The central dogma of molecular biology is best stated as:

DNA ---> RNA ---> Protein

Transcription is the DNA-directed synthesis of ______.  

RNA by the enzyme RNA polymerase

Polypeptide synthesis is directed from:

mRNA

Codons consist of______.

Thre nucleotides.

A degenerate code is one where:

Amino acids are specified by more than one codon

_____are found primarily in prokaryotes and consist of multiple genes transcribed and regulated together.

Operons

What is the role of tRNA in translation?

It brings the amino acid to the ribosome that corresponds to a codon on the mRNA.

Which of the following is NOT part of a bacterial region?

              a.) the -35 sequense

              b.) the -10 sequence

              c.) the gene

              d.) All are part of the promotor

C.) The Gene

When a stop codon is reached _____________.

It is recognized by release factors

DNA binding motifs interact with __ of DNA.

The major groove

What is the central dogma of molecular biology?

informatin passes in one direction from one gene (DNA) to and RNA copy of the gene, and then RNA copy directs the sequential assembly of a chain of aminoa acids into a protein.

DNA ---> DNA

Replication

DNA ---> RNA

Transcription 

(because it contains exact copy of DNA)

RNA --- > Protein

Translation

(because it requires translating from a nucleic acid to a protein)

What is a template strand? What is the coding strand? How do these align with the names sense strand  and antisense strand?

The strand of DNA copied is the template strand. The strand of DNA not used is the coding strand. They call the coding strand the "Sense" strand because it has the same sense as teh RNA. The template strand would be the antisense strand

What type of RNA transcript is used t direct synthesis of polypeptides?

messenger RNA (mRNA)

Why is the process of translation more complex than transcription? How does a cell compensate for a lack of complimentary betwween RNA and amino acids?

RNA cannot be used for a direct template for protein because it does not have a complimentary strand. That is a sequence of amino acids cannot be aligned to RNA template based on any kind of "chemical fit". tRna fizes this problem.

mRNA

Messenger RNA

rRNA

Ribosomal RNA -- Critical to function for ribosome

tRNA

transfer RNA --- act to interpret information in mRNA and to help position the amino acids

snRNA

small nuclear RNA -- part of the machiney involved in nuclear processing of eukaryotic "pre-mRNA"

15.2 Genetic Code 

 How does a sequence of nucleotides in a DNA molecule specify the sequence of amino acids in a polypeptide?

Genetic code most likely consisted of a series of blocks known as codons each cooresponding to an amino acid in the encoded protein. Information with in one codon was probably a sequence of 3 nucleotides.

Why did Crick and Brenner reason codons must consist of 3 nucleotides based on the probabilities?

with 4 DNA nucleotides (GTCA), using 2 in each codon can produce only 4^2, or 16 different codons. --- not enough to code for 20 different amino acids. However using 3 is more than enough

How was it determined that codons are unspaced?

if the information was spaced, altering one word would not make any difference

What happened when single deletion was made?

Genetic message was shifted

What happened when two deletions made near each other were made?

genetic message shifter, altering all of the amino acids after deletion

What happened when 3 deletions were made?

Protein acted as normal

What is the name that refers to these types of mutations? 

Frameshift Mutations

How do these results of shifts reate to a reading frame?

because there is no puncuation, the reading frame established by the first codon in the sequence determins how all subsequent codons are read.

if there are 64 possible 3 nucleotide sequences, and only 20 amino acids, what happens with the other 44 codons?

triplet; binding assay, stop codons, start codons

What is a stop codon?

signals stop

What is a start codon?

signals start

What is meant by saying "The code is degenerate". Is degeneracy uniform? Where does the degenerate base usually occur within the codon?

Some amino acids are specified by more than one codon. it is not uniform, some amino acids have onle one codon, and some have up to six. The DB usually occus in position 3 of a codon.

Does a single codon ever specif more than one amino acid? Why is this important?

This has never been found

Is the genetic code universal? If not, where would we observe difference?

Yes it is universal, mitochondrial genomes

15.3 Prokayotic Transcription

Distinguish between the terms core polymerase and holoenzyme. What componets are parts of each complex? 

The core polymerase can synthesize the RNA using a DNA template but it cannot initiate synthesis accurately. The holoenzyme can accuarately initiate synthesis. 

 Define the following terms: promoter, start site, terminator, and transcription

promoter forms a recognition and binding site for the RNA polymerase and the start site. Termination signals the end of transcription. We refer to the region from promoter to termination as the transcription unit

Where does the DNA helix start to unwind for transcription?

The DNA signals to unwind at the -10 site

How does the polymerase break contacts wit hthe promoter region in order to move down the template?

The enzyme goes through confrontational changes during this clearence stage, and subsequently contacts less of the DNA than it does during the initial promotor binding.

What constitues the transcription bubble ? When is the DNA molecule unwound?

The region contain RNA polymerase, DNA template and growing RNA transcript is the transcription bubble. Contains "unwond bubble" of DNA. After the TB passes-- the DNA is rewound.

What is no longer formed when a stop signal is reached in the DNA? What dissociates? What releases from the DNA?

Causes he formation of phosphodiester bonds to cease, the RNA -DNA hybrid within the transcription bubble to dissociate the RNA polymerases to relase the 

DNA, and the DNA with in the transcription bubble to rewind. 

What does it mean that transcription and translation coupled in prokaryotes

translation occurs before transcripton is finished

What is an operon? Why is the arrangement of DNA useful for bacteria?

Grouping of functionally related genes. By clusting genes they can be related together

 15.4 Eukaryotic Transcription

TRUE OR FALSE: The basic mechanisim of transcription by RNA polymerase is the same as in prokayotes.

TRUE! However details differ enough that they are considered seperate.

RNA POL. I, II, III and their roles in transcription

Pol. I --- Transcribes RNA

Pol. II --- Transcribes mRNA and some other small RNA's

Pol. III --- Transcribe tRNA and some other small RNA's

What are transcription factors and what is their role in production of RNA? Which polymerase do they interact with?

Eukayrotes use a host of factos allowing promotor recognition. Initaes gene expression. Polymerase II.

How does termination of transcription differ in eukaryotes?

They are not as well defined as are prokaryotic terminators. The end of the mRNA is also not formed by RNA pol. II because the primary transcript is modified after transcription.

Differentiate EXONS and INTRONS: 

noncoding DNA that interupts the sequence of gene intervening sequences as introns. We call the coding sequences exons

Describe the parts nessecary for mRNA splicing:

Intron-Exon junction: 

Small nuclear ribonucleoprotein particals

Describe the parts nessecary for mRNA splicing:

snRNPs: 

Complexes composed of snRNA + Protein

Describe the parts nessecary for mRNA splicing:

Splicesome: 

snRNPs cluster together with other associated proteins to form a larger complex called splicesome

What is the role of an aminoactyl-tRNA synthetase?

Covalent attachment

What part of the ribosome is responsible for th edecoding funstion?

small sub unit on ribosome

What part of the ribosome is responsible for forming the peptide bond? What is the name of the enyme involved that is part of the ribosome? Where does it form? 

Resides in large unit. Enzyme is called peptidyl transferase.

Which of the following is a product of translation?

a.) tRNA

b.) rRNA

c.)mRNA

d.) All of the above

C.) mRNA

Why would a mutation that results in changing a lysine to argine not have as great an impact on protein structure as a change of lysine to glutamate?

lysine is + charged and glytamate is a - charged amino acid. Lysine and algine are both + carged amino acids

The prokaryotic promoter has 2 distinct elements (DNA sequences) that are not identical (-35 and -10). What would happen to the transcription of a gene if these 2 sequences were flipped?

-35 holoenzyme binds to DNA

-10 DNA helix start to unwind

If they were flipped before initiationthe process would not be carried out proberly

Based on your knowlege of codons and open reading frames which of the following changes in the coding sequence of a gene would most likely result in teh prodiuction of a functional protein?

a.) Insertion of 3 nucleotides near the beginning of the coding sequence

b.) Insertion of a single nucleotide near the beginning of teh coding sequence.

c.) Deletion of 2 nucleotides near the beginning of the coding sequence

d.) deletion of a nucleotide near the beginning of teh coding sequence

a.) Insertion of 3 nucleotides near the beginning of the coding sequence

List all of the processing of the RNA that is required in eukaryotes?

-5' capping

-3' poly tail

pre-mRNA splicing

Why do prokaryotic mRNAs not require RNA processing?

1.) They are coupled -- translation begins before transcription is finished

2.) organized in groups of functionality , related genes called operons

3.) mRNA may contain multiple genes

4.) No introns

Alternating splicing means That ____.

Multiple mRNA transcripts can be produced from the same gene

In a certain mutant strain of bacteria, the enzyme leucyl-tRNA synthesis mistakenly attaches isoleucine to leucyl-tRNA 10% of the time instead of attaching leucine. These bacteria synthesize:

Proteins in which isoleucine is inserted at some positions normally occupied by leucine

Compare how termination of transcription is different than termination of translation.

Termination transcription: RNA transcription is released and polymerase detaches from DNA. DNA rewinds into double helix and is unaltered throughout this process

Termination Translation: when the ribosome encounters one of the three stop codons it disassembles the ribosome and elease the polypeptide.

What is a lac operon? What genes does it consist of and what do these genes do?

Lac Operon is an operon required for the transport of lactose in escherichia coli.

it has three genes ... LACZ, LACY, and LACA

The genes encode b-galactosidase, lactose permease, and thiogalactoside transacetylose

What is the trp operon? What genes does it consist of and what do these genes do?

a series of genes that encode enzymes involved in the same biochemical pathway. in the case of trp operon, these enzymes are necessary for synthesizing tryptophan.

Genes E,D,C,B,A They create enzymes to carry ou synthesis of tryptophan

What woud happen to the regulation of the ara operon in cells that express a mutant form of AraC protein that cannot bind to arabinose?

Genes of the ara operon would never be expressed whether arabinose was present or not.