Chapter 17 - Gene Expression: From Gene to Protein

The information found in DNA takes the form of ____

Specific nucleotide sequences

Inherited DNA creates specific traits by regulating ___

protein synthesis

Gene Expression

The process by which DNA directs the synthesis of proteins; Includes two stages: transcription and translation

What are the two stages of gene expression?

Transcription and Translation

**What organelle is essential in translation?**

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*Some background info: translation is the protein/polypeptide synthesis stage of gene expression*

Ribosomes

In 1902 _____ suggested that genes dictate phenotypes through enzymes; He said inherited diseases reflect an inability to synthesize a certain enzyme.

Archibald Garrod

In 1902 Archibald Garrod suggested that _____. He said inherited diseases reflect an inability to synthesize a certain enzyme.

genes dictate phenotypes through enzymes

Enzyme

Proteins that catalyze a specific chemical reaction

Beadle and Tatum are known for ____

Their experiments with bread mold and mutants; They developed the one gene-one enzyme hypothesis *(this hypothesis got reviewed and changed later)*

One Gene-One Enzyme Hypothesis

**The hypothesis that a gene dictates the production of a specific enzyme**

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*Extra: This hypothesis got reviewed and changed later to the one gene-one protein hypothesis*

Metabolic Pathway

Series of steps in which a cell synthesizes and degrades molecules

One Gene-One Protein Hypothesis

**The hypothesis that a gene dictates the production of a specific protein**

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*Extra: This hypothesis was first called the one gene-one enzyme hypothesis. The name changed because some proteins aren’t enzymes. This hypothesis is changed later :)*

One Gene-One Polypeptide Hypothesis

**The hypothesis that a gene dictates the production of a specific polypeptide**

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*Extra: This hypothesis was first called the one gene-one enzyme hypothesis, then it was called the one gene-one protein hypothesis because not all proteins are enzymes. Now it’s renamed as the one gene-one polypeptide hypothesis because each polypeptide has its own gene.*

Genome

All the genes for a certain species

Proteome

Collection of all the proteins used in a species

Transcription

The synthesis of any kind of RNA using a DNA template

Messenger RNA (mRNA)

A type of RNA that carries a genetic message from DNA to ribosomes

Translation

The synthesis of a polypeptide using the info in mRNA. Involves tRNA and a change of “language” from nucleotides to amino acids.

Translation takes place on ______

Ribosomes

Ribosomes

The site of protein synthesis

Ribosomes facilitate specific coupling of _____

tRNA anticodons with mRNA codons

Where does transcription take place in eukaryotes?

In the nucleus

Where does transcription take place in prokaryotes?

In the cytoplasm

Transcription & Translations in Prokaryotes vs Eukaryotes

In prokaryotes, transcriptions and translation are _______

**Not separated, immediate, and without more processing**

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*Extra: without more processing means there is no cap, no poly-A tail, and no intron removal*

Transcription & Translations in Prokaryotes vs Eukaryotes

In eukaryotes, transcription and translation are _______

**Separated and there is more processing/modifying**

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*Extra: more processing/modifying means introns are removed, a cap is added, and a poly-A tail is added*

RNA processing (the modifications of pre-mRNA before being sent to the cytoplasm) produces ______

mRNA

Primary Transcript

An initial RNA transcript from any gene; also called pre-mRNA when transcribed from a protein-coding gene

Central Dogma

The idea that the flow of information went only one way

The flow of information from gene to protein is based on a **_____**

**Triplet Code**

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*Extra: a triplet code is a series of non-overlapping, three-nucleotide code words that specify a sequence of amino acids for a polypeptide chain*

Triplet Code

A series of non-overlapping, three-nucleotide code words that specify a sequence of amino acids for a polypeptide chain

Genes determine the sequence of _____

Nucleotide bases

Codon

The basic unit of the genetic code; a three-nucleotide sequence of DNA or mRNA that codes for a specific amino acid

Coding Strand

The nontemplate DNA strand, which has the same sequence as the mRNA except it has thymine (T) instead of uracil (U)

There are how many known amino acids?

20

Template Strand

During transcription, the DNA strand that provides a pattern for ordering the sequence of nucleotides in an RNA transcript

There are two DNA strands per gene How many are transcribed?

**Only one**

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*This strand is also known as the template strand*

During translation, the mRNA codons are read in what direction?

5’ end to 3’ end

There are a total of ___ codons

64

The genetic code is ____

redundant but not ambiguous; no codon specifies more than one amino acid

Codons must be read in the correct ____ in order for the specified polypeptide to be produced

Reading frame/groupings

Frameshifts can be problematic. If they occur in an intron, then ____

it does not make a difference because introns are not expressed

The genetic code is _____

universal

**Component of Transcription:** RNA polymerase

An enzyme that catalyzes the synthesis of RNA; it pries the DNA strands apart and hooks together the RNA nucleotides

RNA synthesis follows the same base-pairing rules as DNA, except uracil substitutes for ____

thymine

**Component of Transcription:** Promoter

The DNA sequence where RNA polymerase attaches and transcription (RNA synthesis) is initiated

RNA polymerase II

**One of three** __**eukaryotic**__ **RNA polymerase that is used for pre-mRNA synthesis**

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*Extra: prokaryotes have only ONE type of RNA polymerase*

**Components of Transcription:** Terminator

__In prokaryotes__, a sequence that signals the end of transcription

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*Extra:* *Eukaryotes do not have this structure.*

**Components of Transcription:** Transcription Unit

A region of DNA that is transcribed into an RNA molecule; Requires modifications __only__ in eukaryotes

Transcription and translation each have 3 stages and all 3 are named the same respectively. What are the 3 stages?

Initiation, elongation, and termination

Start Point

In transcription, the nucleotide position on the promotor where RNA polymerase begins transcription

The direction and location of transcription is determined by the _____

location and orientation of RNA polymerase binding on the promotor

Transcription Factors

__In eukaryotes__, a group of regulatory proteins that mediate the binding of RNA polymerase and the initiation of transcription

Transcription Initiation Complex

The complete assembly of transcription factors and RNA polymerase II bound to a promoter

TATA Box

__In eukaryotes__, a promoter DNA sequence that is crucial in the formation of the transcription initiation complex

What happens during initiation stage of transcription?

RNA polymerase & transcription factors bind to the promoter, causing the DNA to unwind so the enzyme can “read” the bases in the template strand

What happens during elongation stage of transcription?

RNA polymerase moves along the DNA; It untwists the double helix, exposing 10 to 20 bases at a time, and adds a matching RNA nucleotide for each nucleotide in the template.

Transcription progresses at a rate of ____

40 nucleotides per/sec

The mechanisms of termination (of transcription) are different in prokaryotes and eukaryotes. In prokaryotes, the polymerase stops transcription at the end of the terminator. In eukaryotes ____

RNA polymerase II continues transcription after the pre-mRNA is cleaved from the growing RNA chain; the polymerase eventually falls off the DNA

RNA Processing

Modification of the pre-mRNA by enzymes before being sent to the cytoplasm; Includes RNA splicing (removal of introns & joining of exons), and modification of the 5’ and 3’ ends

During RNA Processing, each end of the primary transcript (pre-mRNA) is modified. The 5’ end receives a _____

**5’cap**

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*Extra: The 5’cap is a modified form of guanine nucleotide*

During RNA Processing, each end of the primary transcript (pre-mRNA) is modified. The 3’ end receives a _____

**poly-A tail**

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*Extra: The poly-A tail is a sequence of 50-250 adenine nucleotides*

5’ cap

A modified form of guanine nucleotide

poly-A tail

A sequence of 50-250 adenine nucleotides

The modifications of pre-mRNA during RNA processing share the following three functions:

• Facilitate mRNA export

• Protect mRNA from degradation

• Help ribosomes attach to mRNA

RNA Splicing

The stage of RNA processing that involves the removal of introns and the joining of exons, making a continuous sequence

Introns

the noncoding nucleotide segments of eukaryotic genes and their RNA transcripts that lie between coding regions

Exons

the nucleotide segments of eukaryotic genes and their RNA transcripts that are eventually expressed, usually translated into amino acid sequences

In some cases, RNA splicing is carried out by **_____**

**Spliceosomes**

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*Extra: Spliceosomes are a large complex made of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites*

Spliceosomes

A large complex made of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites

Ribozymes

RNA molecules that function as enzymes and can splice RNA

Alternative RNA Splicing

A type of eukaryotic gene regulation in which some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during RNA splicing

The number of different proteins an organism can produce is much greater than its number of genes because of __________

alternative splicing

Proteins often have a modular architecture consisting of **_____,** which are discrete structural and functional regions

Domains

Domains

discrete structural and functional regions

In many cases, different _____ code for the different domains in a protein

Exons

A cell translates an mRNA message into proteins with the help of ____

Transfer RNA (tRNA)

Transfer RNA (tRNA)

An RNA molecule that is responsible for translating nucleotides to amino acids by transferring an amino acid to a growing polypeptide in a ribosome

Molecules of tRNA are not identical. Each tRNA molecule enables the translation of a ______

given mRNA codon into a certain amino acid

What structures make up a tRNA molecule?

A single RNA strand that is about 80 nucleotides long; Includes a specific amino acid on one end and an anticodon on the other end

Anticodon

Nucleotide triplet at one end of a tRNA molecule that base-pairs with a complementary codon on mRNA

What is the shape of a tRNA molecule?

3D and roughly L-shaped

With regard to the shape of a tRNA, it is 3D and roughly L-shaped; When flattened into one plane to reveal its base pairing, a tRNA molecule looks like a _____

Cloverleaf

Because of ____, tRNA can twist and fold into a 3D molecule

hydrogen bonds

Accurate translation of a genetic message requires the following two steps:

• A correct match between tRNA and amino acids (via aminoacyl-tRNA synthetase)

• A correct match between the tRNA anticodon and an mRNA codon

Aminoacyl-tRNA synthetases

An enzyme that joins each amino acid to the appropriate tRNA; There are 20 different synthetases, one for each amino acid.

Wobble

Flexibility in the base-pairing rules in which the nucleotide at the 5’ end of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position (3’ end) of a codon

What are the structural components of a Ribosome?

**Two subunits (small and large), each consisting of proteins and ribosomal RNA (rRNA), and made in the nucleolus**

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*Extra: Ribosomal RNA (rRNA) is RNA that joins with proteins to make ribosomes; the most abundant type of RNA*

Ribosomal RNA (rRNA)

RNA that joins with proteins to make ribosomes; the most abundant type of RNA

Ribosomes have one biding site for mRNA and ___ for tRNA

three

What are the three ribosome binding sites for tRNA?

P Site, A Site, E Site

P Site

Holds the tRNA that carries the growing **p**olypeptide chain; One of three tRNA binding sites on a ribosome.

A Site

Holds the tRNA that carries the next **a**mino **a**cid to be added to the chain; One of three tRNA binding sites on a ribosome.

E Site

The **e**xit site, where discharged tRNAs leave the ribosome; One of three tRNA binding sites on a ribosome

All three stages of translation (initiation, elongation & termination) require ____, which offer support

Protein factors

What happens during initiation stage of translation?

2 ribosomal subunits, mRNA, and a tRNA holding methionine are joined to each other by initiation factors

More Specific Explanation Below

• The following structures bind to each other: ribosomal subunit, mRNA, & tRNA holding methionine

• The subunit moves along the mRNA until it reaches the start codon (AUG).

• A large ribosomal subunit is finally attached.

All the complexes involved in the initiation stage of translation are brought together by _____

Initiation Factors

Translation Initiation Complex

The complete complex of all the structures involved in the initiation stage of translation (2 ribosomal subunits, mRNA, and a tRNA holding methionine)

What happens during the elongation stage of translation?

Amino acids are added one by one to the preceding amino acid, resulting in an elongated polypeptide chain

During the elongation stage of translation, amino acids are added one by one to the preceding amino acid, resulting in an elongated polypeptide chain.

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Each addition is done in three steps with the help of elongation factors. What are these three steps in order?

Codon recognition, peptide bonding, and translocation

What happens during the termination stage of translation?

A stop codon binds with a release factor at the A site of a ribosome resulting in the release of a polypeptide and the destruction of the translation assembly