Unit I - Cell Biology Flashcards Preview

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Flashcards in Unit I - Cell Biology Deck (63)
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Intron splice site consensus sequences

GU marks the 5' end of an intron
AG marks the 3' end of an intron



Made of small nuclear ribonuclear proteins (snRPS) and snRNAs

U1 snRNA contains a sequence complementary to the mRNA sequence near the 5' splice site of introns

U2 snRNA base pairs with the intron at a point corresponding to the branch point A residue, activating it for nucleophilic attack


Purine accumulation disorders

Defect in hypoxanthine-guanine phosphoribosyl transferase (HGPT); leads to accumulation of purines (uric acid) in tissues

Lesch-Nyhan Syndrome


Deamination of 5mC and C

Deamination of 5-methyl cytosine converts 5mC to thymine

Deamination of C yields U



Antibiotic; inhibits bacterial translation by mimicking the 3; tRNA acceptor region and interacting with the ribosome to cause premature peptide release


Functions of RNA Poly I, II, III

RNA Polymerase I - synthesizes pre-ribosomal RNA

RNA Polymerase II - synthesizes mRNA

RNA Polymerase III - synthesizes tRNA


TATA Box / Initiator sequence

DNA control element located 25-30bp upstream from the transcription start site; bound by TATa-binding protein (TBP); this is the site at which general TFs bind



Contains TATA-binding protein (TBP) as well as TBP-associated factors (TAFs)

Part of RNA Polymerase II pre-initiation complex



Antibiotic; binds to RNA polymerase at the exit channel and sterically occludes the formation of mRNA chains > 2-3 nucleotides long



Phosphorylates RNA Polymerase II, which activates it

Part of RNA Polymerase II pre-initiation complex



CDK7 subunit phosphorylates Pol II CTD; has some helicase activity and functions in nucleotide excision repair (NER)

Part of RNA Polymerase II pre-initiation complex


Nucleotide Excision Repair (NER)

Removes DNA lesions that distort the DNA structure (i.e. dimers) and therefore block RNA or DNA polymerase from binding

Cockayne Syndrome & Xeroderma Pigmentosum are caused by defects in NER, often TFIIH


PolyA tail cleavage site consensus sequence

AAUAAA 10 to 30 nucleotides upstream from the cleavage site


DNA Polymerase III

The main polymerase involved in DNA replication; Pol III "holds on" to the DNA via a sliding clamp protein and has 3-5' exonuclease activity that enables proofreading


DNA Polymerase I

Mostly involved in replacing RNA primer with DNA; has exonuclease activity in the 5-3; direction


DNA Mismatch repair

MutS/MutL (in prokaryotes) or MSH/LH (in eukaryotes) recognize mismatched DNA nucleotides on the newly synthesized strand, which is unmethylated

Defects in this pathway cause hereditary non-polyposis colorectal cancer (HNPCC)/Lynch Syndrome


Base Excision Repair (BER)

Removes DNA lesions that do not cause distortions in the backbone and therefore may be missed by NER; glycosylase enzymes hydrolyze the N-glycosidic bond to remove the damaged base, producing an AP site which is removed by AP-specific endonuclease


Homologous Recombination & Non-homologous end joining (NHEJ)

Both repair double-stranded DNA breaks; HR repairs breaks between homologous ends; it requires the presence of a homologous chromosome (S & G2 phase)

NHEJ repairs breaks between non-homologous ends, which may lead to insertion/deletion of nucleotides at the break point


4 categories of DNA binding domains

Helix-Turn-Helix (Homeodomain)
Zinc Finger
Basic Leucine Zipper Proteins (bZLP)
Basic Helix-Loop-Helix motif (bHLH)


Histone structure

Histones are octameric proteins consisting of dimers of subunits H2A, H2B, H3, and H4

Histone H1 is bound to linker DNA between histones and functions to "slide" histones along DNA during modification


Histone De/Acetylation

Histone Acetyltransferases (HATs) and Histone De-acetyltransferases (HDATs) are classes of reversible chromatin modifiers; acetylation of histone N-termini Lysine residues neutralizes the positive charge and "frees" the histone tails from electrostatic reactions with the DNA phosphate backbone


Stop Codons



Shine-Delgarno Sequence

Prokaryotic ribosomal binding site; essentially corresponds with initiator AUG codon


Initiation Factor 4E (IF4E)

Binds the 7-methyl guanosine cap on the 5' end of the mRNA, facilitating scanning of the ribosome down the primary transcript to the start AUG codon


Elongation Factors (Prok and Euk)

Ef-Tu (in bacteria) & Ef1A (in eukaryotes); deliver charged aa-tRNA complexes to the A site of the ribosome, burning GTP when it dissociates


Initiation of Translation - Bacteria

IF1 and IF3 bind the small subunit, which binds the mRNA at the AUG start codon via base pairing with the Shine Delgarno sequence

IF2 (bound to GTP) delivers initiation Met-tRNA to the P site to pair with the AUG codon

GTP hydrolysis on IF2 releases all IFs and signals binding of the large subunit


DNA Polymerase delta

Performs DNA synthesis on the lagging strand in eukaryotes; contains 3-5' exonuclease activity


DNA Polymerase alpha

Functions in the synthesis of the first ~20 DNA nucleotides immediately following the RNA primers; also synthesizes the first basepairs of each Okazaki fragment

DNA polymerase alpha has primase activity


DNA Polymerase epsilon

Performs DNA synthesis on the leading strand in eukaryotes; contains 3-5' exonuclease activity


Release Factor (RF)

Enters the A site (bound to GTP) in conjunction with a stop codon; hydrolysis of GTP induces release of the ribosomal subunits