Step 1 - Biochem 1

denniskwinn's version from 2015-04-25 15:56


Question Answer
Chromatin structureDNA exists in the condensed, chromatin form in order to fit into the nucleus.
(-)charged DNA loops twice around (+) charged histone octamer (2 sets of H2A, H2B, H3, and H4) to form nucleosome bead.
Octamer subunits consist primarily of lysine and arginine amino acids (+ charged)
H1 Histone ties nucleosome beads together in a string = only histone not in the nucleosome core.
In mitosis, DNA condenses to form mitotic chromosomes.
Heterochromatincondensed transcriptionally inactive sterically inacessible HighlyCondensed
Euchromatinless condensed, transcriptionally active, sterically accessible
PurinesPure As Gold A and G - 2 rings
guanine has a ketone
- the a.a. Glycine, Aspartate, Glutamine are needed for synthesis
- Made from IMP precursor
PyrimidinesCUT the Py
Thymine has a methyl. uracil is found in RNA and thymine in DNA.
- deamination of C⇢U
Made from orotate precursor with PRPP added later
G-C bond has3 H bonds - ⇡G-C content = higher melting temp.
Ribonucleotides are converted to DNA byribonucleotide reductase
Carbamoyl phosphate metabolic pathways involvedde novo pyrimidine synthesis and urea cycle.
Carbamoyl Phosphate accumulation causeOrnithine transcarbamoylase deficiency (urea cycle) leads to an accumulation of carbamoyl phosphate which is then converted to orotic acid.
Hydroxyurea inhibitsribonucleotide reductase
6-mercaptopurine (d-MP) blocks de novo purine svnthesis.
5-fluorouracil (5-FU) inhibitsthymidylate synthase - ⇣dTMP
Methotrexate (MTX) inhibitsdiihydrofolatc reductase (⇣dTMP).
Trimethoprim inhibitsbacterial dihydrofolate reductase- (⇣dTMP)
Orotic aciduriainability to convert orotic acid to UMP (de novo pyrimidine synth pathway) due to defect in either orotic acid phosphoribosyltransferase or orotidine 5’ phosphate decarboxylase - autosomal recessive
Orotic aciduria findingshigh orotic acid in urine, megaloblastic anemia that doesn’t improve with administration of Vitamin B12 or folic acid. . Failure to thrive. No hyperammonemia (vs. OTC deficiency- Increased orotic acid with hyperammonemia).
Orotic aciduria treatmentoral uridine administration
Adenosine deaminase deficiencymajor cause of SCID - excess ATP and dATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase prevents DNA synth and decreased lymphocyte count.
Lesch-Nyhan syndromedefective purine salvage - absence of HGPRT & results in excess uric acid production. x linked recessive
Lesch-Nyhan findingsretardation, self-mutilation, aggression, hyperuricemia, gout, choreoathetosis
HGPRTconverts hypoxanthine to IMP and guanine to GMP


Question Answer
Genetic Code Features1.Unambiguous(each codon specifies only 1 amino acid) 2.Degenerate/redundant(more than 1 codon may code for same aa-except methionine encoded only by aug) 3.Commaless/nonoverlapping(Read from a fixed starting point as a contiuous sequence of bases- except some viruses) 4.Universal(genetic code conserved thru evolution- except mitochondria, archaebacteria, mycoplasma and some yeasts)
Transitionsubstituting purine for purine or pyrimidine for pyrimidine
Transversionsubstituting purine for pyrimidine or vice versa
Silent mutationssame amino acids often base changes in 3rd position of codon (tRNA wobble)
Missense mutationschanged amino acids (conservative- new aa is similar in chemical structure)
Nonsense mutationschange resulting in early stop codon
Frame shift mutationchange resulting in misreading of all nucleotides downstream, usually resulting in a truncated nonfunctional protein.


Question Answer
HelicaseUnwinds DNA template at replication fork.
Single -stranded binding proteinsprevent strands from reannealing
DNA topoisomerasecreates a nick in the helix to relieve supercoils created during replication
Primasemakes an RNA primer on which DNA polymerase III can initiate replication.
Fluoroquinolonesinhibit DNA gyrase (a prokaryote topoisomerase)
DNA poly IIIProkaryotic only. Elongates leading strand by adding deoxynucleotidesto the 3' end. Elongates lagging strand until it reaches primer of preceding fragment. Has 5' to 3' synthesis and proofreads with 3' to 5' exonuclease.
DNA poly 1prokaryotic only - degrades RNA primer and fills in the gap w/DNA. It excises RNA primer with 5' to 3' exonuclease.
DNA ligaseseals
Nucleotide excision repairspecific endonucleases release the oligonucleotides containing damged bases; DNA poly and ligase fill and reseal the gap, respectively.
Xeroderma pigmentosamutated Nucleotide excision repair - dry skin with melanoma and other cancers - can’t repair thymine dimers from UV light
Base excision repairSpecific glycosylases recognize and remove damaged bases- AP endonuclease cuts DNA at apyrimidinic site, empty sugar is removed and the gap is filled and resealed.
mismatch repairunmethylated, newly synthesized string is recognized, mismatched nucleotides are removed and the gap is filled and resealed. Mutated in Hereditary nonpolyposis colorectal cancer.
DNA repairnon homologous end joining - brings together 2 ends of DNA fragments -


Question Answer
mRNA read5' to 3'. Protein synthesis is N to C.
DNA/ RNA/protein synthesis direction5' to 3'. 5' of incoming nucleotide bears the triphospate which is the target of the 3' hydroxyl attack. Drugs blocking DNA replicatn often have modified 3' OH preventing addition of the next nucleotide aka chain termination
most abundant rnarRNA
longest type of rnamRNA
smallest rna typetRNA
mRNA start codonsAUG (or rarely GUG)
AUG in eukaryotescodes for methionine which may be removed before translation is completed
AUG in prokaryotescodes for formyl-methionine (f-Met)
mRNA stop codonsUGA, UAA, UAG
Gene promoter regionsite where RNA poly and multiple other transcription factors bind to DNA upstream from gene locus( AT- rich upstream sequence with TATA and CAAT boxes). Promoter mutation commonly results in dramatic decrease in amount of gene transcribed.
Gene enhancer regionstretch of DNA that alters gene expression by binding transcription factors
Gene silencer regionsite where negative regulators (repressors) bind
Location of Enhancer, Silencer may be located close to , far from or even within (in an intron) the gene whose expression it regulates
RNA poly I makesrRNA
RNA poly II makesmRNA. RNA poly II opens DNA at promoter site. alpha amanitin(death cap mushrooms) inhibit it and causes liver failure if ingested
RNA polyIII makestRNA
Prok RNA polymerasemakes all 3 kinds of RNA
RNA processing in eukaryotes (3)Occurs in nucleus after transcription - 1. Capping on 5’ end (7-methylguanosine) 2. Polyadenylation on 3’ end (200A’s) 3. Splicing out of introns - initial transcript is called heterogenous nuclear RNA. capped and tailed transcript is called mRNA. only processed rna is transported out of the nucleus. AAUAAA=polyadenylation signal. Poly-A polymerase doesnt require template.
Splicing of pre-mRNA1. Primary transcript combines w/snRNPs and other proteins to form splicesome. 2. Looped intermediate is generated. 3. Loop is released to remove intron precisely and join 2 exons. patients with lupus make antibodies to spliceosomal snRNPs. Pre-mRNA splicing occurs in eukaryotes.
Exonscontain the actual genetic info coding for protein. Different exons can be combined by alternative splicing to make unique proteins in different tissues ex Bthalassemia mutations
Intronsintervening noncoding segments of Dna
tRNA structure75-90 nucleotides, secondary structure, cloverleaf form, anticodon end is opposite 3' aminoacyl end. All tRNAs both eukaryotic and prokaryotic have CCA at 3' end along with a high percentage of chemically modified bases. the amino acid is covalently bound to the 3' end of the tRNA.
tRNA chargingAminoacyl-tRNA synthetase (1 per aa, matchmaker uses atp) scrutinizes aa before and after it binds to tRNA. If incorrect, bond is hydrolyzed. the aa-tRNA bond has energy for formation of peptide bond. A mischarged tRNA reads usual codon but inserts wrong amino acid.
tetracycline moabind 30 s subunit, preventing attachment of aminoacyl-tRNA
Aminoacyl-tRNA synthetaseaminoacyl-tRNA synthetase and binding of charged tRNA to the codon are responsible for accuracy of aa selection.
tRNA wobbleaccurate base pairing is required only in the first 2 nucleotides positions of an mRNA codon -
Initiation of protein synthesisactivated by GTP hydrolysis, initiation factors(eIFs) help assemble the 40S ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal subuit assemble with the complex.
Protein elongation1. Aminoacyl tRNA binds to A site(except for initiator methionine) 2.ribosomal rRNA (aka ribozyme) catalyzes peptide bond formation, transfers growing polypeptide to amino acid in A site 3. Ribosome advances 3 nucleotides toward 3’ end of RNA moving peptidyl RNA to P site (translocation)
Protein synth TerminationStop codon is recognized by release factor, and Completed protein is released from ribosome
Aminoglycosides inhibitformation of the initiation complex and cause misreading of mRNA
Chloramphenicolinhibits 50S peptidyltransferase
Macrolidesbind 50S blocking translocation
Clindamycinbinds 50S blocking translocation
tRNA aminoacylation ATP requirementATP to AMP
Energy requirement of TranslationATP to AMP, and two GTPs to GDP
Posttranslational trimmingremoval of N- or C-terminal propeptides from zymogens to generate mature proteins
Posttranslational covalent alterationsPhosphorylation, glycosylation and hydroxylation
Posttranslational Proteasomal degradationAttachment of ubiquitin to defective proteins to tag them for breakdown
CDKs and cell cycleCyclin-dependent kinases, constitutive and inactive
Cyclins and cell cycleregulatory proteins that control cell cycle events; phase specific: activate CDKs
Cyclin-CDK and cell cycleMust be both activated and inactivated for cell cycle to progress
Tumor suppressors and cell cycleRb and p53 normally inhibit G1 to S progression; mutations in these genes result in unrestrained growth
Permanent cell typesRemain in G0, regenerate from stem cells - Neurons, skeletal and cardiac muscle, RBCs
Stable cell typesEnter G1 from G0 when stimulated - Hepatocytes, lymphocytes
Labile cell typesNever go to G0, divide rapidly with a short G1 - bone marrow, gut epithelium, skin, hair, follicles


Question Answer
Rough ERsite of synthesis of secretory proteins and N-linked oligosaccharide addition to many proteins. Mucus-secreting goblet cells of the small intestine and anitbody- secreting plasma cells are rich in RER.
Nissl bodiesRER in neurons - synthesize enzymes(ex. ChAT) and peptide neurotransmitters
Free ribosomesunattached to any membrane, site of synthesis of cytosolic and organellar proteins
Smooth endoplasmic reticulumsite of steroid synthesis and detoxification of drugs and poisons - liver hepatocytes and steroid hormone-producing cells of the adrenal cortex are rich in SER
Golgi Apparatus fxns1Distribution center of proteins and lipids from ER to the plasma membrane, lysosome, and secretory vesicles 2. Modifies N-oligosaccharides on asparagine 3. Adds O-oligosaccharides to serine and threonine residues 4. Addition of mannose6 phospate to specific lysosomal proteins, targets the protein to the lysosome. 5. proteoglycan assembly from core proteins. 6. Sulfation of sugars in proteoglycans and of selected tyrosine on proteins.
Vesicular Trafficing Proteins COPI= retrograde golgi to ER, COPII=anterograde, RER to cis-Golgi, Clathrin= trans-Golgi to lysosomes, plasma membrane to endosomes(receptor mediated endocytosis)
I-cell disease (inclusion cell disease)inherited lysosomal storage disorders: failure of addition of mannose-6-phosphate to lysosome proteins (enzymes are secreted outside the cell instead of being targeted to the lysosome).
I-cell disease sxcoarse facial features, clouded corneas, restricted joint movement, high plasma levels of lysosomal enzymes - often fatal in childhood
Drugs that act on microtubules (5)1. Mebendazole/thiabendazole (antihelminthic) 2. Griseofulvin (antifungal) 3. Vincristine/vinblastine (anti-cancer) 4. Paclitaxel (anti-breast cancer) 5. Colchicine (anti-gout)
Chediak-Higashi syndromemicrotubule polymerization defect resultin in decrease in phagocytosis - recurrent pyogenic infections, partial albinism, peripheral neuropathy
Microtuble structurepolymerized dimers of alpha and beta tubulin. Each dimer has 2GTP bound- incorporated into flagella, cilia, mitotic spindles - grows slowly, collapses quickly. Also involved in slow axoplasmic transport in neurons
Molecular motor proteinstransport cellular cargo toward opposite ends of microtubule tracks. - dynein = retrograde to microtubule (+ to -) . . Kinesin = anterograde to microtubule (- to +)
Cilia Structure9 + 2 arrangement of microtubules. Axonemal dynein- ATPase that links peripheral 9 doublets and causes bending of cilium by differential sliding of doublets.
Kartagener’s syndromeimmotile cilia due to dynein arm defect - male and female infertility, bronchiectasis and recurrent sinusitis (bact and particle not pushed out) - assoc w/ situs inversus
Cell structures with Actin and myosinMicrovilli, muscle contractions, cytokinesis, adherens junctions
Cell structures with MicrotubulesCilia, flagella, mitotic spindle, neurons, centrioles
Cell structures with IFsVimentin, desmin, cytokeratin, glial fibrillary acid proteins (GFAP), neurofilaments
Effect of cholesterol in plasma membranehigher cholesterol in membranes or long saturated fatty acid content decreases fluidity and increases melting temperature
Plasma membrane compositionAsymmetric lipid bilayer. contains cholesterol (50%), phospholipids (50%), sphingolipids, glycolipids, and proteins.
Vimentinconnective tissue
Desmin muscle
Cytokeratinepithelial cells