Molecular Flashcards
Heterochromatin
Condensed
Appears darker on EM
Transcriptionally inactive, sterically inaccessible
Barr bodies (inactive X chromosomes) are heterochromatin
Euchromatin
Less condensed
Lighter on EM
Transcriptionally active and sterically accessible
DNA methylation
Template strand cytosine and adenine are methylated in DNA replication, which allows MMR enzymes to distinguish between old and new strands in prokaryotes
DNA methylation at CpG islands represses transcription
Histone Methylation
Usually reversibly represses DNA transcription, but can activate it in some cases depending on methylation location
Histone Acetylation
Relaxes DNA coiling, allowing for transcription
Nucleoside
Base + (deoxy)ribose
Base + Sugar
Nucleotide
Base + (deoxy)ribose + phosphate
Linked by 3’-5’ phophodiester bond
Purines
A & G 2 rings PURe As Gold GAG - amino acids necessary for purine synthesis =Glycine, Aspartate, Glutamine
Pyrimidines
C, U, T
1 ring
CUT the PY (pie)
Deaminations of cytosine makes uracil (found in RNA)
Disrupting Pyrimidine Synthesis: Leflunomide
Inhibits dihydroorate dehydrogenase
Inhibits change Carbomoyl phosphate into orotic acid
Disrupting Pyrimidine Synthesis: Methotrexate, Trimethoprim & pyrimethamine
Inhibit dihydrofolate reductase
Decreases deoxy thymidine monophosphate in humans, bacteria and Protozoa
Inhibits change of DHF to THF
Disrupting Pyrimidine Synthesis: 5-Fluorouracil
Forms 5-F-dUMP, which inhibits thymidylate synthase (decreased dTMP)
Inhibits change from dUMP to dTMP
Disrupting Purine Synthesis: 6-Mercaptopurine
Inhibits de novo purine synthesis
Inhibits change of PRPP to IMP
Disrupting Purine Synthesis: Mycophenolate and Ribavirin
Inhibits inosine monophosphate dehydrogenase
Inhibits change from IMP to GMP
Disrupting both Purine and Pyrimidine synthesis: Hydroxyurea
Inhibits ribonucleotide reductase
Inhibits the change of UDP to dUDP
Adenosine deaminase deficiency
ADA is required for degradation of adenosine and deoxyadenosine
In ADA deficiency increase in dATP which is toxic for lymphocytes
One of the major causes of AR SCID
Lesch-Nyhan syndrome
Defective purine salvage due to absent HGPRT which converts hypoxanthine to IMP and guanine to GMP
Results in excess uric acid production and de novo purine synthesis
X-linked recessive
Findings: intellectual disability, self-mutilation, aggression, hyperuricemia (orange ‘sand’ in diaper), gout, dystonia
Treatment: allopurinol or febuxostat (second line)
Genetic code features: Unambiguous
Each codon specifies only 1 AA
Genetic code features: Degenerate/redundant
Most AA are coded my multiple codons
Exceptions: methionine and tryptophan encoded by only 1 codon (AUG & UGG)
Genetic code features: Commaless, non-overlapping
Read from a fixed starting point as a continuous sequence of bases
Exceptions: some viruses
Genetic code features: Universal
Genetic code is conserved throughout evolution
Exception in humans: mitochondria
DNA replication
Eukaryotic DNA replication more complex than prokaryotes DNA replication (in both) is semi conservative and involves both continuous and discontinuous (Okazaki fragment) synthesis
Origin of Replication
Particular consensus sequence of base pairs in genome where DNA replication begins
May be single (prokaryotes) or multiple (eukaryotes)
AT-rich sequences are found in promoters and origins of replication
Replication fork
Y-shaped region along DNA template where leading and lagging strands are synthesized
Helicase
Unwinds DNA template at replication fork
Single-Stranded binding proteins
Prevent strands from reannealing
DNA topoisomerases
Crease a single or double stranded break in the helix to add or remove super oils
Topo inhibitors: fluoroquinolones (topo II and IV in prokaryotes) and Etoposide/Teniposide (eukaryotic Topo II)
Primase
Makes an RNA primer on which DNA polymerase III can initiate replication
DNA pol III
Prokaryotic only
Elongates leading strand by adding deoxy nucleotides to the 3’ end (5’-3’ synthesis)
Elongates lagging strand until it reaches the primer of the preceding fragment
3’-5’ exon unleash activity proof reads each added nucleotide
DNA pol I
Prokaryotic only
Degrades RNA primer and replaces it with DNA
Has same functions at DNA pol III but excises RNA primer with 5’-3’ exonuclease
DNA ligase
Catalyzes the formation of a phosphodiesterase bond within a strand of dsDNA (i.e. Joins Okazaki fragments)
Telomerase
An RNA-dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material with every duplication
Eukaryotes only
Often dysregulated in cancer cells, allowing unlimited replication
Mutations in DNA: severity
Severity of damage: silent
Mutation in DNA: Transition
Purine to purine (A to G) or Pyrimidine to Pyrimidine (C to T)
Mutation in DNA: Transversion
Purine to Pyrimidine (A to T) or Pyrimidine to purine (C to G)
Silent mutation
Nucleotide substitution but codes for same (synonymous) AA
Often base change in 3rd position of codon (tRNA wobble)
Missense Mutation
Nucleotide substitution resulting in changed amino acid (called conservative if new AA is similar in chemical structure)
E.g. Sickle cell disease - glutamic acid with valine
Nonsense Mutation
Nucleotide substitution resulting in early stop codon
Usually results in non-functional protein
Frameshift mutation
Deletion or insertion of a number of nucleotides not divisible by 3, resulting in misreading of all nucleotides downstream
Protein may be shorter or longer and its function may be disrupted or altered
E.g. Duchenne Muscular Dystrophy, Tay-Sachs disease
Splice Site mutation
Mutation at splice site - retained intron in mRNA - protein with impaired or altered function
E.g. Rare causes of cancers, dementia, epilepsy and some types of beta-thalassemia
Lac Operon
Genetic response to environmental change
Glucose preferred metabolic substrate of E. Coli, but when absent and lactose is available can switch metabolism
Mechanism of shift: Lac Operon
Low glucose: increased adenylate cyclase activity to increase generation of cAMP from ATP causing activation of catabolite activator protein (CAP) and increase transcription
High Lactose: unbinds repress or protein from repressor/operator site to increase transcription
Nucleotide excision repair
Single stranded repair
Specific ending leases release the oligonucleotides containing damaged bases
DNA pol and ligase fill and reveal the gap
Repairs bulky helix-distorting lesions. Occurs in G1 phase of cell cycle
Defective: xeroderma pigmentosum, which prevents repair of Pyrimidine dimers because of UV light damage
Base excision repair
Single stranded repair
Base-specific glucose last removes altered base and creates AP site
One or more nucleotides are removed by AP-endonuclease, which cleaves the 5’ end
Lyse cleaves the 3’ end
DNA polymerase Beta fills gap and DNA ligase seals it
Throughout cell cycle
Important repair of spontaneous/toxic deamination
Mismatch Repair
Single stranded repair
Newly synthesized strand is recognized, mismatched nucleotides are removed, and the gap is filled and resealed
Occurs mostly in G2 phase of cell cycle
Defective: Lynch syndrome - hereditary non-polyposis CRC)
Nonhomologous end joining
Double strand repair
brings together 2 ends of DNA fragments to repair dsDNA breaks
No requirement for homology, some DNA may be lost
Mutated in ataxia telangiectasia, Fanconi anemia
DNA/RNA/Protein synthesis direction
DNA and RNA - 5’-3’ synthesis
The 5’ end of the incoming nucleotide bears the triphosphate (energy source)
Drugs blocking DNA replication often have modified 3’OH preventing addition of the next nucleotide (chain termination)
Protein: N-terminus to C-terminus
Start and Stop Codons: mRNA start codons
AUG
Eukaryotes: codes for methionine which may be removed before translation is complete
Prokaryotes: codes for N-formylmethionine (fMet) - stimulates neutrophil chemotaxis
Start and Stop Codons: mRNA stop codons
UGA
UAA
UAG
Promoter
Site where RNA pol II and multiple transcription factors bind to DN upstream from the gene locus (AT-rich region with TATA and CAAT boxes)
Promoter mutation commonly results in dramatic decrease in gene transcription
Enhancer
Stretch of DNA that alters gene expression by binding transcription factors
May be located close or far from or even within the gene
Silencer
Site where negative regulators (repressors) bind
May be located close, far from or within gene
RNA pol I: eukaryotes
Makes rRNA (most numerous RNA, rampant)
RNA pol II: Eukaryotes
Makes mRNA (largest RNA, massive)
Opens DNA at the promoter site
Alpha-amanitin, found in Amanita phalloides (death cap mushrooms) inhibits RNA pol II and causes severe hepatoxicity if ingested
RNA pol III: Eukaryotes
Makes 5S rRNA, tRNA (smallest RNA, tiny)
RNA pol: Prokaryotes
Multisubunit complex makes all three kinds of RNA
Rifampin: inhibits RNA pol in prokaryotes
Actinomycin D: inhibits RNA pol in both pro and eu
RNA processing (eukaryotes)
Initial transcript = heterogeneous nuclear RNA - modified to mRNA
In the nucleus: capping of 5’ end (7-methylguanosine cap), polyadenylation of 3’ end (AAUAAA - signal), splicing out of introns = mRNA
Then mRNA transported out of nucleus into cytosol for translation
Quality control in P-bodies
Chromatin Structure
DNA exists in the condensed, chromatin form in order to fit into the nucleus
Negatively charged DNA loops 2x around positively charged his tone octamer to form nucleosides (beads on a string)
Histones rich in AA lysine and arginine
H1 binds to the nucleosome and to linker DNA thereby giving stabilization
In mitosis, DNA condenses to form chromosomes
DNA and histone synthesis occur during S phase
Splicing of pre-mRNA
- Primary transcript combines with small nuclear ribonucleoproteins and other proteins to form the spliceosome
- Lariat-shaped (looped) intermediate is generated
- Lariat is released to precisely remove intron and join two exons
Ab to spliceosome like snRNPs (anti-Smith Ab) are highly specific for SLE
Anti-U1 RNP Ab are highly associated with mixed CT disease
Exon
Contain actual genetic information for coding proteins
Different exons are frequently combined by alternative splicing to produce larger numbers of unique proteins
Abnormal splicing variants are implicated in oncogenes is and many genetic disorders (e.g. Beta-thalassemia)
Intron
Are intervening non-coding segments of DNA
Stay in the nucleus once spliced out
MicroRNAs
Small, noncoding RNA molecules that post-transcriptionally regulate protein expression
Introns can contain miRNA genes
They have multiple mRNA targets, typically related to complementary base pairing: miRNA - degradation or inactivation of target mRNA - decreased translation into protein
Abnormal expression of miRNAs contribute to certain malignancies (e.g. By silencing an mRNA from a tumor suppressor gene)
tRNA: Structure
Secondary structure cloverleaf form with anticodon end is opposite 3’ aminoacyl end
All tRNAs have CCA (Can Carry Amino acids) at 3’ end along with a high percentage of chemically modified bases
The AA is covalently bound to the 3’ end of the tRNA
tRNA: T-arm
Contains the ribothymidine, pseudouridine, cytidine sequence necessary for tRNA-ribosome binding
tRNA: D-arm
Contains dihydrouidine residues necessary for tRNA recognition by the correct aminoacyl tRNA synthetase
tRNA: Acceptor stem
The 5’ CCA 3’ is the amino acid acceptor site
tRNA: Charging
Aminoacyl-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 a peptide bond
Am is harmed tRNA reads usual codon but inserts the wrong AA
tRNA: Wobble
Accurate base pairing is usually required only in the first 2 nucleotide positions of an mRNA codon, so codons differing in the 3rd ‘wobble’ site may code for the same tRNA/AA (as a result of degeneracy of the genetic code)
Protein synthesis: Initiation
Initiated by GTP hydrolysis
Initiation factors help assemble the 40S ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal 60S subunit assemble with the complex
ATP-tRNA (Activation = charging)
GTP-tRNA (Gripping and Going places = translocation)
Ribosomal Subunits
Eukaryotic: 40S + 60S = 80S (Even)
PrOkaryotic: 30S + 50S = 70S (Odd)
Protein Synthesis: Elongation
- Aminoacyl-tRNA binds to A site (exception: initiator methionine)
- rRNA (ribozyme) catalyzes peptide bond formation, transfers growing polypeptide to amino acid in A site
- Ribosome advances 3 nucleotides toward 3’ end of mRNA, moving peptidyl tRNA to P site (translocation)
Ribosome Sites
A site = incoming Aminoacyl-tRNA
P site = accommodates growing Peptide
E site = holds Empty tRNA as it Exits
Protein Synthesis: termination
Stop codon is recognized by release factor and completed polypeptide is released from ribosome
Post translational modifications: trimming
Removal of N or C-terminal propeptides from zymogen to generate mature protein
E.g trypsinogen to trypsin
Posttrasnlational modifications: Covalent alterations
Phosphorylation, glycosylation, hydroxylation, methylation, acetylation and ubiquitination
Chaperone protein
Intracellular protein involved in facilitating and/or maintaining protein folding
E.g. Yeast heat shock proteins are expressed at high temps to prevent protein denaturing/misfolding
