DNA/RNA Flashcards
What is contained in the nucleus?
Proteins, nucleotides, carbohydrates, and lipids
What is posttranslational modification?
once protein synthesis is complete, they need to be modified to change function whether they are going to be intracellular or extracellular proteins
What is the precurser to protein synthesis?
mRNA
What is the function of nuclear pores?
nucleus membrane channels that actively transport RNA, ribosomes, proteins, carbohydrates and lipids (smaller molecules simply diffuse)
What is the role of importins or exportins?
They are carrier proteins (nucleoporins); proteins with nuclear export sequence (NES) are actively transported out of the nucleus via these carrier proteins
RNA uses a NES-containing RNA-binding protein that also uses exportin
What is the most important structure inside the nucleous and how many are they? What is their role?
Chromatin; 46 chromosomes
unwinding exposes genes for DNA replication, DNA to RNA transcription and mRNA translation
What are the six classes of Histones?
H1, H2A, H2B, H3, H4, H5
What is the primary role of Histones?
post-translationally modified which either expose or conceal DNA sequences for gene transcription or repair of DNA damage
What are Histones made of?
Protein (positive/negative/uncharged/AA/primary structure/alpha helices(secondary structure)
What is the role of nuclear matrix/scaffold?
protect and maintain the structure and integrity of the DNA molecule
What are laminopathies?
groups of disorders associated with the mutations that affect the proteins of the nuclear membrane or lamina (dystrophies and dysplasias)
What must take place before DNA replication?
pre-replication complex which is composed of 4 proteins
What are the four steps for pre-replication complex?
- origin recognition complex binds to the origin of replication
2 & 3. Two regulatory proteins (CDC6 and CDT1) ensure the cell is prepared for DNA replication
- minichromosome maintenance complex contains the proteins essential for the establishment of the REPLICATION FORK
What is the replication fork?
point where the two DNA strands separate into leading strand and lagging strand and DNA copying occurs
What enzyme is responsible for the first step in DNA replication after the pre-replication complex?
DNA Helicase unwinds the DNA double helix
What happens on the leading strand?
DNA polymerase replicates the DNA strand from the 5’ to 3’ direction towards the replication fork; process is continuous
What happens on the lagging strand?
DNA polymerase adds short chains of nucleic acids, called Okazaki fragments in the 5’ to 3’ direction away from the replication fork
What is the role of the enzyme DNA ligase?
Joins the Okazaki fragments on the lagging strand
What is the role of DNA topoisomerase?
cuts the phosphate backbone, “untangles” the DNA strands, and then repairs the cut leaving the DNA unaltered
What is Transcription?
synthesis of mRNA from DNA; RNA polymerase transcribes DNA strand (only one strand - known as template trand) from 3’ to 5’ direction
What is the main difference between replication and transcription?
in transcription, multiple RNA polymerase can transcribe on a single DNA gene sequence. CANNOT have this during DNA replication
How does reverse transcriptase inhibitors (retrovirals) effect HIV?
inhibit the enzyme for reverse transcriptase (viral enzyme that copies its RNA to DNA, aka Retrovirus)
What is the genetic code?
3 bases = 1 codon and 1 codon = 1 AA. **AA can be represented by more than 1 codon
What is the complex that must be formed in order to have protein synthesis?
Ribosome made up of 60S subunit and 40S subunit
What does protein synthesis require?
mRNA, tRNA, ribosome and accessory proteins called initiation factor and elongation factor
What is the purpose of tRNA?
has to line up with and bind to the initiating codon (mRNA); composed up the anticodon and carries AA
What is the role of 60S subunit in Ribosome?
stabilize ribosome, peptide bond formation and movement of the ribosome along the mRNA strand
What is the role of 40s Subunit in Ribosome?
helps in establishing the proper AUG codon start site on the mRNA
What is the P-site?
peptide chain that grows on the 60S subunit when the tRNA is at this site on the 40S subunit
What is the A-site?
new AAs bind here
What are macrolides and how do they effect protein synthesis?
Antibiotics that inhibit protein synthesis in bacteria by taking advantage of the 50S subunit (blocking movement of ribosome along the mRNA) and does not effect the 60S subunit in humans
What is the function of the post-translational chaperones?
preventing misfolding and aggregation
Mad Cow Disease/Bovine Spongiform Encephalopathy (human equivalent Creutzfeldt-Jakob disease)
infectious, misfolding proteins known as prions; misfolding proteins aggregate into amyloid plaques creating holes in normal brain tissue
S&S: dementia, hallucinations, seizures, memory and speech problems, nervous tissue damage
TxT: chaperone proteins
What is post-translational trafficking?
directs a protein to its correct (final) destination after synthesis; if misfolding happens, it is sent to a retention center to get fixed
What is the final step in protein synthesis and why does it happen?
Post-translational modification (phosphorylation, lipidation, disulfide bond, acetylation, glycosylation, or ubiquitination)
It happens based on the body’s needs
Why is control of gene expression important?
Regulated by DNA promoter regions and allows for selective initiation and cessation of metabolic pathway; without it would be total chaos in the body
What is Gene Expression?
Binding of different transcription factors and/or enhancers to promoter sequences are essential for positive or negative control of transcription
What is the similarity between the 4 methods to control gene expression?
bind to enhancer promoter region of DNA
What are the 4 methods to control gene expression?
helix-turn-helix
Leucine zipper
helix-loop-helix
Zinc finger
What enzymes control gene expression by reversible acetylation of histone and what do they do?
histone acetyl transferases (HATs): adds acetyl group
histone deacetylases: remove acetyl group which blocks access of RNA polymerase to DNA
What is neutral mutation?
change of codon making a change in the AA however the new AA has the same chemical properties (hydrophilic, hydrophobic, charge, etc.)
What is Silent Mutation?
Change of codon results in the same AA
What is missense mutation?
change in codon resulting change in AA with different chemical properties
What is nonsense mutation?
change of codon resulting premature stop codon in the middle of the sequence. Stop codon is not at the end
What are Frameshift -1 and Frameshift +1
can add or delete at the same time; removal or add codon letter resulting in an entire shift of AA sequence
What is transition mutations?
single purine nucleotide is changed for a different purine or a pyrimidine to pyrimidine
( A G or T C)
What is transverse mutation?
Pyrimidine to purine or purine to pyrimidine
T –> A or G C –> G or A
A—>T or C G—>C or T
What and how do mutations occur in DNA?
chemical, radiation and viral can cause single or double strand breaks or DNA cross-linking with itself or proteins
What are the enzymes and steps involved with DNA repair?
Single-nucleotide mutations, endonucleases enzymes sense and remove (excision) the incorrect base and the correct nucleotide is replaced by a polymerase and ligase
Cell cycle checkpoints also verify accuracy of DNA replication prior to division
characterstics, S&S, TXT of Xeroderma Pigmentosa
autosomal recessive mutations in the enzymes required for the repair of thymidine dimers
Thymidine dimers are a common cross link that occurs between adjacent thymidine dimers to form a cyclobutane ring (hydrocarbon ring) when exposed to UV; this ring compromises the shape and function of DNA
S&S: basal cell carcinoma, squamous cell carcinoma and malignant carcinoma
TxT: reduce sun exposure and supportive care (die by age 20)
What is the cell cycle?
cell pathway which defines times of cell division, replication, cell growth and functional activities
Where do the two checkpoints occur in the cell cycle to check for DNA damage and what is involved?
G1-S checkpoint and G2-M checkpoint; p53 protein will detect damage of DNA and if there is damage, it will activate the inhibitor p21 which blocks the cyclin D-CDK4 complex and subsequently the G1 to S transition or G2 to Mitosis transition
Activity during interphase G1 of cell cycle?
prep for DNA synthesis, cell growth and protein production, cyclin E activates CDK2 allowing progression into S-phase
Activity during interphase S of cell cycle?
DNA replication; RNA transcription low except for that involved in histone production
Activity during interphase G2 of cell cycle?
synthesis of micrtobules for mitotic spindle and chromosome packing; process controlled by dephosphorylation of tyrosine in the maturation/mitosis-promoting factor complex; CDK2 leads to mitosis (point of no return; if cell is unprepared, Cdc25 inactivated
What are the phases in mitosis and what enzyme and phase is responsible for separating the sister chromosome?
Prophase, metaphase, anaphase and telophase
separase is the protein and it happens during anaphase
Activity during interphase G0?
no cell replication/division; cell cycle progression inhibited by protein cyclin-dependent kinase inhibitor 2A (blocks CDK4 with cyclin D interaction); G0 cells lose cell cycle proteins including cyclins and CDKs.
How are microtubules related to cancer treatment? (non-hodgkin’s lymphoma, wilm’s tumor and acute lymphoblastic leukemia)
Vincristine can block growth of microtubule polymerization during G2 and M phase, stopping mitosis at metaphase
How does TAXOL effect cancer treatment? (breast, lung, ovaries, head and neck cancers and Kaposi’s sarcoma)
stabilizes microtubules preventing sister chromatid separation in M phase
