Chapter 10 Bio

termination of transcription

RNA polymerase reaches a terminator sequence (Stop codon) and RNA transcript disassociates from the DNA.

Polypeptide

Refers to a linear sequence of amino acids; it denotes structure.

In transcription a DNA sequence is copied into...

A RNA sequence

ribozyme

a type of RNA that can act as an enzyme and catalyze a chemical reaction.

Step 1: Initiation

mRNA, the first tRNA, and the ribosomal subunits assemble into a complex.

tRNA (transfer RNA) is needed to make...

polypeptides during translation.

Ribosomal-binding site

this site is located near the 5' end of the mRNA and provides a location for the ribosome to bind to the mRNA

initiation of translation of bacteria

1. An mRNA binds to the small ribosomal subunit. The binding of bacterial mRNA to this subunit is facilitated by a short ribosomal-binding site near the 5' end. The start codon is found just a few nucleotides downstream from the ribosomal binding site. 2. A specific tRNA, which functions as a initiator tRNA recognizes the start codon in mRNA (AUG) and binds to it. In bacteria, it carries a formyl methionine. 3. To compete initiation stage, the large ribosomal subunit associates with the small subunit.

translation elongation

1. Binding of charged tRNA: a charged tRNA carries a single amino acid and binds to the A site. This occurs because the anticodon in the tRNA is complementary to the codon in mRNA. The hydrolysis of GTP by proteins that function as elongation factors provides energy for the binding of tRNA to the A site. 2. Peptide bond formation and peptide transfer: a peptide bond is formed between amino acid in the A site and the growing polypeptide. As this occurs, the polypeptide is removed from the tRNA in the P site and transferred to the amino acid at the A site. (This is called peptidyl transfer reaction) 3. Translocation and exit of uncharged tRNA: ribosome moves, or translocates, toward the 3' end of the mRNA by exactly one codon. The uncharged tRNA exits the E site.

Differences between initiation phase between eukaryotic species and bacteria

1. Eukaryotic mRNAs have a guanosine cap (5' cap) at their 5' end. Cap-binding proteins recognize this and promote binding of mRNA to the small ribosomal subunit site. ( Eukaryotes do not have a RNA sequence that functions as a ribosomal binding site.) 2. The first AUG codon is not always the start codon. 3. In Eukaryotes, the initiator tRNA carries a methionine not formyl-methionine.

Splicing steps

1. First two snRNP subunits bind to the 5' splice site and branch site. 2. Additional snRNP subunits bind to the 3' splice site and other locations to create a spliceosome. The intron forms a loop. 3. The 5' splice site is cut. The 5' end of intron is covalently attached to the branch site. Two snRNP subunits are removed. 4. The 3' splice site is cut. Exon 1 is covalently attached to exon 2. The intron is released along with the rest of the snRNP subunit and degraded.

How spliceosomes process RNA

1. Spliceosome subunits bind to specific sequences at three locations in the intron RNA: one is termed the branch site and two sequences at the intron-exon boundaries are called the 5' splice site and the 3' splice site. 2. The binding causes the intron to loop outward which brings two exons closer. 3. The 5' splice site is then cut, and the 5' end of the intron becomes covalently attached to the branch site. 4. The 3' splice site is cut, and the two exons are covalently attached to each other. The intron, in the form of a loop, is released and eventually degraded.

tRNAs of all species share common features:

1. Two-dimensional structure of tRNA exhibits a cloverleaf pattern. The structure has three stem-loops and a fourth stem herb a 3' single-stranded region. 2. The anticodon is located in the middle loop. 3. The 3' single-stranded region is the amino acid attachment site. 4. Three-dimensional structure of tRNA molecule involves additional folding of the secondary structure.

alternative splicing

Allows a single gene to encode two or more polypeptides with differences in their amino acid sequences.

mRNA is used to make a polypeptide with a specific...

Amino acid sequence

Gene

An organized unit of nucleotide sequences that enables a segment of DNA to be transcribed into RNA and ultimately results in the formation of a functional product.

Ribosome (In General)

Are in the cytosol, mitochondria, and chloroplast. Unless otherwise noted, eukaryotic ribosomes refers to the ribosomes in the cytosol.

Pre-mRNA and how it's modified

Before they become mature mRNA, eukaryotic pre-mRNA are modified by the addition of caps and tails to their ends. In addition, many have coding sequences that are separated by sequences that are later removed. Many pre-mRNAs undergo RNA splicing to become functional mRNA.

Mature mRNA (in eukaryotes) have a modified form of... *(Capping)

Guanine covalently attached at the 5' end. (* Also known as capping)

During RNA modification, the RNA transcript is modified...

In a way that makes it a functionally active mRNA.

Initiation stage of transcription

In bacteria, a protein called sigma factor binds to RNA polymerase. Sigma factors also recognize the base sequence of a promoter and binds there. Role of sigma factor is to enable RNA polymerase to bind to the promoter. The initiation stage is completed when the DNA strands are separated near the promoter to form an open complex.

Transcription occurs in three stages:

Initiation, elongation, and termination.

introns and exons

Introns: intervening sequences that are not translated. (Not expresses) Exons: sequences contained in the mature mRNA. (Considered expressed)

rRNA (ribosomal RNA) forms

Part of the ribosome which provides the site where translation occurs.

Mature mRNAs also have a _________ _______ tail at the 3' end.

Poly A. (String of adenine nucleotides 100-200 in length.

Central Dogma

DNA -> RNA -> Protein (polypeptide)

Peotein

Denotes function

Polypeptide synthesis occurs in which stage

Elongation stage

Transcription and translation occurs where in eukaryotes vs. bacteria?

Eukaryotes: transcription occurs in the nucleus. mRNA exits the nucleus through a nuclear pore, and translation occurs in the cytosol. Bacteria: in the same place, in the cytoplasm.

Transcription:

Produces a RNA copy of a gene, also called an RNA transcript. Most genes, which are termed protein-encoding genes or structural genes are used to make an RNA molecule that contains the information to specify a polypeptide with a particular amino acid sequence. This type of RNA is called messenger RNA.

3 forms of RNA polymerase and their roles

RNA polymerase 2 is responsible for transcribing the mRNA from eukaryotic protein-encoding genes, whereas RNA Polymerase 1 and 3 transcribe non-coding genes such as the genes that encode tRNA and rRNA.

elongation (transcription)

RNA polymerase synthesizes the RNA transcript. Sigma factor is releases and RNA polymerase slides along the DNA in a way that maintains the open complex. The opposite DNA strand is called the coding strand.

To translate a nucleotide sequence of mRNA into an amino acid sequence...

Recognition occurs between mRNA and transfer RNA (tRNA) molecules. tRNA function as a translator between an mRNA codon and an amino acid. The anticodon is complementary to a codon in mRNA. The anticodon in tRNA binds to a codon in mRNA.

RNA splicing

Removing introns and the remaining exons are connected to each other.

Step 2: Elongation

Ribosome moves in the 5' to 3' direction from the start codon in the mRNA toward the stop codon, synthesizing a polypeptide according to the sequence of codons in the mRNA.

Regulatory sequences

Sequences that function as sites for the binding of regulatory proteins that affect the rate of transcription.

Release factor

a protein that recognizes a stop codon in the termination stage of translation and promotes the termination of translation. (Has a three dimensional structure and mimics the structure of tRNAs, which allows it to fit in the A site.

Promoter:

a site in DNA where transcription begins.

N-terminus

amino end of a polypeptide

C-terminus

carboxyl end

Genetic code is said to be...

degenerate or redundant. More than one code can specify the same amino acid.

aminoacyl-tRNA synthetases

enzymes that catalyze the attachment of amino acids to tRNA molecules

mRNA

messenger RNA; type of RNA that carries instructions from DNA in the nucleus to the ribosome

transcription factors

proteins that influence the ability of RNA polymerase to transcribe genes, to initiate transcription.

template strand of DNA

the DNA strand that is copied into mRNA and has the complementary sequence to the mRNA. (Serves as template for transcription.)

Elongation stage involves...

the covalent bonding of amino acids to each other, one at a time, to produce a polypeptide.

Translation:

the process of synthesizing a specific polypeptide on a ribosome.

Ribosome is the site where...

translation occurs.

Translation occurs in which three steps?

1. Initiation 2. Elongation 3. Termination

A ribosome is a large complex composed of structures called the...

Large and small subunits.

For many genes, the functional product is...

The RNA itself. These RNAs are called non-coding RNAs (ncRNA)

Peptide bonds

Connect amino acids together

rRNAs and ribosomal proteins are assembled within the nucleolus to make the...

40S and 60S subunits that are exported into the cytosol where they associate to form an 80S ribosome during translation.

RNA polymerase 2 always requires _____ transcription factors.

5

During the initiation stage...

A complex is formed between an mRNA molecule, the first tRNA, and the ribosomal subunits. The assembly of this complex requires the help of translation factors called initiation factors. This assembly requires an input of energy. GTP is hydrolyzed by certain initiation factors to provide the necessary energy.

Capping occurs while...

A pre-mRNA is being made by RNA polymerase. Usually when the transcript is only 20 to 25 nucleotides in length.

Initiation factors

A protein that facilitates the interactions between these components. (mRNA, tRNA, and ribosomal subunits.)

coding sequence

A region that begins with the start codon and specifies the entire amino acid sequence of a polypeptide

ribosomal binding site

A sequence of bases that is complementary to a portion of the 16S rRNA within the small ribosomal subunit.

Termination occurs when...

A stop codon is reached in the mRNA

Elongation continues until...

A stop codon moves into the A site of the ribosome. The three stop codons, UAA UAG UGA, are recognized by a protein known as a release factor.

To elongate a polypeptide...

A tRNA brings a new amino acid to the ribosome, where it is attached at the end of the growing polypeptide.

spliceosome

Composed of different subunits known as snRNPs (small nuclear RNA and a set of proteins) they remove introns from eukaryotic Pre-mRNA

pre-mRNA

The RNA transcript

tRNA is names according to...

The amino acid it carries. Ex. tRNA^ser carries a serine.

Translation is initiated by...

The assembly of mRNA, tRNA, and ribosomal subunits.

start codon (AUG) (*Reading frame*)

The first codon that is used in translation. Also defined the READING FRAME.

Step 3: Termination

The ribosome reaches a stop codon and the complex disassembles, releasing the completed polypeptide.

Terminator:

The site on a DNA strand at which transcription ends

Codons

Three nucleotide bases

Anticodon

Three-base sequence in a transfer RNA molecule base that pairs with a complementary codon in mRNA

examples of ncRNAs are

Transfer RNA, Ribosomal RNA, promoter, terminator, and regulatory sequences

RNA polymerase

Type of enzyme that synthesizes strands of RNA.

Stop codon

UAA, UAG, UGA; signals end of translation.