Biochemistry - Molecular Flashcards
1
Q
Chromatin structure
- DNA
- Histones
A
- DNA
- DNA exists in the condensed, chromatin form in order to fit into the nucleus.
- Negatively charged DNA loops twice around positively charged histone octamer to form nucleosome “bead.”
- Think of “beads on a string.”
- In mitosis, DNA condenses to form chromosomes.
- DNA and histone synthesis occur during S phase.
- Histones
- Histones are rich in the amino acids lysine and arginine.
- H1 binds to the nucleosome and to “linker DNA,” thereby stabilizing the chromatin fiber.
- H1 is the only histone that is not in the nucleosome core
2
Q
Heterochromatin
A
- Condensed, transcriptionally inactive, sterically inaccessible.
- HeteroChromatin = Highly Condensed.
3
Q
Euchromatin
A
- Less condensed, transcriptionally active, sterically accessible.
- Eu = true, “truly transcribed.”
4
Q
DNA methylation
A
- Template strand cytosine and adenine are methylated in DNA replication, which allows mismatch repair enzymes to distinguish between old and new strands in prokaryotes.
- DNA methylation at CpG islands represses transcription.
- CpG Methylation Makes DNA Mute.
5
Q
Histone methylation
A
- Usually reversibly represses DNA transcription, but can activate it in some cases.
- Histone Methylation Mostly Makes DNA Mute.
6
Q
Histone acetylation
A
- Relaxes DNA coiling, allowing for transcription.
- Histone Acetylation makes DNA Active.
7
Q
Nucleotides
- Purines
- Pyrimidines
- Thymine
- Uracil
- Bonds
- Amino acids necessary for purine synthesis
- Nucleosides
- Nucleotides
A
- Purines
- Purines (A, G)—2 rings.
- PURe As Gold
- Pyrimidines
- Pyrimidines (C, T, U)—1 ring.
- CUT the PY (pie)
- Thymine
- Has a methyl.
- THYmine has a meTHYl
- Found in DNA
- Has a methyl.
- Uracil
- Deamination of cytosine makes uracil.
- Found in RNA
- Bonds
- G-C bond (3 H bonds) stronger than A-T bond (2 H bonds).
- Increased G-C content –> increased melting temperature of DNA.
- Amino acids necessary for purine synthesis (GAG)
- Glycine
- Aspartate
- Glutamine
- Nucleosides
- NucleoSides = base + (deoxy)ribose (Sugar).
-
Nucleotides
- NucleoTides = base + (deoxy)ribose + phosphaTe
- Linked by 3′-5′ phosphodiester bond.
8
Q
De novo pyrimidine and purine synthesis
- Purines
- Pyrimidines
- Ribonucleotides
- Carbamoyl phosphate
A
- Purines
- Start with sugar + phosphate (PRPP)
- Add base
- Pyrimidines
- Make temporary base (orotic acid)
- Add sugar + phosphate (PRPP)
- Modify base
- Ribonucleotides
- Synthesized first
- Converted to deoxyribonucleotides by ribonucleotide reductase.
- Carbamoyl phosphate
- Involved in 2 metabolic pathways: de novo pyrimidine synthesis and the urea cycle.
9
Q
Various antineoplastic and antibiotic drugs function by interfering with nucleotide synthesis:
- Leflunomide
- Mycophenolate and ribavirin
- Hydroxyurea
- 6-mercaptopurine (6-MP) and its prodrug azathioprine
- 5-fluorouracil (5-FU)
- Methotrexate (MTX), trimethoprim (TMP), and pyrimethamine
A
- Leflunomide
- Inhibits dihydroorotate dehydrogenase
- Mycophenolate and ribavirin
- Inhibit IMP dehydrogenase
- Hydroxyurea
- Inhibits ribonucleotide reductase
- 6-mercaptopurine (6-MP) and its prodrug azathioprine
- Inhibit de novo purine synthesis
- 5-fluorouracil (5-FU)
- Inhibits thymidylate synthase (decrease deoxythymidine monophosphate [dTMP])
- Methotrexate (MTX), trimethoprim (TMP), and pyrimethamine
- Inhibit dihydrofolate reductase (decrease dTMP) in humans, bacteria, and protozoa, respectively
10
Q
Purine salvage deficiencies
- HGPRT + PRPP
- APRT + PRPP
- Adenosine deaminase (ADA)
- Xanthine oxidase
A
- HGPRT + PRPP [1]
- Guanine –> Guanylic acid (GMP)
- Hypoxanthine –> Inosinic acid (IMP)
- APRT + PRPP [2]
- Adenine –> Adenylic acid (AMP)
- Adenosine deaminase (ADA) [3]
- Adenosine –> Inosine
- Xanthine oxidase [4]
- Hypoxanthine –> Xanthine
- Xanthine –> Uric acid
11
Q
Adenosine deaminase deficiency
A
- Excess ATP and dATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase –> prevents DNA synthesis and thus decreases lymphocyte count.
- One of the major causes of autosomal recessive SCID.
12
Q
Lesch-Nyhan syndrome
- Definition
- Findings
- Treatment
A
- Definition
- 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, gout, dystonia.
-
HGPRT:
- Hyperuricemia
- Gout
- Pissed off (aggression, self-mutilation)
- Retardation (intellectual disability)
- DysTonia
-
Treatment
- Allopurinol or febuxostat (2nd line).
13
Q
Genetic code features
- Unambiguous
- Degenerate / redundant
- Commaless, nonoverlapping
- Universal
A
- Unambiguous
- Each codon specifies only 1 amino acid.
- Degenerate / redundant
- Most amino acids are coded by multiple codons.
- Exceptions: methionine and tryptophan encoded by only 1 codon (AUG and UGG, respectively).
- Commaless, nonoverlapping
- Read from a fixed starting point as a continuous sequence of bases.
- Exceptions: some viruses.
- Universal
- Genetic code is conserved throughout evolution.
- Exception in humans: mitochondria.
14
Q
DNA replication:
Eukaryotic vs. Prokaryotic
A
- Eukaryotic DNA replication is more complex than the prokaryotic process but uses many analogous enzymes.
- In both prokaryotes and eukaryotes, DNA replication is semiconservative and involves both continuous and discontinuous (Okazaki fragment) synthesis.
15
Q
DNA replication (69)
- Origin of replication
- Replicaiton fork
- Helicase
- Single-stranded binding proteins
- DNA topoisomerases
- Primase
A
- Origin of replication [A}
- Particular consensus sequence of base pairs in genome where DNA replication begins.
- May be single (prokaryotes) or multiple (eukaryotes).
- Replicaiton fork [B]
- Y-shaped region along DNA template where leading and lagging strands are synthesized.
- Helicase [C]
- Unwinds DNA template at replication fork.
- Single-stranded binding proteins [D]
- Prevent strands from reannealing.
- DNA topoisomerases [E]
- Create a single- or double-stranded break in the helix to add or remove supercoils.
- Fluoroquinolones—inhibit DNA gyrase (prokaryotic topoisomerase II).
- Primase [F]
- Makes an RNA primer on which DNA polymerase III can initiate replication.
16
Q
DNA replication (69)
- DNA polymerase III
- DNA polymerase I
- DNA ligase
- Telomerase
A
- DNA polymerase III [G]
- Prokaryotic only.
- Elongates leading strand by adding deoxynucleotides to the 3′ end.
- Elongates lagging strand until it reaches primer of preceding fragment.
- 3′ –> 5′ exonuclease activity “proofreads” each added nucleotide.
- DNA polymerase III has 5′ –> 3′ synthesis and proofreads with 3′ –> 5′ exonuclease.
- DNA polymerase I [H]
- Prokaryotic only.
- Degrades RNA primer; replaces it with DNA.
- Has same functions as DNA polymerase III but also excises RNA primer with 5′ –> 3′ exonuclease.
- DNA ligase [I]
- Catalyzes the formation of a phosphodiester bond within a strand of double-stranded DNA (i.e., joins Okazaki fragments).
- Seals.
- Telomerase
- An RNA-dependent DNA polymerase that adds DNA to 3′ ends of chromosomes to avoid loss of genetic material with every duplication.
25
Q
Functional organization of a eukaryotic gene
A
28
Q
Eukaryotic RNA processing
- hnRNA
- The following processes occur in the nucleus following transcription:
- mRNA
- Poly-A polymerase
- Polyadenylation signal
A
- hnRNA
- Initial transcript is called heterogeneous nuclear RNA (hnRNA).
- hnRNA is then modified and becomes mRNA.
- The following processes occur in the nucleus following transcription:
- Capping of 5′ end (addition of 7-methylguanosine cap)
- Polyadenylation of 3′ end (≈ 200 A’s)
- Splicing out of introns
- mRNA
- Capped, tailed, and spliced transcript is called mRNA.
- mRNA is transported out of the nucleus into the cytosol, where it is translated.
- mRNA quality control occurs at cytoplasmic P-bodies, which contain exonucleases, decapping enzymes, and microRNAs
- mRNAs may be stored here for future translation.
- Poly-A polymerase
- Does not require a template.
- Polyadenylation signal
- AAUAAA
29
Q
Splicing of pre-mRNA
- Splicing process
- Antibodies
A
- Splicing process
- Primary transcript combines with small nuclear ribonucleoproteins (snRNPs) and other proteins to form spliceosome.
- Lariat-shaped (looped) intermediate is generated.
- Lariat is released to precisely remove intron and join 2 exons.
- Antibodies
- Antibodies to spliceosomal snRNPs (anti-Smith antibodies) are highly specific for SLE.
- Anti-U1 RNP antibodies are highly associated with mixed connective tissue disease.
30
Q
Introns vs. Exons
- Introns
- Exons
- Abnormal splicing variants
A
- Introns
- Introns are intervening noncoding segments of DNA.
- Introns are intervening sequences and stay in the nucleus.
- Exons
- Exons contain the actual genetic information coding for protein.
- Different exons are frequently combined by alternative splicing to produce a larger number of unique proteins.
- Exons exit and are expressed.
- Abnormal splicing variants
- Implicated in oncogenesis and many genetic disorders (e.g., β-thalassemia).
31
Q
tRNA Structure
- Structure
- T-arm
- D-arm
- Acceptor stem
A
- Structure
- 75–90 nucleotides, 2º 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.
- CCA Can Carry Amino acids.
- T-arm
- Contains the TΨC (thymine, pseudouridine, cytosine) sequence necessary for tRNA-ribosome binding.
- D-arm
- Contains dihydrouracil residues necessary for tRNA recognition by the correct aminoacyl-tRNA synthetase.
- Acceptor stem
- The 3′ CCA is the amino acid acceptor site.
32
Q
tRNA Charging
A
- Aminoacyl-tRNA synthetase (1 per amino acid; “matchmaker”; uses ATP) scrutinizes amino acid before and after it binds to tRNA.
- If incorrect, bond is hydrolyzed.
- The amino acid-tRNA bond has energy for formation of peptide bond.
- A mischarged tRNA reads usual codon but inserts wrong amino acid.
- Aminoacyl-tRNA synthetase and binding of charged tRNA to the codon are responsible for accuracy of amino acid selection.
34
Q
Protein Synthesis:
Initiation
- Initiation
- Eukaryotic vs. prokaryotic subunits
- ATP vs. GTP
A
- Initiation
- Initiated by GTP hydrolysis
- Initiation factors (eukaryotic IFs) 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.
- Eukaryotic vs. prokaryotic subunits
- Eukaryotic subunits: 40S + 60S –> 80S (Even).
- PrOkaryotic subunits: 30S + 50S –> 70S (Odd).
- ATP vs. GTP
- ATP—tRNA Activation (charging).
- GTP—tRNA Gripping and Going places (translocation).
35
Q
Protein Synthesis:
Elongation & Termination
- Elongation
- Termination
- Mnemonic
A
- Elongation
- Aminoacyl-tRNA binds to A site (except for 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)
- Termination
- Stop codon is recognized by release factor, and completed polypeptide is released from ribosome.
-
Think of “going APE”:
- A site = incoming Aminoacyl-tRNA.
- P site = accommodates growing Peptide.
- E site = holds Empty tRNA as it Exits.
