Cell and Molec Lecture 7

What is the central dogma of molecular biology?

The central dogma describes the direction of information flow in biological systems: DNA → RNA → protein.

What are the two major information-transfer processes in the central dogma?

Transcription, which transfers information from DNA to RNA, and translation, which transfers information from RNA to protein.

Why is the DNA → RNA → protein pathway called the "central dogma"?

Because it describes the fundamental direction of genetic information flow shared by essentially all living organisms.

What organisms or biological systems are an important exception to the central dogma?

Retroviruses, such as HIV, can transfer information from RNA → DNA.

What enzyme allows retroviruses to reverse transcribe RNA into DNA?

Reverse transcriptase.

Where is reverse transcriptase found in retroviruses?

It is an enzyme carried within the viral capsid.

What is reverse transcription?

the process of using an RNA template to synthesize DNA.

Why is HIV considered an exception to the usual direction of information flow?

HIV has an RNA genome and uses reverse transcriptase to convert its RNA genome into DNA.

What is transcription?

the process of making an RNA copy of DNA.

What type of information is preserved during transcription?

Information is copied from one nucleic acid molecule into another, so the information remains in the language of nucleotides.

Why is transcription compared to copying a page from a textbook?

Because DNA information is copied into RNA while remaining in essentially the same nucleotide-based "language."

What molecule serves as the template during transcription?

DNA

What molecule is produced during transcription?

RNA

What enzyme synthesizes RNA during transcription?

RNA polymerase.

What is translation?

Translation is the process of using the instructions in messenger RNA (mRNA) to synthesize a polypeptide/protein.

What is the basic information flow during translation?

RNA → protein

Why is translation different from transcription in terms of "language"?

Transcription copies information between nucleic acids using nucleotides, while translation converts nucleotide information into a sequence of amino acids, which are chemically different building blocks.

What molecule provides the instructions for protein synthesis during translation?

Messenger RNA (mRNA).

What is the product of translation?

A polypeptide, which can fold and function as a protein.

At what two major levels can gene expression be regulated?

At the levels of transcription and translation.

What happens when a gene is transcribed and translated with high efficiency?

A large amount of protein is produced from that gene.

What happens when a gene has low transcription and low translation efficiency?

The gene produces a low level of protein.

Can transcription and translation efficiencies be different for the same gene?

Yes. A gene can be transcribed efficiently but translated inefficiently, or vice versa.

Can gene-expression efficiency change over time?

Yes. Gene expression can change depending on time and circumstances.

Can the expression of the same gene differ between different cells?

Yes. Different cells can express the same gene at different levels depending on their needs.

Why is it beneficial for cells to regulate gene expression?

It allows cells to produce proteins according to their needs rather than producing every protein at the same level all the time.

Why is gene expression described as dynamic?

Because the level of gene expression can change over time, in response to circumstances, and between different cell types.

How is RNA chemically similar to DNA?

RNA has a sugar-phosphate backbone connected by phosphodiester bonds between nucleotides.

What is the major sugar difference between RNA and DNA?

RNA's ribose contains an extra hydroxyl (-OH) group on the 2′ carbon, while DNA's deoxyribose has a hydrogen instead.

Why is the 2′ hydroxyl group on RNA important?

It makes RNA chemically distinct from DNA and contributes to properties that allow processes such as RNA splicing

Why is it useful for cells that DNA and RNA are chemically different?

The chemical differences allow enzymes and proteins that interact with nucleic acids to distinguish DNA from RNA.

Which nitrogenous base does RNA use instead of thymine?

Uracil

How are uracil and thymine chemically similar

They are very similar pyrimidine bases; thymine differs from uracil by the presence of a methyl group.

Is RNA always completely single-stranded?

No. Although RNA is synthesized as a single-stranded molecule, it can fold back on itself and form regions of base pairing.

What is RNA secondary structure?

It consists of regions within an RNA molecule where complementary bases pair with one another, causing the RNA to fold.

How can a single-stranded RNA molecule form double-stranded regions?

The RNA can fold so that complementary sequences within the same molecule come together and base-pair.

What allows RNA to fold into secondary structures?

Complementary base sequences within the RNA can hydrogen bond with one another.

Why is RNA folding important?

It can allow RNA molecules to form stable three-dimensional structures that are important for their functions.

What is the relationship between RNA structure and RNA function?

The three-dimensional shape of an RNA molecule can be essential for its biological function

What types of RNA molecules can depend on three-dimensional folding for their function?

tRNAs, ribozymes, and riboswitches.

What is a ribozyme?

A catalytic RNA molecule that can perform biochemical reactions

What is a riboswitch?

An RNA structure that can change its conformation in response to a small molecule and thereby regulate gene expression.

Do cells generally contain more RNA or DNA?

more RNA

How can scientists visualize RNA in the laboratory?

RNA can be visualized using agarose gel electrophoresis.

What does agarose gel electrophoresis allow scientists to determine about RNA?

It allows scientists to visualize RNA molecules and assess their sizes and overall integrity

What makes up a large proportion of the RNA in a cell?

Ribosomal RNA (rRNA) and other ribosomal components make up a large proportion.

What are ribosomes?

the cellular machinery responsible for translation and protein synthesis.

What are the prominent RNA bands seen on an agarose gel from intact eukaryotic RNA?

The 28S and 18S rRNA bands

Why are the 28S and 18S bands so intense on an RNA gel?

Because ribosomal RNA makes up a large proportion of total cellular RN

What does the RNA smear below the ribosomal bands represent?

many other RNA molecules of different sizes.

Approximately what size range does much of the non-ribosomal RNA smear occupy?

0.5–6 kb

Why are cellular RNAs found in many different sizes?

Different RNA molecules are encoded by different genes and can differ in length, structure, and the number and size of exons.

Is RNA stable or labile?

RNA is extremely labile, meaning it can degrade relatively easily.

What are RNases (Ribonucleases)?

enzymes that degrade RNA

Why are RNases a major problem when working with RNA in the laboratory?

RNases are extremely common and can be found practically everywhere, making accidental RNA degradation easy.

What happens to RNA on an agarose gel when it has degraded?

The strong 28S and 18S bands disappear or become much weaker, while the RNA shifts toward smaller molecular sizes and appears more heavily smeared.

Why does degraded RNA appear toward the lower end of the gel?

RNases break RNA into smaller pieces, which migrate farther through the gel

What would intact RNA look like compared with degraded RNA on a gel?

Intact RNA shows prominent 28S and 18S rRNA bands and a relatively defined RNA distribution, whereas degraded RNA loses those strong bands and shows a smear toward smaller fragments.

What is the primary function of RNA polymerase?

RNA polymerase synthesizes RNA using a DNA template during transcription.

What process is performed by RNA polymerases?

Transcription

What process is performed by DNA polymerases?

DNA replication

What is one major difference between RNA polymerase and DNA polymerase?

What is one major difference between RNA polymerase and DNA polymerase?

Does RNA polymerase require a separate DNA helicase to continuously unwind DNA during transcription?

No. RNA polymerase can melt/unwind the DNA itself as it transcribes.

What is the central channel of RNA polymerase used for?

It provides a path through which double-stranded DNA is threaded toward the active site.

What happens to the DNA just ahead of the RNA polymerase active site?

The DNA double helix is melted/unwound, breaking the hydrogen bonds between the strands.

What does the active site of RNA polymerase do?

It is where incoming ribonucleotides are positioned and incorporated into the growing RNA transcript.

What enters RNA polymerase through the ribonucleoside triphosphate uptake channel?

Ribonucleoside triphosphates (NTPs), the substrates used to synthesize RNA.

What are the four ribonucleoside triphosphates used during RNA synthesis?

ATP, GTP, CTP, and UTP.

What ion helps coordinate incoming ribonucleotides at the RNA polymerase active site?

A magnesium ion (Mg²⁺).

What happens when an incoming ribonucleotide correctly base-pairs with the exposed DNA template?

It is added to the growing RNA transcript.

What provides energy for RNA synthesis?

The hydrolysis of the high-energy phosphate bonds of incoming ribonucleoside triphosphates.

How does the energy from ribonucleoside triphosphates help RNA polymerase?

Hydrolysis of their high-energy bonds provides energy that drives nucleotide incorporation and RNA synthesis.

What is a DNA-RNA hybrid helix?

A short region where the newly synthesized RNA remains base-paired with the DNA template during transcription

Approximately how long is the DNA-RNA hybrid inside RNA polymerase?

About 9 base pairs.

Is the DNA-RNA hybrid stable for a long time?

No. It is very short-lived and rapidly separates.

What happens to the RNA after the DNA-RNA hybrid separates?

The newly synthesized RNA is released, while the DNA double helix reforms.

Why is the short-lived DNA-RNA hybrid important?

Its transient nature allows RNA polymerases to rapidly move along the DNA and allows additional polymerases to begin transcribing the same gene.

Can multiple RNA polymerases transcribe the same gene simultaneously?

Yes. Multiple RNA polymerases can be transcribing the same gene at the same time.

Why can multiple RNA polymerases transcribe the same gene at once?

Because the DNA-RNA hybrid is short-lived, allowing RNA polymerases to follow one another along the gene.

Approximately how fast does RNA polymerase transcribe DNA?

About 50 base pairs per second.

In what direction is RNA synthesized?

5′ —> 3

Can adjacent genes on the same DNA molecule be transcribed simultaneously?

Yes. Different RNA polymerases can simultaneously transcribe different genes on the same DNA molecule.

Can multiple ribosomes translate the same mRNA simultaneously?

Yes

What is a polysome?

A group of multiple ribosomes simultaneously translating the same mRNA molecule.

How is a polysome analogous to multiple RNA polymerases transcribing one gene?

In both cases, multiple molecular machines work on the same nucleic acid molecule simultaneously.

What does fidelity mean in the context of DNA or RNA polymerases?

The accuracy with which the polymerase copies genetic information.

Does DNA polymerase have high or low fidelity?

High fidelity

Why does DNA polymerase have high fidelity?

DNA polymerase has proofreading activity that helps correct copying errors.

Does RNA polymerase have the same level of proofreading as DNA polymerase?

No. RNA polymerase has much more modest proofreading activity.

Approximately how often does RNA polymerase make an error?

Approximately 1 error per 1,000 nucleotides copied.

Why are RNA polymerase errors less consequential than DNA polymerase errors?

RNA errors do not permanently alter the gene, and individual RNA molecules are generally short-lived.

Why might RNA polymerases not have evolved extremely high fidelity?

Extremely high fidelity is not as necessary for RNA because RNA molecules are temporary and errors generally do not become permanent genetic mutations.

What does mRNA stand for?

Messenger RNA.

What does tRNA stand for?

Transfer RNA.

What does rRNA stand for?

Ribosomal RNA.

Which type of RNA generally represents the most common type because most genes code for proteins?

mRNA.

What are non-coding RNAs?

RNAs that do not encode proteins and instead function as RNA molecules themselves.

Which major RNA type is NOT considered a non-coding RNA?

mRNA, because it carries information used to produce proteins.

Approximately how many genes in the human genome encode non-coding RNAs?

10,000 genes

What does snRNA stand for?

Small nuclear RNA.