Chp 2 Gene Expression

Explains how genetic information, stored as DNA, is used to regulate the synthesis of proteins (polypeptides)

central dogma of molecular biology

Information stored in DNA is copied, or transcribed, into a more mobile form known as RNA

transcription

Multiple types of RNA are involved in gene expression, but only _____ contains the information needed to synthesize a protein via _____.

messenger RNA; translation

During this phase, a ribosome and two other forms of RNA are used to decode the information in mRNA, resulting in a protein product

translation

Transcription occurs first, in the ____, and translation occurs later _____ of the nucleus

nucleus; outside

The promoter and the DNA sequences before the transcription unit are considered ______, and the region to be transcribed is considered _______

upstream; downstream

Transcription is similar to DNA replication in that the enzyme that synthesizes mRNA molecules (_________) can assemble nucleotides in the 5' --> 3' direction only.

RNA polymerase III

Unlike DNA polymerase III, RNA polymerase II does not need a ___ to begin assembling nucleotides.

primer

Transcription occurs in three broad stages:

initiation, elongation, and termination

This stage begins with the recognition of the promoter sequence, which is generally located approximately 25-50 nucleotides upstream of the transcription start site

Initiation

This complex is formed when RNA polymerase II and other regulatory proteins known as general (basal) transcription factors bind to a specific nucleotide sequence called the promoter.

Transcription initiation complex

TATA box

A promoter DNA sequence crucial in forming the transcription initiation complex.

What unwinds the DNA helix so that transcription can begin at the transcription start site?

RNA polymerase II

One strand is known as the coding (sense) strand _____, and the other is the noncoding (antisense) strand _____.

5'--> 3'; 3'-->5'

During this phase, the noncoding DNA strand (3'-->5' DNA strand) is used as a template to build the mRNA molecule

elongation

RNA polymerase II synthesizes the mRNA transcript in the _______ direction by complementary base pairing with the noncoding DNA strand.

5' --> 3'

During this phase of transcription, the transcription complex reaches the terminator sequence in the DNA

termination

In eukaryotes, RNA polymerase II transcribes a sequence in the DNA known as the _________, which is then bound by proteins that separate the mRNA transcript from RNA polymerase II.

polyadenylation signal sequence (3'-TTATTT-5')

The 5' end of pre-mRNA is modified almost immediately after it is transcribed with the addition of a ______, which is a modified _______ nucleotide.

5' cap; guanosine triphosphate (GTP)

This 5' cap is recognized by the _____ during _____ and prevents _______.

ribosome; translation; degradation of mRNA in the cytoplasm

When transcription is complete, a chain of adenine nucleotides known as the _____ is added to the ___' end of mRNA, directly downstream of the transcribed polyadenylylation signal sequence.

poly-A tail; 3

Like the 5' cap, the poly-A tail also functions to prevent _________. In addition, the poly-A tail facilitates export of ___________.

mRNA degradation; mature mRNA from the nucleus to the cytoplasm

To produce mature mRNA transcripts, the intervening noncoding regions (___) must be ______, and coding regions (___) must then be ____.

introns; removed; exons; linked together

Process of removing noncoding regions, is carried out by a type of molecular machine called

RNA splicing; spliceosome

Splice donor sites are located at the _' end of ___, adjacent to teh _' end of the upstream ____.

5; introns; 3; exons

Splice acceptor sites are found at the _' end of ___, adjacent to the _' end of the ____ directly downstream.

3; introns; 5; exons

Allows for the synthesis of multiple distinct proteins (isoforms) from a single mRNA transcript based on differential inclusion or exclusion of exons during splicing.

Alternative mRNA splicing

A cell converts genetic information encoded within the nucleotide sequence into a protein.

translation

Start codon

AUG (methionine)

Stop codons

UAA, UAG, UGA

During translation, each codon in the mRNA transcript is read by the translation machinery in the _____ direction.

5' --> 3'

The key to matching the correct amino acid with its specific codon is found in another type of RNA, called

transfer RNA (tRNA)

A small molecule, that is a single-stranded RNA molecule that base pairs with itself to form a complex three-dimensional L-shaped structure, which is often depictd as a cloverleaf shape for simplicity

tRNA

A three-nucleotide sequence found in each tRNA that is complementary to a particular mRNA codon

Anticodon

The tRNA molecule is the necessary link to ______ or convert the information found in the nucleotide sequence of the mRNA to specify the correct order of amino acids during translation

decode

tRNA molecules are transcribed by a different RNA polymerase

RNA polymerase III

A family of enzymes helps pair amino acids with the correct tRNA molecules

aminoacyl-tRNA

There are how many possible combinations of three nucleotides?

64

The genetic code is considered ____, or redundant, meaning that multiple codons code for the same amino acid.

degenerate

How do ribosomes participate in translation?

By providing a location where mRNA and tRNA molecules can interact and by catalyzing the formation of peptide bonds between amino acids to create a protein chain

Eukaryotic ribosomes are composed of two parts:

a large (60S) subunit and a small (40S) subunit, which are assembled to form a complete (80S) ribosome

Prokaryotic 70s Ribosome

50S + 30S

Ribosomes are composed of

rRNA and proteins

Like mRNA and tRNA, rRNA must be transcribed from

DNA in the nucleus

In eukaryotes, rRNA genes are clustered in a specialized region of the nucleus called the

nucleolus

rRNA genes are mostly transcribed by

RNA polymerase I

The small ribosomal subunit contains an ____ binding site

mRNA

The large ribosomal subunit contains _______ binding sites and catalyzes peptide bond formation via its ________ activity

three tRNA; peptidyl transferase

The three tRNA binding sites include the

-peptidyl-tRNA binding site (P site)

-aminoacyl-tRNA binding site (A site)

-exit site (E site)

Like transcription, translation can be divided into three phases:

initiation, elongation, and termation

Some steps of translation require the hydrolysis of ______ for energy.

guanosine triphosphate

Eukaryotic translation initiation begins when

The small (40S) ribosomal subunit binds to a specific initiator tRNA carrying the amino acid methionine

Along with the initiation factors, the initiator tRNA binds to the

small ribosomal subunit

The small ribosomal subunit then binds to the mRNA _' cap.

5

The small subunit glides along the mRNA in the ____ direction unit it detects the first AUG codon.

5'--> 3'

When the initiator tRNA anticodon recognizes and base pairs with the mRNA start codon, the reading frame is established

true

The portion of the mRNA that is translated by ribosomes

open reading frame

During the elongation phase in translation

tRNA molecules deliver amino acids to the ribosome for incorporation into the growing protein chain in a cycle

The steps in the cycle for elongation (translation)

1.The mRNA codon following the start codon dictates the next tRNA that will bind. Base pairing between the mRNA codon and the anticodon of the next tRNA occurs within the ribosome's A site.

2. The peptidyl transferase center within the ribosome's large subunit catalyzes the formation of a peptide bond between the carboxyl end of the growing protein (attached to the tRNA in the P site) and the amino end of the amino acid attached to the tRNA in the A site. This step results in the attachment of the growing protein to the amino acid of the tRNA in the A site.

3. The empty tRNA in the P site is translocated to the E site, and the tRNA containing the growing protein is translocated from the A to P site. The mRNA moves along with the bound tRNAs, advancing the next codon into the A site.

4. The discharged tRNA exits from the E site and the ribosome is now ready to accept the next charged tRNA at the A site.

Elongation process continues until it reaches a

stop codon (UGA, UAA, UAG)

When a stop codon is encountered instead of a tRNA, a ____ binds to the codon in the _ site, leading to the ____ of translation.

release factor; A; termination

The release factor promotes ______ of the ____ linkage between the protein and the tRNA in the P site, separating the protein from the ribosome.

hydrolysis; ester

Ribosomes can be found in the _____ and attached to the ____ side of the ER.

cytosol; cytosolic

Protein folding often requires the assistance of other proteins called molecular

chaperones

Additional chemical modifications may be necessary for the protein to become functional, and such modifications may include

- addition of carbohydrates (glycosylation)

- lipids (lipidation)

- certain proteins (ubiquitination)

- phosphate groups (phosphorylation)

Protein glycosylation plays a role in

stability, cellular localization, and molecular trafficking

Protein phosphorylation plays a role in

activation and deactivation of proteins during cell signaling

Ubiquitin plays a role in

membrane trafficking proteins and the timing of protein degradation

Chemical, physical, or biological agents that can lead to mutations in DNA

mutagens

Physical agents (e.g, ionizing radiation, UV light)

- Nucleic acid strand breaks

- Pairing of noncomplementary bases

Chemical agents (e.g, base analogs, intercalating agents)

- Direct interaction with nucleic acids leading to chemical alteration of bases

- Insertion of agents between bases

- Strand breaks

Biological agents (e.g, viruses, transposons)

- Incorrect proofreading by DNA polymerase during genome replication

- Nucleic acid strand breaks caused by reactive oxygen species

- Insertion of transposons (mobile DNA elements) or viral DNA into the genome

Agents that lead to cancer-causing mutations

carcinogens

The result of the replacement of a single nucleotide and its complementary partner with a different pair of nucleotides

Point mutations

Substitutions that occur within the open reading frame of a gene and cause a different amino acid to be placed into the protein during translation

Missense mutations

Single base pair change that gives rise to a stop codon

Nonsense

Single base pair change that does not change the amino acid sequence

Silent

Addition of one or more base pairs into the DNA sequence

Insertion

Removal of one or more base pairs from the DNA sequence

Deletion

Addition or removal of one or more base pairs that results in a new reading frame

Frameshift

housekeeping genes

genes that are switched on all the time because they are needed for life functions vital to an organism

Heterochromatin is more densely arranged, and genes present within regions of heterochromatin are

rarely expressed

Euchromatin is more openly arranged and is associated with

higher levels of gene expression

The addition of acetyl groups to histone tails is catalyzed by the enzyme

histone acetylase

Histone acetylation influences gene transcription by promoting

the formation of more openly arranged euchromatin, making that region of DNA more readily accessible to transcription machinery

Histone deacetylases (HDACs) enzymes downregulate gene expression by

removing acetyl groups from histones, which promotes a denser heterochromatin conformation and restricts access of transcriptional machinery

Histone tails may also be modified by the addition of

methyl or phosphate groups, which may also affect chromatin conformation and transcriptional activity

Addition of a methyl group to cytosine nucleotide by a family of enzymes known as

DNA methyltransferases

Removal of such methyl groups by DNA demethylation enzymes can _____ expression levels.

restore

To achieve a higher level of expression under appropriate conditions, additional proteins are required

transcription factors

Enhancers are found mostly in _______ regions

noncoding

Transcription factors often have two types of structural domains

- a DNA-binding domain, which interacts with DNA binding sites in the enhancer

- an activation domain which interacts with other regulatory proteins or transcription machinery to facilitate transcription initiation

Flagging a protein for destruction involves the addition of a series of ubiquitin proteins that are covalently linked to form a

polyubiquitin chain

when a protein becomes polyubiquitinated, it can be recognized by a type of molecular machine known as

proteasomes

Once the protein is inside the proteasome, it is ____ into small ____, which are released into the ____, where the oligopeptides can be further degraded into amino acids and recycled for future use

hydrolyzed; oligopeptides; cytosol

Two major classes of small ncRNAs:

microRNAs (miRNAs) and small interfering RNAs (siRNAs)

miRNAs typically originate as ______ RNAs, which exhibit ______ and are processed to form __________.

single-stranded; self-complementarity; shorter double-stranded mature miRNAs

siRNAs are first observed as _______ RNAs which are further processed into a mature form.

double-stranded

The major functional difference between these two types of ncRNA is that siRNA molecules are _____ specific and regulate a _____ mRNA target, whereas miRNA molecules are _____ specific and regulate _____ mRNA targets.

highly; single; less; multiple

An ncRNA-protein complex interacts with an mRNA molecule to either

trigger mRNA degradation or block mRNA translation