the bond connecting a purine to its deoxyribose sugar is broken by a molecule of water (hydrolysis) resulting in a purine free nucleotide that can’t act as a template during DNA replication (results in a deletion)

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what is the spontaneous removal of the amine (NH2) group from ~100 cytosines per cell per day to form uracil

deamination

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when does deamination occur?

when hydrolysis wipes away the NH2 from cytosine and replaces it with an oxygen to form uracil and an ammonium ion (results in a substitution

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List the spontaneous DNA mutations that require DNA repair

depurination
deamination
spontaneous oxidative destruction
uncontrolled methylation
hydrolytic attack

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reactive oxygen radical or chemical exposure causes base damage

spontaneous oxidative destruction

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forms pyrimidine dimers via covalent linkage between 2 bases

UV damage

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DNA glycosylases are specific for altered DNA bases. it is detected by the glycosylase enzyme “flipping out” each nucleotide so it can be checked by the endonuclease and repaired if necessary

base excision repair

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recognition of dimer begins with this repair

delete

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BRCA1

breast and ovarian cancer; repair by homologous recombination is affected

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Ataxia Telangiectasia (AT)

leukemia, lymphoma, gamma ray sensitivity, genome instability; ATM protein is affected

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cockayne syndrome

UV sensitivity, developmental abnormalities; coupling of nucleotide excision repair to transcription process is affected

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xeoderma pigmentosum

skin cancer, UV sensitivity, neurological abnormalities; nucleotide excision repair is affected

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DNA is transcribed into RNA

transcription

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a sequence of DNA nucleotides that signal the starting point for RNA synthesis

promoter

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comparing many sequences with the same basic function and tallying up the most common nucleotides found at each position. it serves as a summary or “average” of a large number of individual nucleotide sequences

consensus nucleotide sequences

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genes carried in a cells DNA, specify the amino acid sequence of proteins, and the RNAs that are copied from these genes (which ultimately direct the synthesis of proteins)

mRNAs

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do not code for a protein

non coding RNAs

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will form to compensate for each 10 nucleotide pairs that are open (unwound). the formation of this is energetically favorable because it restores a normal helical twist to the base paired regions that remain

DNA supercoiling

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state the central dogma

dna to mrna to protein

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transcribes the genes 5.8S, 18S, 28S rRNA genes

RNA Polymerase I

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transcribed all protein coding genes, plus snoRNA genes, miRNA genes, siRNA genes, incRNA genes and most snRNA genes

RNA Polymerase II

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transcribes tRNA genes, 5S rRNA genes, some snRNA genes and genes for other small RNAs

RNA Polymerase III

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function in a variety of nuclear processes, including the splicing of pre-mRNA

snRNA (small nuclear RNA)

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help to process and chemically modify rRNAs

snoRNA (small nucleolar RNA)

regulate gene expression by blocking translation of specific mRNAs and causing their degredation

miRNA (micro RNAs)

a transcribed segment of DNA; information in just one gene for just one RNA molecule or single protein (or group of mRNAs if there is splicing)

transcription unit

a sequence of DNA Ts and As located ~30 nucleotides upstream from the transcription start site.

TATA box

form the basic structure of the ribosome and catalyze protein synthesis

rRNA

joins together different portions of an RNA transcript to eliminate the intron sequences; also provides eukaryotes with the ability to synthesize several related but different proteins from the same gene

RNA splicing

allows activator proteins to communicate properly with the RNA polymerase II and with the general transcription factors

mediator

the large assembly of RNA and protein molecules that performs pre-mRNA splicing in the cell, snRPs form the core

spliceosomes

the nucleotide sequence of a gene, through intermediary of mRNA, is instead translated into the amino acid sequence of a protein by rules

genetic code

each group of three consecutive nucleotides in mRNA is called (this) and each (this) specifies either one amino acid or a stop to the translation process

codon

allows an RNA sequence to be translated in anyone of 3 different frames

reading frame

a set of three consecutive nucleotides that pairs with the complementary codon in an mRNA molecule

anticodon

mismatch at the third position, can base pair with any nucleotide listed in the shown column; explains why so many of the alternative codons for an amino acid differ only in their third nucleotide

wobble

a complex catalytic machine made from more than 50 proteins and several RNA molecules

ribsomes

RNA molecules that posses catalytic activity

ribozymes

small set of RNA molecules that allow the binding to both the codon and the amino acid

tRNAs

sugar group is ribose, uracil replaces thymine (loses methyl group), sometimes there are unique base pairings G wit U

RNA

how does tRNA become attached to the appropriate amino acid?

tRNA requires aminoacyl-tRNA synthetase for recognition and attachment of the correct amino acid to the 3' end

what direction are proteins synthesized in

N-terminal end to C-terminal end

this ribosomal subunit is important for matching tRNA to codon on mRNA

small subunit

this ribosomal subunit catalyzes the formation of peptide bonds between amino acids

large subunit

Four major steps to chain elongation

tRNA binding peptide bond formation large subunit translocation small subunit translocation

what speeds up eukaryotic translation process?

elongation factors EF1 and EF2

how is codon-anticodon match checked?

small rRNA subunit forms hydrogen bonds between codon and anticodon; if match is correct, GTP hydrolysis occurs which moves the translation process along

what does the mRNA 5' cap do?

marker to cell that this is an mRNA essential for translation binds a protein complex as a recognition factor: cap binding complex

this is considered a molecular mimic, similar in 3D conformation to tRNA which helps it bind to the A site

release factor

allows more than one protein to be synthesized from a single mRNA by changing reading frame by ignoring a start or stop codon

translational frameshifting

21st amino acid can be inserted directly into a growing polypeptide using

translation recoding

produced from serine tRNA that is enzymatically altered, binds to stop codon

selenocysteine

misplaced STOP codon

nonsense mediated mRNA Decay

a collection of rare disorders involving impaired ribosome biogenesis and function; mutations affect translation and protein synthesis

ribosomopathies

caused by truncated protein bc STOP codon is misplaced (Nonsense mutations)

CF mutations Duchennes MD betathalassemia hurlers syndrome

Disorders of missense mutation

sickle cell certain types of CF mutations certain cancers

Have specific functions in altering a misfolded protein hsp60 and hsp70 are examples

chaperones

initiates early protein folding; looks for stretches of hydrophobic amino acids which trigger ATP hydrolysis

HSP70

aids in helping incorrectly or incompletely unfolded proteins fold completely

HSP60

contains proteases for digestion of proteins

proteasomes

serve as a recognition marker for proteasomes when it is bound to misfolded proteins

ubiquitin

histone regulation

monoubiquiliation

endocytosis

multiubiquitylation

proteasomal degradation and DNA repair

polyubiquitylation

surface amino acid sequences recognized by a set of enzymes

degrons

brain/spinal cord are sensitive to protein aggregates. protein aggregates can cause

alzheimers huntingtions ALS parkinsons

RNA polymerase is part of the repair process by stalling at DNA alterations (specifically NER) during transcription and calls fourth coupling proteins which direct excision repair machinery to these sites

transcription-coupled repair

this syndrome is caused by a defect in transcription coupled repair

cockayne syndrome

methods for repairing double stranded DNA breaks

non-homologous end joining and homologous recombination

involves removing a set of nucleotides, then ligating the strands back together

non-homologous end joining

occurs after replication (S and G2 phases) when nearby daughter DNA duplex and serve as template for repair

homologous recombination

group of enzymes that form phosphodiester bonds between ribonulceotides

RNA polymerases

unwinds DNA at the transcription start point, phosphorylates Ser5 of the RNA polymerase CTD; releases RNA polymerase from the promoter

TFIIH

RNA polymerase I transcribes......

rRNAs