From DNA to Protein

How are the shape and chemical properties of a protein determinedeach protein has a unique sequence of amino acids determines shape and chemical properties
what are the two manners by which genetic information is expressedTranscription and translation
why is RNA capable of folding in a variety of different shapesRNA can fold into a variety of shapes because it is singled stranded

Name two other ways that RNA differs from DNARNA comes in different varieties structural and catalytic function
how does transcription beginwith the opening and unwinding of a small section of DNA
what is produced by this processnewly synthesized RNA drops away from the DNA template a double helix is reformed
how does RNA polymerase function in transcriptionRNA polymerase carry out transcription
in which direction does the growth occurRNA chain grows in 5 to 3
name four molecules that power this reactionATP, CTP, UTP, GTP
Why is accuracy not required for transcriptionRNA does not function to permanently store genetic information
rRNACore of ribosome
tRNAadapters that select amino acids and holds them on the ribosome until incorporated into protein
miRNAregulation of gene expression
what signals the starting point of transcription on the DNA strandRNA polymerase binds to DNA looking for the promoter region
What terminates transcriptionRNA chain is elongated until polymerase reaches a terminator
Discuss the sigma factor in bacteriaBacteria polymerase has factor that recognizers promoter
Discuss four manners by which transcription in eukaryotes differs from the process in prokaryotes1. Eukaryotes have 3 types of polymerases
2. eukaryotes RNA polymerase requires general transcription factores(accessory proteins)
3. Mechanisms of control less elaborate in eukaryotes (genes are far apart)
4. Eukaryotic DNA is packed into nucleosomes
What other components are necessary for eukaryotic RNA polymerases to function
TFIIDbinds to a DNA sequence rich in T and A nucleotides, causes distortion DNA that function to mark the promoter for other transcription factors
TATA boxlocated 25 nucleotides upstream from transcription, binding of other factors hepls form a complete transcription intiation complex
Cappingaddition of guanine nucleotide with CH3 to 5 end
polyadenylationadenine repeatedly added to 3 end
where does transcription and processing of RNA occur in eukaryotesin the nucleus
how are exons different from introns
how are introns removedby RNA splicing
name 2 molecules that play a role in the removal of intronsnucleotide squences
what governs the amount of protein produced by an mRNA moleculenuclear pore complex
what is the life span of prokaryotic and eukaryotic mRNAsbacterial mRNAs have lifespan of 3 mins, eukaryotic mRNAs have lifespan of 30 mins to 10hrs
what controls the lifespan of mRNA moleculeslifespans controlled by nucleotides in 3 untranslated region
discuss the genetic codetranslation involves conversion of RNA into protein using the genetic code
charged tRNAmolecules match amino acids to codons in mRNA
anticodonset of three nucleotides that base pair with the complementary codon
aminoacyl tRNA synthestasescovalently joins each amino acid to the proper tRNA molecule
where within a cell is the RNA message decoded in order to synthesize a protienin the ribosomes
what is a complete ribosome composed of and what is the function of each compoenenta large and small subunit
name the four binding sites on a ribosomea-site, aminoacyl-tRNA p-site, peptidyl-tRNA e-site
discuss the steps involved in translation1. charged tRNA molecule enters the a-site
2. the amino acid attached to the newly added tRNA is linked by a peptide bond to the polypeptide chain held by the
3. the large subunit shifts
4. the small subunit moves exactly 3 nucleotides along the mRNA molecule
define the term ribozymemolecule that have catalytic activity
which codon starts the translation process and which amino acid does it code forAUG and tRNA
what does the term polycistronic indicatethese mRNA molecules encode different proteins
name the three codons involved in termination of protein synthesisUAA, UAG, UGA
what happens to the structure of a ribosome once the stop codon is encountered and the mRNA molecule is releaseddissociates into two components
what are polyribosomeslarge cytoplasmic components made of many ribosomes that are closely spaced along a single strand of mRNA
discuss on way that inhibitors of protein synthesis can be utilizedantibiotics
name two sources of these inhibitorsno effect on protien synthesis in eukaryotes, can be taken in high doses without being toxic in human
what is the function of the proteasomesact on proteins that have been tagged with ubiqutin
between DNA and RNA which is more efficient at storing genetic informationDNA emerged and became more efficient at storing genetic information
has this always been the casethe earliest cells are thought to have stored hereditary information in RNA
Mutagensomething known to cause mutations (inherited genotypic changes)
One-gene, One-enzyme Hypothesis
(one-gene, one-polypeptide relationship)
Garrods idea that genes act through the production of enzymes, with each gene responsible for producing a single enzyme that in turn affects a single step in a metabolic pathway
One-Gene, One-polypeptide relationshipMany proteins, including many enzymes, are composed of more than one polypeptide chain (or subunit).

*The function of a gene is to inform the production of a single, specific polypeptide. (But not all genes code for polypeps.)

How does information flow from Genes to Proteins?-Transcription
-Translation

The question in another sense is also asking how does Central Dogma take place?

TranscriptionInformation from DNA sequence is copied to form RNA seq.

-3 Steps:
+ Initiation: PROMOTER
+ Elongation: done by RNA poly.
+Termination

TranslationRNA seq. is used to create amino acid seq. of a polypeptide
RNA vs DNA-Consists of one polynucleotide strand
-Sugar molecue = ribose (rather than deoxyribose in DNA)
-“U” uracil instead of “T” (in DNA)
Messenger RNA– carries a copy of a gene seq. in DNA to the site of protein
-Transcript region of one of the strands of DNA
-Carries a copy of the gene sequence in the form of codons to the ribosome for protein synthesis.
Transfer RNAA family of double-stranded RNA molecules. Each tRNA carries a specific amino acid and anticodon that will pair with the complementary codon in mRNA during translation.
Ribosomal RNAcatalyzes peptide bond formation and provides a structural framework for the ribosome.
Central DogmaInformation flows from DNA to RNA to polypeptide.

-RNA viruses are exceptions to the central dogma (reverse transcript)

How is the Information content in DNA transcribed to produce RNA?-RNA synthesis is directed by DNA.
-Transcription Requires:
+DNA template (for complementary base pairing)
+Appropriate nucleoside triphosphates (ATP, GTP, CTP, UTP) to act as substrate
+* RNA Polymerase enzyme
RNA Polymerase vs DNA Polymerase– RNA does NOT require a primer and it does NOT double check.

-Even thought there will be errors in the replication , RNA

Transcript Step 1: INITIATIONDone by promoter.
Promoter-tells RNA polymerase where to start transcription and which strand to transcribe.

– (special seq. of DNA) is required in order to cataylze RNA polymerase to start working.

Transcript Step 2: Elongation-Once RNA poly. binds to promoter, it unwinds the DNA and reads it from 3-5 direction.
-Like DNA polymerase, it adds nucleotides to the 3 ends of the growing strand but doesnt require primer to start working.
Consequence of RNA poly not proofreading.There will be a lot of mutations/ errors.
-However, many correct copies of RNA are made at the same time and because RNA has a short life span, these errors are not as harmful as mutations to DNA.
Mutations in DNA vs Mutations in RNA-It is deleterious (usually) to have mutated DNA because DNA is the main set of genes that will be replicated and not many are replicated (in comparison to RNA). On the other hand,many RNA are created and RNAs life span is short so a mutation is not really that harmful
Transcription and Translation OccurencePro: At the same time in the cytoplasm
Euk: Transcribe in Nucleus and translate in Cytoplasm
Gene StructurePro: DNA seq. is read in the same order as the amino acid seq.
Euk: Noncoding introns within coding seq.
Modification of mRNA after initial transcription but before translationPro: None
Euk: Introns spliced out; 5 cap and 3 poly A added
pre-mRNA-primary mRNA transcript where introns and exons are.
-still processing in the nuclues
-mRNA is the mature product that leaves the nuclues and goes into cytoplasm to be translated
intronsnoncoding base sequences. (intervening regions)
-introns are removed before the pre-mRNA becomes mature mRNA.
exons(expressed regions) introns may be interspersed with coding seq.

(only exons are left to create mRNA)