EXAM 2 review Flashcards
What evidence did the experiment w/ nutritional mutants in Neospora provide?
-Genes specify enzymes
What is the Central Dogma of molecular biology?
- How info passes through the cell
- DNA to RNA to Protein
- RNA to DNA (reverse transcription)
What are the characteristics of a Codon in the genetic code?
- Consists of 3 bases
- Specifies SINGLE amino acid
What is the difference between Eukaryotic & Prokaryotic transcription in terms of number of RNA pol?
- Eukaryotes have 3 RNA pol
- Prokaryotes only have 1
What kind of RNA can an Anticodon be found on?
-On tRNA
What does RNA pol bind to initiate Transcription?
-It binds to the Promoter
What is the codon in mRNA read by?
-It is read by the anticodon in a tRNA
What is a special characteristic of the Splicing process?
-It can join multiple mRNA’s in the same transcript
What is the job of the Peptidyltransferase enzyme?
-It transfers the growing peptide from a tRNA to the next amino acid
In comparing gene expression in Prokaryotes vs Eukaryotes:
- Eukaryotic genes can make 1 protein
- Prokaryotic genes make more than 1 protein
- Both produce mRNA’s that are colinear w/ the protein
What would happen to the CCA codon if it was mutated?
-It would produce a silent codon
What will an Inversion mutation do?
-Only cause a mutant phenotype if the inversion breakpoints fall within a gene
What is the relationship between Mutations & evolution?
-Mutations can create new inheritable alleles
What occurs in Huntington’s disease?
-High levels of repeats of triplet sequence of DNA that encodes glutamate
What is true about individuals on autism spectrum or MSSNG data?
- Majority of DNA changes occur in non-protein coding regions
- 1% of genomic changes involve epigenetics
- 25% of those w/ autism have seizure disorder
What would NOT occur in Central Dogma?
- Polypeptides used to create other polypeptides
- DNA directly directing production of polypeptides
What are Operons in Prokaryotes?
-They are single promotor that transcribes multiple genes
What does it mean that the genetic code is Redundant?
-1 codon can encode for multiple amino acids
What is the role of RNA Haloenzyme?
- It is the sigma factor that attaches to form initiation complex
- Helps w/ phosphodiester bonds & accurate initiation for transcription by recognizing promotor
What is the Anti-sense strand of DNA?
-The template for production of RNA base pairs in transcription
What is the Sense strand of DNA?
-The coding strand
What is unique about Prokaryotes in terms of transcription & translation?
-Its coupled= once 5’ end of mRNA is freed up translation for proteins begins
What 3 things is true about tRNA?
- Transcribed w/ the assistance of RNA pol 3 in nucleus
- It has a 3’ acceptor stem
- May be charged w/ the help of Aminoacyl-tRNA synthase=by covalently bonding an amino acid to tRNA
What is the role of Peptidyl-Transferase?
- RNA enzyme in large ribosomal subunit
- Helps peptide bond formation for amino acids on growing amino acid chain in P-Site
What is the role of Spicosomes?
- They cause intronic sequences to loop into Lariat Structure
- Contains proteins that are in the nucleus
What are Splicosomes made of?
- Small Nuclear RNA= snRNA
- Proteins
What causes the correct positioning of RNA on a ribosome for initiation in Eukaryotes?
-The 5’ methyl cap of mRNA
What requires energy input?
- tRNA charging (ATP)
- Translocation & Charged tRNA delivery (GTP)
What is a Single Nucleotide Polymorphism?
-It is the one base difference between individuals in a population
What is Linkage Disequilibrium?
-Non-random association between a genotype at one locus and the genotype at another locus
How many naturally occurring Amino acids are there?
20
How many codons are there?
64
How many codons codes for amino acids?
61 which includes AUG for methionine
How many stop codons are there?
3
What are the stop codons?
UAA
UAG
UGA
How is the genetic code read as?
-Units for 3 bases
What is an exception to the universality of the coding language?
-Mitochondria & Chloroplasts read the code differently (don’t read stop codons as STOP, instead they are read as amino acids)
What are the 4 Key characteristics in Prokaryotic Transcription?
- It involves only 1 RNA pol= 2 pieces
- Transcription & Translation are coupled
- 2 Initiation sites
- mRNA doesn’t need a primer
What are the 2 pieces of the RNA polymerase for Prokaryotic Transcription?
- Core Polymerase
- Holoenzyme
What is the role of the Core Polymerase?
- Can synthesize RNA using DNA template (won’t be accurate)
- Has 2 alpha, 1 beta, 1 beta’ subunit
- It binds to DNA template & ribonucleotide triphosphate precursors
What are the 2 sites of DNA to initiate transcription in Prokaryotes?
- Promotor
- Actual Start site
What is the role of the Promotor in Prokaryotic Transcription?
-It forms recognition & binding site for RNA pol
Where is the Promotor for Prokaryotic Transcription located?
- Located upstream of start site
- 35nt and -10nt upstream
What is the overview of Prokaryotic Transcription?
- RNA pol binds to the promotor @ -35nt upstream
- Then the RNA unwinds the helix at -10nt upstream
Why is Prokaryotic Transcription coupled to Translation?
- It all occurs in the same site within the cell
- Translation starts when the 5’ end of mRNA is available
- This way the mRNA can contain multiple genes=encodes for multiple proteins
How does Termination occur in Prokaryotic Transcription?
-Occurs at stop markers
G-C pairs followed by A-U pairs= allows the RNA to form hairpin
What are the 4 key characteristics of Eukaryotic Transcription?
- Uses transcription factors
- Transcription takes place in Nucleus
- Has 3 RNA pol each w/ own promotor (RNA pol 2 is the star)
- mRNA goes through extensive modification
What are the 3 different polymerases that Eukaryotic Transcription uses?
- RNA Pol 1
- RNA Pol 2
- RNA Pol 3
What is the role of RNA pol 1?
-Transcribes rRNA
What is the role of RNA pol 2?
- Transcribes mRNA & SnRNA
- Consists of CTD subunit
What is the role of RNA pol 3?
-Transcribes tRNA & sRNA
What is the promotor for RNA pol 1?
-It is specific for each species
What is the promotor for RNA pol 2?
-It is the Core promotor w/ TATA box
What is the promotor for RNA pol 3?
-It is found within the actual gene
What is the purpose of the CTD subunit in RNA pol 2?
- Carboxyl Termination Domain
- Recruits other factors w/ polymerase to make Transcription Elongation Complex (7aa repeated 52x)
What is the role of the Transcription Factors?
-Interact w/ RNA pol 2 to create Initiation complex @ promotor
What does the Initiation complex for Eukaryotic Transcription consist of?
- Core promotor w/ TATA box
- Other transcription factors
- RNA Pol 2 comes in & binds last
What modifications does the mRNA go through in Eukaryotic Transcription?
5’ Methyl G cap
3’ poly a tail
What is the purpose of the 5’ methyl G cap on mRNA?
- Important for translation
- RNA stability
- Further processing
What is Polydenylation?
- Occurs in Eukaryotic Transcription
- Causes a transcript to be cleaved off of 3’ end & adds the Poly-A tail
What is Transcription in general?
DNA to RNA
- Uses RNA pol= has NO proofreading abilities
- Consists of using Coding strand & Template strand
What is the Coding strand for Transcription?
- It is the mRNA strand produced w/ complementary bases to DNA strand
- Known as the SENSE strand bc read from 5’ to 3’= helps direct polypeptide synthesis in translation
What is the Template strand for Transcription?
- It is 2nd strand of DNA
- Known as ANTI-SENSE strand bc read from 3’ to 5’
What is Translation in general?
RNA to Proteins
- takes place on ribosomes
- tRNA is the star here
What are the 6 types of RNA?
- tRNA
- rRNA
- mRNA
- Small RNA
- srpRNA
- snRNA
What is the role of tRNA?
- Used in translation bc used as intermediary between mRNA and amino acids
- Helps position Amino acids on Ribosome
What is the role of rRNA?
- Critical to the function of Ribosomes
- found on both small & large ribosomal subunits
What is the role of mRNA?
-Used in transcription
What is the role of Small RNA?
- Consists of siRNA and miRNA
- Both control gene expression
What is the role of srpRNA?
- Signal Recognition Particle for protein synthesis on RER=drags the proteins to RER for further modification
- srpRNA consists of RNA & proteins
What is Pre-mRNA splicing ?
- Removal of introns (non-coding sequences)
- Then joining the Exons together (coding-sequences) to make mature mRNA
What are the 4 steps for pre-mRNA splicing?
1) snRNA forms base pairs w/ 5’ end of intron & branch side (3’ end)
2) snRNPS associate to make a spliceosome
3) 5’ end of intron is removed & forms bond @ branching site and 5’ attaches to the 2’ OH to form lariat
4) Exons are joined & spliceosomes disassemble
How does the Splicesome recognize the introns for removal?
-The introns begins w/ same 2 base sequence and ends w/ another 2 base sequence= tags them for removal
When does pre-mRNA splicing occur?
-in the nucleus BEFORE export to the cytoplasm
What is Alternative Splicing?
- Primary transcript can be spliced into different mRNA by including different sets of exons
- 1 gene can produce 25 distinct mRNA’s
What is the Proteasome?
-Proteins produced from a genome
What is Transcriptome?
-When RNA is produced from genome
What are Introns?
- Non-coding sequences= makes gene non-colinear w/ protein product which is why it needs to be removed
- Makeup 24% of human genome
What are Exons?
-Coding sequences that are expressed
What are the 4 key characteristics of Ribosomes?
- Key organelle in translation=can only ensure correct codon & anticodon pairing
- Has 3 tRNA binding sites
- It moves horizontally during translation
- Has decoding & enzymatic funtions
What are the 3 tRNA binding sites?
Read like 5’ E, P, A 3’
- E site is where the uncharged tRNA exits
- P site=Peptidyl site= Where the polypeptide chain grows
- A site=Amincoacyl site= where the tRNA enters
What are the 3 key characteristics of tRNA?
- It can be folded into Leaf clover shape=has 2 functional ends
- tRNA is charged when it carries an amino acid
- Needs Aminoacyl-tRNA synthase to bind to amino acids
What is the tRNA leaf clover shape?
- Anticodon Loop
- Acceptor stem
What is the role of the Anticodon loop of the tRNA leave clover shape?
- It is located at the bottom of the leaf
- It base-pairs w/ codons in mRNA
What is the role of the Acceptor stem?
- It is located at the 3’ end
- Is joined w/ the carboxyl terminus of an amino acid
- Always read as 5’ CCA 3’
What is tRNA charging reaction?
- It joins the acceptor stem w/ the carboxyl terminus of an amino acid
- Product= amino acid + charged tRNA
What does a ribosome do with is decoding function?
-It decodes at a small subunit of the ribosome
What does a ribosome do with its enzymatic function?
-Uses peptidyl transferase for peptide bond formation in the LARGE subunit
What is the overview of Translation?
1) mRNA is threaded through ribosome
2) tRNA carrying the amino acid bind to ribosome
3) Ribosome & tRNA position amino acid= allows for peptide bond formation between new amino acid & growing peptide chain
How does translation begin?
-The ribosome uses the first AUG it encounters in mRNA to signal intiation
What is Translation like in Prokaryotes?
-They use an Initiation Complex= initiator charged w/ chemically modified methionine + small ribosomal subunit & mRNA strand
How is the small ribosomal subunit positioned on mRNA for Prokaryotic translation?
- Ribosomal Binding Sequence (RBS)
- Located on 5’ end & complementary to the 3’ end of small subunit rRNA
What happens after the complex of mRNA, initiator tRNA and small ribosomal subunit are added in Prokaryotic Translation?
-The large ribosomal subunit is added
What is translation like in Eukaryotes?
- Similar to prokaryotes EXCEPT
- their initiation amino acid is methionine
- their mRNA’s lack RBS
- Small subunit binds to mRNA by binding to it’s 5’ cap
- more complex than prokaryotes
What results from the fact that there are fewer tRNA’s than Codons?
-Wobble Pairing= tRNA’S wobbly on mRNA so that it can be read by more than one codon
What does Termination of translation require?
- STOP codons move into A site & recognized by released factors
- Then proteins may be sent to RER w/ the help of SRP
What is the structure of the growing peptide during Translation?
Top= Amino Terminus (N terminus) Middle= all amino acids bonded to eachother Bottom= Carboxyl End (C terminus) which is bound to tRNA
What happens in the Transcription bubble in both Prokaryotes & Eukaryotes?
-RNA nucleotides match up w/ their complementary bases on temporary DNA strand
What is unusual about initiator tRNA?
-Carries modified amino acid fMET & only binds to ribosome on P site
Why is Ubiquitin associated w/ toxic damage?
-Damaged proteins are tagged w/ ubiquitin for degeneration
What are the 6 different points where Eukaryotes can regulate gene expression?
- Initiation of Transcription
- RNA splicing
- Passage through nuclear membrane
- Protein synthesis
- RNA inference
- Post-translational modification
What is the difference between the mature mRNA in Prokaryotes & Eukaryotes?
- Prokaryotes can specify for more than one protein
- Eukaryotes can only specify for one
How could drug developers use RNA inference ina medical application?
-They could stop the production of a defective protein
What are the 3 important functions of Gene Splicing?
- They allow one coding sequence to be expressed differently according to each cell type
- They change all gene types randomly
- Add another layer to gene regulation
What supresses Transcription?
- They methylation of DNA at cytosines followed by guanines
- Treating histones w/ histone deacetylase
What are the 3 characteristics of Epigentic changes?
- They’re heritable
- May alter patterns in DNA methylation
- May alter gene expression
What are the characteristics of Histamines?
- It would effect nearby cells by initiating a signal transduction pathway
- It is also a ligand
What is the correct positioning of RNA on a ribosome in initiation aided by?
-the 5’ Methyl cap in eukaryotes
What would happen to the cells that use chaperone proteins if the chaperone proteins are damaged?
-It would be unable to restore its tertiary structure
How do you make histones positively charged?
-You would add Histone Deacetylase which decreases the rate of gene expression
What are characteristics of Estrogen & Progesterone?
- They have intracellular receptors
- Function to affect gene expression directly
Why do Prader-Willi syndrome & Angelman syndrome have different phenotypes?
-Individuals affected by either syndrome have a deletion in chromosome 15 but have different imprint on homologue
The receptor for Insulin-Like growth factor is a receptor tyrosine kinase. what happens when the factor binds to the receptor?
- They autophosphorylate
- Initiate a signal transduction cascade
What is true about Denaturation?
-It may be caused by an increase in salt concentration= causes protein to lose its tertiary structure
If only one of your autosomal genes is only paternally imprinted, which allele do you express?
-Maternal allele
What is Paracrine Signaling?
-It is the response that Histamine does that causes your finger to swell when you prick it
Who received a nobel prize after their death?
-Ralph Steinman
Who receive a nobel prize for identifying the alpha helix?
-Linus Pauling
How many deaths were drug over dose deaths in 2016 in indiana?
1500
