BIO 189A: Chapter 7 DNA Structure and Function

What are nucleic acids?

The information-bearing molecules of all life on Earth

What are pyrimidine bases?

Cytosine and Thymine

What are Purine Bases?

Adenine and Guanine

How are chromosomes formed?

DNA is wrapped around histone proteins

What are chromosome pairs 1-22 called?

Autosomes

What is chromosome pair 23 called?

Sex chromosomes

What are homologous chromosomes?

Two chromosomes that are the same size and contain the same genes

What is a gene?

It contains instructions on how to build a protein

What chromosome pair is not homologous?

Pair 23, X & Y

What is DNA?

A polymer composed of nucleotides

What nucleotides make up DNA?

Adenine, Thymine, Guanine, Cytosine

What makes up the backbone of the DNA helix?

Sugars and phosphates

What makes up the rungs of the helix?

Nitrogenous bases bond with each other through hydrogen bonding

How is DNA replication semi-conservative?

1 strand of the DNA molecule is old, and the other strand is new

What is DNA polymerase?

It adds new nucleotides and proofreads each new nucleotide against the template

What is the error rate before proofreading?

1 error/100,000 base pairs

What is the error rate after proofreading?

1 error/1 billion base pairs

What are mutations?

Errors that change the original DNA sequence

Can mutations be beneficial, harmful, or neutral?

They can be all

What is point mutation?

A change in sequence without a change in length

What are large-scale mutations?

Chromosomal mutations

What is the central dogma of biology?

DNA is transcribed into RNA, which is translated into proteins

What nucleotides make up RNA?

Adenine, Uracil, Guanine, Cytosine

Which nucleic acid is single-stranded?

RNA

Where does transcription take place?

Nucleus

What performs transcription?

RNA polymerase

What is the first stage of transcription called?

Initiation

Where does RNA polymerase bind to begin initiation?

The "promoter" sequence

What is the stage of transcription where RNA Polymerase continues to build the growing RNA product after initiation?

Elongation

What is the final stage of transcription called?

Termination, which ends the transcription process

What happens to RNA Polymerase during the termination phase?

It is released from the terminator sequence in the DNA template

What must happen to pre-RNA before it can be released from the nucleus?

It must be processed into mature mRNA

What are the modifications required to process pre-RNA into mature mRNA?

5' cap addition

Poly-A tail addition

Splicing

Where does mRNA processing occur, and where is the mature mRNA sent next?

It takes place in the nucleus, and the mature mRNA is then released into the cytoplasm.

What is splicing?

The process of removing introns and connecting exons from pre-RNA to form mature mRNA

Where does translation occur?

In the cytoplasm or is associated with the rough er

Which cellular structure performs the process of translation?

Ribosomes

What specifies the sequence of a polypeptide chain during translation?

The codons on the mRNA strand

How many different kinds of amino acids are there?

20

What does tRNA stand for?

Transfer RNA

Where do tRNA molecules and amino acids float freely before translation begins?

The cytoplasm

What is the step-by-step pathway of tRNA during translation?

1. tRNA and amino acids float freely in the cytoplasm.

2. tRNA links to an amino acid and transfers it to the ribosome.

3. tRNA binds to the appropriate mRNA codon at the ribosome.

4. A polypeptide chain is produced.

What is the average rate or speed of protein synthesis by a ribosome?

4 amino acids per second

How are amino acids joined to their correct tRNA molecules?

By an enzyme that recognizes the subtle differences in shape of each tRNA.

What type of bonding occurs between the tRNA anticodon and the mRNA codon during translation?

Complementary base pairing via hydrogen bonding.

Why must a genetic codon consist of at least 3 nucleotides?

3 nucleotides yield 64 combinations, which is enough to code for all 20 amino acids. 1 or 2 nucleotides (yielding 4 and 16 combinations) are not enough

What is a codon, and what is shown mapping to polypeptides in the process?

A codon is a nucleotide triplet in mRNA (e.g., matching DNA template strands) that codes for a specific amino acid sequence (like Lysine, Serine, and Valine) during translation.

Why does the genetic code exhibit redundancy, and what is its biological purpose?

Redundancy means multiple different codons can code for the same amino acid (64 codons for 20 amino acids). Its purpose is to protect against point mutations and transcription errors, preventing small DNA changes from altering the final protein sequence.

What are the key steps during the Initiation phase of translation?

1. The small ribosomal subunit binds to the 5' G-cap of the mRNA.

2. It scans down the mRNA until it reaches the start codon (AUG).

3. A special initiator tRNA (tRNA-met) binds to the start codon via its anticodon.

4. The large ribosomal subunit is recruited to complete the ribosome.

What are the key steps during the elongation phase of translation?

1. The "P"-site holds the tRNA attached to the growing peptide chain.

2. A new tRNA enters the "A"-site and stays if its anticodon forms hydrogen bonds with the mRNA codon.

3. The ribosome forms a peptide bond between the amino acids in the P and A sites.

4. The empty tRNA exits via the "E"-site, and the remaining tRNA shifts from the A-site into the P-site to continue the process.

What occurs during the Termination phase of translation when a stop codon is reached?

1. A stop codon enters the ribosome's "A"-site (no tRNAs bind to it).

2. A Release Factor protein is recruited and binds to the stop codon.

3. The ribosome releases both the mRNA molecule and the newly synthesized peptide chain.

What are polysomes?

Multiple ribosomes simultaneously translating a single mRNA

In what state is the lac operon typically found in prokaryotes, and what protein keeps it that way?

It is typically in the "off" position, kept blocked by the lac repressor protein bound to the operator region, which prevents RNA polymerase from accessing the DNA template.

How does lactose turn the lac operon "on"?

Lactose binds to the repressor protein, causing a conformational change so it can no longer bind to the DNA operator, allowing RNA polymerase to transcribe the gene.

What are the three main levels of eukaryotic gene regulation in the nucleus?

1. DNA availability/accessibility (chromatin structure).

2. Transcription Factors (activator and repressor proteins interacting with enhancer and silencer sequences).

3. mRNA processing (5' cap, poly-A tail, and splicing).

What are the levels of eukaryotic gene regulation that occur in the cytoplasm?

1. RNA degradation by microRNAs.

2. Protein processing and degradation.

What is post-translational modification (PTM), and what are its primary functional outcomes?

1. It is the modification of proteins after synthesis (e.g., via proteolytic processing, PIM-dependent proteolysis, or reversible multi-site PTMs).

2. Its primary functions include activation, degradation, interaction, localization, and dynamic regulation of protein activity and protein-DNA interactions.

How does the cell expand genome coding capacity from a relatively small number of genes (20,000-25,000) to a much larger proteome (>1,000,000 proteins)?

Through various steps, including alternative promoters, alternative splicing, mRNA editing, and post-translational modifications.

What is a virion?

Genetic material (DNA or RNA) contained within a protein coat.

What is the primary function of a virus?

Propagation

What are the six basic steps of viral infection and propagation?

1. Attachment & Entry into target cell

2. Genetic information decoded

3. Host translation of viral mRNA

4. Genome replication

5. Genome assembled/packaged into virions

6. Host cell releases virions

What is a Lytic pathway?

The virus forces the host to make viral parts and assemble new virions, then "blows up" (lyses) the cell to release them.

What is a Lysogenic pathway?

The viral DNA integrates into the host chromosome as a prophage, replicating passively along with the host cell's DNA.

What terminology is used to describe a bacterium that carries an integrated prophage in its chromosome?

A lysogen

What is the primary role of reverse transcriptase during the HIV infection cycle?

It transcribes single-stranded viral RNA into double-stranded DNA.

What happens after HIV viral DNA is formed inside the host cell?

The double-stranded viral DNA is incorporated into the host cell's genome.

What is a prion?

A proteinaceous infectious particle (an infectious agent composed purely of protein with no genetic material).

How do prions propagate or cause disease in cells?

An abnormal prion protein interacts with a normal protein, triggering the normal protein to refold into the abnormal shape, accumulating and causing cellular damage (such as holes in brain tissue).