Biochemistry - First Aid Flashcards
Charges/Composition of DNA and histones
DNA: negatively charged; nucleic acids linked by phosphodiester bonds
Histones: positively charged; rich in amino acids lysine and arginine ;
8 subunits make up a nucleosome core (two each of 4 histone types - H2A, H2B, H3, H4)
Note that DNA loops around histones 2x.
Both DNA and histone synthesis occurs during S phase
DNA methylation
Represses transcription when methylated at CpG islands.
During replication, the template stand is IDed by the mismatch repair enzymes via methylation of A and C.
Nucleotide excision repair defect
xeroderma pigmentosum
predisposes to SCC, BCC, and melanoma
*Nucleotide excision repairs prymidine dimers during G1 phase because of UV light exposure; via specific endonucleases, DNA poly, and ligase;
Mismatch repair defect
HNPCC (hereditary nonpolyposis colorectal cancer (Lynch syndrome)
*mismatch repair fixes new strands during G2 phase
Base excision repair
Important in repair of spontaneous/toxic deamination throughout the cell cycle.
Via: base specific glycosylases remove altered base, endonuclease cleaves 5’ and lyase cleaves 3’, DNA poly, and ligase.
alpha-amanitin
found in amanita phalloides (death cap mushrooms) - inhibits RNA poly II (which makes mRNA, snRNA, microRNA)
RNA polymerase and rifampin
Prokaryotes only have 1 type of RNA poly that carries out the cell functions.
Note that rifampin inhibits it in prokaryotes
RNA polymerase and Actinomycin D
Inhibits RNA poly in both prokaryotes and eukaryotes
Splicing of pre-mRNA
- Primary transcript (heterogenous RNA) combines with snRNPs and other proteins to make spliceosome.
- lariat shaped (loop) intermediate is generated
- lariat released to precisely remove intervening introns and join 2 exons
Ab to spliceosome snRNPs (anti-smith ab) are highly specific for SLE.
Anti-U1 RNP ab are highly specific for mixed connective tissue disease.
tRNA structure
Acceptor stem: 3’ end CCA to carry amino acids via covalent bond
T arm: contains thymine, pseudouracil, cytosine sequences necessary for tRNA ribosome binding
D arm: contains dihydrouracil residues necessary for tRNA recognition by correct amino acyl tRNA synthetase
anticodon loop opposite the 3’ acceptor stem
Hydroxyurea
inhibits ribonucleotide reductase in pyrimidine production;
leads to inhibtoin of UDP to dUDP
Posttranslational modifications
Trimming: Removal of N or C terminal propeptides from zymogen to generate mature protein (ex. trypsinogen to tryspsin
Covalent alterations: phosphorylation, glycosylation, hydroxylation, methylation, acetylation, ubiquitination
Bonds in the primary structure of proteins
Peptide bonds
Typically the genetic code is considered universal (i.e., conserved throughout evolution). What is one noteworthy exception to this rule?
Human mitochondrial DNA, which is not conserved
Frameshift mutation
Deletion or insertion of number of nucleotides not divisible by 3 which leads to misreading of all nucleotides downstream, usually causing truncated, nonfunctional protein.
Ex. duchenne muscular dystrophy
DNA Polymerase 3
Prokaryote only
Elongates leading DNA strand adding to 3’,
elongates lagging DNA strand until it reaches primer of preceding fragment
3’ to 5’ exonuclease activity “proofreads” each added nucleotide
DNA polymerase1
Prokaryote only
Has same functions as DNA poly 3, but also excises RNA primer since it has 5’ to 3’ exonuclease activity, and replaces it with DNA
lac operon
Glucose normally surpresses adenylate cyclase.
If glucose absent, then increased AC, increased cAMP, increased CAP activation, and increased transcription (CAP acts as an activator for RNA poly)
High lactose unbinds the repressor (lactose acts as an inducer), so there is increased transcription.
Nonhomologous end joining
Brings together 2 ends of DNA fragments to repair ds breaks. No requirement for homology. Some DNA may be lost.
Mutated in ataxia telangiectasia and fanconi anemia
RNA polymerase 1
**Note the nucleolus is the primary site of ribosomal RNA transcription.
Also the nucleolus is involved in maturation of ribosomal subunits.
Ribosomal protein components are made in cytoplasm and then go to nucleolus where they combine with the rRNA to make the 40s and 60s . Then they go back to cytoplasm.
Generally as cells grow mature, they require less ribosomes and this process slows. But malignant cells with high metabolic activity use this process and have large numbers of active rRNA genes and prominent mucleoli.
ribosomal RNA (18s, 5.8s, 28S)
RNA polymerase 2
mRNA
snRNA
microRNA
RNA polymerase 3
tRNA
5S rRNA
P bodies
Where mRNA quality control occurs in the cytoplasm.
P bodies contain exonucleases, decapping enzymes, and microRNAs
mRNAs may be stored in P bodies for future translation
Rough ER function
The synthesis of secretory (exported) proteins and the addition of N-linked oligosaccharides to proteins
Goblet cells and plasma cells are very rich in RER!!
Nissl bodies
synthesis of peptide NTs for secretion
Free ribosome function
Unattached to any membrane; site of synthesis of cytosolic and organellar proteins
Smooth ER
Steroid synthesis; detoxification of drugs and poisons
adrenal cortex and hepatocytes are rich in SER!
Golgi
Distribution center for proteins and lipids from ER to vesicles and plasma membrane.
Modifies N oligosaccharides on asparagine.
Adds O oligosaccharides on serine and threonine.
Adds mannose 6P to proteins for lysosomal trafficking
Endosomes
sorting centers for material from outside the cell or from the golgi, sending it to lysosomes for destruction or back to the membrane / golgi for further use.
Signal recognition particles (SRPs)
abundant, cytosolic ribonucleoproteins that traffic proteins from ribosome to RER. Absent or dysfunctional SRP means that proteins accumulate in the cytosol!!
Vesicular trafficking proteins
COPI: golgi to golgi retrograde transport; cis golgi to ER
COPII: ER to cis golgi (anterograde)
Clathrin: trans-golgi to lysosomes; plasma membrane to endosomes
Microtubules
Movement and cell division; microtubules
cilia, flagella, mitotic spindles, centrioles, and axonal trafficking (ex. dynein and kinesin)
Intermediate filaments
maintain cell structure.
vimentin, desmin, cytokeratin, lamins, glial fibrillary acid proteins (GFAP), neurofilaments