Chapter 17: Gene Expression From Gene to Protein

Three properties of RNA allow some RNA to function as enzymes:

(1) RNA is single stranded so it can base pair with itself in the same molecule, giving it a particular 3D structure (2) some bases in RNA contain functional groups that can participate in catalysis (3) ability of RNA to hydrogen bond with other nucleic acid molecules (RNA or DNA) adds specificity to its catalytic activity

Two reasons why the "one gene one polypeptide hypothesis" is incorrect?

(1) a eukaryotic gene can code for a set of closely related polypeptides via alternative splicing (2) quite a few genes code for RNA molecules with important functions for cells even though they are never translated into proteins

The 5' and poly-A tail share three important functions:

(1) facilitate the export of mature mRNA from nucleus (2) protect mRNA from degradation by hydrolytic enzymes (3) help ribosomes attach 5' end of mRNA once mRNA reaches cytoplasm

The accurate translation of a genetic message requires two instances of molecular recognition:

(1) tRNA that binds to mRNA codon specifying a particular amino acid must carry that amino acid to the ribosome (2) pairing of tRNA anticodon with proper mRNA codon

How many of the nucleotide triplets code for amino acids? What do the remainder code for?

- 61/64 - termination codons marking the end of translation

What are the two functions of the codon AUG?

- amino acid methionine - initiation codon

How did the one gene one enzyme hypothesis evolve over time?

- became the one gene one protein hypothesis, then the one gene one polypeptide hypothesis

How many types of RNA polymerase do bacteria have? Eukaryotes?

-1 -at least 3

Bacteria and eukaryotes differ in the way they terminate transcription. How is termination initiated in eukaryotes?

-RNA polymerase II transcribes polyadenylation signal sequence which specifies signal in pre-mRNA - proteins cut RNA transcript free from polymerase and release pre-mRNA - pre-mRNA undergoes processing

Although cleavage marks the end of mRNA, the RNA polymerase continues to transcribe in eukaryotes. How does it eventually dissociate from the DNA?

-enzymes degrade RNA starting at newly exposed 5' end - polymerase continues transcribing, pursued by enzymes, until they catch up to it and it dissociates from DNA

The key to translating a genetic message into a specific amino acid sequence is the fact that each tRNA molecule enables translation of a given mRNA codon into a certain amino acid. How is this made possible?

-tRNA has a specific amino acid on one end, and nucleotide triplet that an base pair with complementary codon on mRNA on other end

Bacteria and eukaryotes differ in the way they terminate transcription. How do bacteria terminate transcription?

-transcription proceeds through terminator sequence in DNA -transcribed terminator (RNA sequence) functions as termination signal, causing polymerase to detach from DNA and release transcript which requires no further modification before translation

Do transcription and translation occur in all organisms? For which kingdom is our data most limited?

-yes -archaea

How is RNA different from DNA?

1) has ribose not deoxyribose 2) contains Uracil (U) instead of Thymine 3) usually single stranded

How many aminoacyl-tRNA synthetases are there?

20, one for each amino acid

During translation, the sequence of codons along an mRNA molecule is translated into a sequence of amino acids making up a polypeptide chain in the _______________ direction.

5' -> 3'

Each end of a pre-mRNA molecule is modified in a particular way in RNA processing. The 5' end, which is synthesized first, receives a __________, a modified form of a ______________ nucleotide added onto the 5' end after transcription of the first 20-40 nucleotides.

5' cap, guanine (G)

The _______________________ of ribosomes holds the tRNA carrying the next amino acid to be added to the growing polypeptide chain.

A site (aminoacyl-tRNA binding site)

In bacteria or eukaryotes, the start codon (________) signals the start of translation and establishes the ___________________ for mRNA.

AUG, reading frame

tRNA molecules are transcribed from ___________________ and originate in the nucleus, then travels to the __________________ where it will participate in translation.

DNA templates, cytoplasm

The _____________________________ of ribosomes discharges tRNAs (it is where they can leave the ribosome).

E site (exit site)

______________________ is the process by which DNA directs the synthesis of proteins (or in some cases, just RNA).

Gene expression

State the central dogma of biology

Genetic information flows from DNA to RNA to proteins

Who deciphered the first codon in 1961?

Marshall Nirenberg

The _______________________ of ribosomes holds the tRNA carrying the growing polypeptide chain.

P site (peptidyl-tRNA binding site)

In addition to a binding site for mRNA, each ribosome has 3 binding sites for tRNA. What are each of these called?

P site, A site, E site

Why is the mRNA molecule complementary rather than identical to its DNA template?

RNA nucleotides are assembled on the template according to base pairing rules, and synthesized antiparallel to the template strand of DNA

Transcription: An enzyme called an _______________________ pries the two strands of DNA apart and joins together RNA nucleotides complementary to the DNA template strand, thus elongating the RNA polynucleotide.

RNA polymerase

The enzyme used for pre-mRNA synthesis in eukaryotes is known as ______________________.

RNA polymerase II

How are RNA polymerases different from DNA polymerases?

RNA polymerases do not require a primer to begin creating a chain

In a process known as __________________, enzymes in the eukaryotic nucleus modify pre-mRNA in specific ways at the ends and interior before the genetic message is dispatched to the cytoplasm.

RNA processing

____________________ is a stage of RNA processing in the eukaryotic nucleus where large portions of RNA molecules are removed and remaining portions are reconnected.

RNA splicing

Briefly describe the experiment Marshall Nirenberg undertook to decipher the UUU codon

Synthesized artificial mRNA by linking together many identical RNA nucleotides containing uracil as their base and as such, they only contained UUU over and over. He added this to a test tube with components for protein synthesis, and translated mRNA into many units of phenylalanine, so he determined UUU codes for phenylalanine

A crucial promoter DNA sequence called the ______________________ forms the initiation complex at a eukaryotic promoter.

TATA box

In some organisms, RNA splicing can occur without proteins or even additional RNA molecules. What catalyzes the excision?

The intron RNA functions as a ribozyme and catalyzes its own excision!

_____________ explains why the synonymous codons for a given amino acid most often differ in their third nucleotide base.

Wobble

Each end of a pre-mRNA molecule is modified in a particular way in RNA processing. at the 3' end, an enzyme adds 50-250 more ________________ nucleotides, forming a _______________.

adenine (A), poly-A tail

Many genes are known to give rise to two or more different polypeptides depending on which segments are treated as exons during RNA splicing; this is known as ______________________________.

alternative RNA splicing

Because of ___________________, the number of different protein products an organism produces can be much greater than its number of genes.

alternative splicing

The protruding 3' endpoint on tRNA serves as the attachment site for an _______________________.

amino acid

The correct matching of tRNA and amino acid is carried out by a family of related enzymes named _______________________. The active site of each one only fits a specific combination of amino acid and tRNA.

aminoacyl-tRNA synthetases

The loop extending from the end of the tRNA molecule opposite the 3' and 5' ends includes the ______________________, which base pairs to a specific mRNA codon.

anticodon

The small RNAs in the spliceosome not only participate in spliceosome assembly and splice site recognition, by also _____________ the splicing reaction

catalyze

The nontemplate DNA strand is often referred to as the ___________________________, which is, by convention, used when a gene's sequence is reported.

coding strand

The mRNA nucleotide triplets are called _______________, and they are customarily written in the 5' -> 3' direction.

codons

The term for DNA nucleotide triplets along the nontemplate strand is ________________.

codons

A ____________________ contains all nutrients needed for growth

complete medium

Proteins often have a modular architecture consisting of discrete functional and structural regions called __________________. In a few cases, different exons can code for different versions of these.

domains

As the translated polypeptide grows larger, it passes through an ____________________ in the ribosome's large subunit. When the polypeptide is complete, it is released through this _____________________.

exit tunnel (both)

The presence of introns in a gene may facilitate the evolution of new and potentially beneficial proteins as a result of a process known as ________________________.

exon shuffling

In the process of _____________________, ___________ increase the probability of crossing over between exons of alleles of a gene by providing more terrain for crossovers without interrupting coding sequences. This may result in new combos of exons and proteins with altered structure and functions.

exon shuffling, introns

The coding segments of nucleic acids are known as ___________ because they are eventually expressed by being translated into amino acid sequences.

exons

What are the monomers in DNA or RNA?

four types of nucleotides, amino acid monomers

Some steps of initiation and elongation in DNA translation require energy. What molecule provides this energy?

guanosine triphosphate (GTP)

The aminoacyl-tRNA synthetase catalyzes the covalent attachment of the amino acid to its tRNA in a process driven by the ____________________. The resulting aminoacyl tRNA, also called a _______________________, is released from the enzyme and is then available to deliver its amino acid to a growing polypeptide chain on a ribosome.

hydrolysis of ATP, charged tRNA

What is the largest difference between the flow of genetic material in bacteria v eukaryotes?

in bacteria, there is no nucleus, so nuclear membranes do not separate bacterial DNA and mRNA from ribosomes and other protein synthesizing structures, which allows translation of mRNA to begin while transcription is till in process

Translation, the synthesis of a polypeptide, can be divided into 3 stages:

initiation, elongation, termination

What are the three stages of transcription?

initiation, elongation, termination

The noncoding segments of nucleic acid that lie between coding regions are called ___________________________.

intervening sequences (introns)

In making a primary transcript from a gene, RNA polymerase II transcribes both ____________ and _________ from the DNA, but mRNA molecule that enters cytoplasm is abridged. In RNA splicing, the _____________ are cut out from the molecule and the __________ joined together, forming an mRNA molecule with a continuous coding sequence.

introns, exons, introns, exons

In bacteria and eukaryotes, a large and small ribosomal subunit join to form a functional ribosome when attached to an __________ molecule.

mRNA

One type of RNA molecule produced via transcription is known as _______________________ because it carriers genetic information from the DNA to the protein synthesizing machinery of the cell.

messenger RNA

Cells synthesize and degrade most organic molecules via _________________________________, in which each chemical reaction in a sequence is catalyzed by a specific enzyme.

metabolic pathways

A _____________________ is a simple solution containing minimal nutrients for growth - inorganic salts, glucose, and vitamin biotin - incorporated into agar, a support medium.

minimal medium

How can a single gene be transcribed simultaneously by several molecules of RNA polymerase?

multiple RNA polymerases follow one another and transcribe sequentially, helps cell made encoded proteins in large amounts

The sequence of DNA molecules that codes for a eukaryotic polypeptide is usually ________________________.

not continuous/ split into segments

British physician Archibald Garrod hypothesized that a gene dictates the production of a specific enzyme, later named the _________________________________ hypothesis

one gene one

What is the strand that is used as the template for transcription determined by?

orientation of the enzyme that transcribes the genes, which depends on the DNA sequence associated with that gene

Certain sections of a promoter are especially important for binding RNA polymerase in a way that ensures that transcription will begin at the right place. How does this occur in bacteria?

part of the RNA polymerase itself specifically recognizes and binds to the promoter

Termination is initiated in eukaryotes by RNA polymerase II transcribing a sequence on DNA called the ______________________ sequence, which specifies a _________________________ signal (AAUAAA) in the pre-mRNA.

polyadenylation signal (both)

The transcription of a protein coding eukaryotic gene results in _______________, and further processing yields the finished mRNA. The initial RNA transcript from any gene, including those specifying RNA that is not translated into proteins is more generally called a _____________________________.

pre-mRNA, primary transcript

What determines where transcription starts and which of the two strands of the DNA helix is used as the template?

precise location and orientation of the binding of RNA polymerase on the promoter

The DNA sequence where RNA polymerase attaches and initiates transcription is known as the _________________

promoter

About 1/3 of the mass of a ribosome is made up of ____________________ and the rest consists of _____________________.

proteins, RNA molecules (3 in bacteria, 4 in eukaryotes)

The widely accepted model is that _____________ are primarily responsible for both the structure and function of ribosomes.

rRNAs (rather than ribosomal proteins)

Our ability to extract the intended message from DNA depends on reading the symbols in the correct groupings, or __________________________.

reading frame

There is ____ in the genetic code but no ______.

redundancy, ambiguity

A ribosome consists of a large subunit and a small subunit, each made up of proteins and one or more _________________________.

ribosomal RNAs (rRNAs)

The sites of translation are ___________________, molecular complexes that facilitate the orderly linking of amino acids into polypeptide chains

ribosomes

Which structure adds each amino acid brought to it by tRNA to the growing end of a polypeptide chain?

ribosomes

The idea for the catalytic role for RNAs in the spliceosome arose from the discovery of ___________________, RNA molecules that function as enzymes.

ribozymes

The removal of introns in RNA splicing is accomplished by a large complex made of proteins and small RNAs called a ______________________.

spliceosome

The promoter of a gene includes within it the transcription _____________________ - the nucleotide where RNA polymerase actually begins synthesis of the mRNA.

start point

During transcription, the __________________________ of the gene determines the sequence of nucleotide bases along the length of the RNA molecule that is being synthesized. For any given gene, (the same/ a different) strand is used as the template every time the gene is transcribed

template strand, the same

In bacteria, the sequence that signals the end of transcription is called the __________________.

terminator

The redundancy in the genetic code is not random. In many cases, codons that are synonyms for a particular amino acid differ only in the ___________ nucleotide base of the triplet.

third

_____________________ is the general term for synthesis of ANY kind of RNA on a DNA template

transcription

_____________________ is the synthesis of RNA using information in the DNA. A DNA strand serves as a template for assembling a complementary strand of RNA nucleotides, producing a transcript of the gene's protein making instructions

transcription

In eukaryotes, a collection of proteins called _________________________ mediate the binding of RNA polymerase and the initiation of transcription. Only after these are attached does RNA polymerase bind to the promoter.

transcription factors

the whole complex of transcription factors and RNA polymerase II bound to the promoter is called a ________________________________.

transcription initiation complex.

The stretch of DNA downstream from the promoter that is transcribed into an RNA molecule is called a _____________________________.

transcription unit

Expression of genes that code for proteins include two stages:

transcription, translation

The translator in the process of translation is ____________________, which functions by transferring an amino acid from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome.

transfer RNA (tRNA)

_________________________ is the synthesis of a polypeptide using information in mRNA. The cell must convert the nucleotide sequence of an mRNA molecule into amino acid sequence of a polypeptide.

translation

In lab experiments, genes can be transcribed and translated after being ___________________ from one species to another, sometimes with quite striking results.

transplanted

The flow of information from gene to protein is based on a _________________________: the genetic instructions for a polypeptide chain are written in DNA as a series of nonoverlapping, 3 nucleotide segments.

triplet code

_____________ of nucleotide bases are the smallest units of uniform length that can code for all of the amino acids.

triplets

__________________ are portions of mRNA at the 5' and 3' ends that will not be translated into proteins but possess other functions like ribosome binding

untranslated regions (UTRs)

The promoter sequence of DNA is said to be ________________ from the terminator.

upstream

The nucleotide base U at the 5' end of a tRNA anticodon can pair with either A or G in the third position (at the 3' end) of an mRNA codon. This flexible base pairing at this codon position is called _______________.

wobble