Unit 1 Study Questions –DNA Structure, Function, Replication, RNA, Protein Synthesis, Regulation and Mutations)

Vocabulary flashcards covering key terms from Unit 1 notes on DNA, RNA, replication, transcription, translation, and regulation.

DNA

Deoxyribonucleic acid; the molecule that stores genetic information in cells.

Genome

The complete set of genetic material present in an organism or cell.

Nucleotide

The repeating subunit of DNA, consisting of a sugar, a phosphate group, and a nitrogenous base.

Deoxyribose

The five-carbon sugar in DNA.

Phosphodiester bond

Covalent bonds that connect nucleotides along the DNA backbone.

Nitrogenous bases (A, T, C, G)

The bases that encode genetic information in DNA: adenine, thymine, cytosine, and guanine.

A–T base pair

Adenine pairs with thymine via two hydrogen bonds.

G–C base pair

Guanine pairs with cytosine via three hydrogen bonds.

Complementary base pairing

Specific pairing of A with T and G with C, enabling accurate DNA copying.

Antiparallel Strands

run in opposite directions (5’-3’ and 3’-5’)

Double helix

The right-handed spiral structure formed by two antiparallel DNA strands.

Hydrogen bonds

Weaker bonds between bases that stabilize the interior of DNA.

Covalent bonds (phosphodiester bonds)

Strong bonds linking nucleotides in the DNA backbone.

Chargaff's Rules

In DNA, A = T and G = C; base composition varies by species.

Franklin’s Contribution

X-ray diffraction evidence suggesting DNA is a helix with a uniform 2nm width.

Watson–Crick Model

Proposed the DNA double helix with antiparallel strands and base pairing.

Origin of replication

Site where DNA replication begins.

DNA replication

Process of copying DNA so each daughter cell receives an identical genome.

Leading strand

The DNA strand synthesized continuously toward the replication fork.

Lagging strand

The DNA strand synthesized discontinuously away from the fork as Okazaki fragments.

Okazaki fragment

Short DNA fragments on the lagging strand synthesized during replication.

Replication Fork

Y-shaped region where DNA unwinds and replication occurs.

Helicase

Enzyme that unwinds the DNA double helix at the fork.

DNA Polymerase

Enzyme that adds nucleotides to the growing DNA strand in the 5'→3' direction.

Ligase

Enzyme that seals nicks in the DNA backbone after fragment joining.

Topoisomerase

Enzyme that relieves supercoiling ahead of the replication fork.

Replication fork

The active site where DNA unwinds and new strands are synthesized.

Proofreading

DNA polymerase proofreading activity that removes mispaired nucleotides for fidelity.

RNA

Ribonucleic acid; single-stranded polymer involved in transcription and translation.

mRNA

Messenger RNA; carries genetic code from DNA to the ribosome for protein synthesis.

tRNA

Transfer RNA; delivers specific amino acids to the ribosome during translation.

rRNA

Ribosomal RNA; core component of ribosomes and helps catalyze protein synthesis.

Start Codon

AUG; signals the start of translation and codes for methionine.

Codon

Triplet of nucleotides in mRNA that encodes a specific amino acid.

Anticodon

Three-nucleotide sequence on tRNA that pairs with a codon in mRNA.

A site

Ribosome site that accepts the incoming aminoacyl-tRNA.

P site

Ribosome site where the growing polypeptide is held during translation.

Stop codons

UAA, UAG, and UGA; terminate translation.

Genetic code redundancy

Multiple codons can encode the same amino acid, reducing the impact of some mutations.

Translation

Process by which ribosomes read mRNA and synthesize a polypeptide using tRNAs.

How many different kinds of monomers are there in DNA?

Known as nucleotides, which include adenine (A), thymine (T), cytosine (C), and guanine (G).

How do the different kinds of monomers in DNA differ from one another?

They differ in the nitrogenous base attached to the sugar phosphate backbone.

How are the different kinds of monomers in DNA alike?

They all contain a sugar, phosphate group, and a nitrogenous base.

What are 3 functions of DNA in the cell?

Genetic information used to make more DNA, genetic information passed from parent to offspring (inherited), and is instructions used for making RNA, protein/molecules, carrying out everyday activities, and carrying out cellular processes.

What is the main purpose of DNA replication?

Creates two identical copies of DNA from one original DNA molecule, ensuring genetic information is accurately passed on during cell division.

What are 2 reasons why DNA would replicate?

To ensure genetic information is accurately passed on during cell division and to provide a copy for daughter cells during growth and repair.

What are the enzymes involved in DNA replication?

Topioisomerase, DNA helicase, DNA polymerase, and DNA ligase

Role of DNA Helicase

Unwinds the double helix structure of DNA, separating the two strands to allow for replication.

Role in DNA Polymerase

Synthesizes new DNA strands by adding nucleotides complementary to the template strand during replication.

Role in DNA Ligase

Connects Okazaki fragments on the lagging strand and seals it

What are the steps of DNA replication?

• Topoisomerase unwinds the DNA, making it accessible to other molecules

• DNA Helicase breaks the DNA hydrogen bonds, opening up DNA at ORI, exposing the nucleotides in each strand

• DNA Polymerase attaches to exposed nucleotides, placing the first 2 complementary base pairings, and forms covalent bonds

• DNA Polymerase moves along the DNA strands adding new nucleotides and proofreading

• DNA Polymerase follows DNA Helicase being the leading strand, and the other strand is the lagging strand due to wait

• DNA Ligase seals the lagging strand fragments, forming covalent bonds between nucleotides on same strand

• TWO IDENTICAL DNA MOLECULES ARE PRODUCED

What main factors allow DNA replication to occur so quickly?

The presence of multiple origins of replication, high processivity of DNA polymerases, and the action of accessory proteins like helicases and ligases streamline the process for rapid DNA synthesis.

What are some advantages to DNA replication?

Accuracy in genetic transmission, the ability to repair damaged DNA, and the generation of multiple copies for quicker cell division and response to environmental changes.

Why would a cell replicate/copy its DNA?

Ensure that each daughter cell receives an identical set of genetic information during cell division, which is essential for growth, development, and repair.

What is proofreading for DNA Replication?

A mechanism by which DNA polymerases check and correct errors in newly synthesized DNA strands, ensuring high fidelity during replication.

Why is DNA replication said to be semi-conservative?

Because each new DNA molecule consists of one original strand and one newly synthesized strand, preserving half of the original DNA.

Describe the role of complementary base pairing in DNA replication?

Ensures that adenine pairs with thymine and cytosine pairs with guanine, allowing accurate replication of the genetic code and stability of the DNA structure.

What is the importance of hydrogen bonds in DNA replication?

Plays a crucial role in maintaining the structure of the DNA double helix, providing stability during unwinding and allowing the complementary bases to pair accurately, which is essential for proper replication.

What is the importance of covalent bonds in DNA replication?

Plays a crucial role in linking the sugar-phosphate backbone of DNA, providing structural integrity and stability to the molecule. They ensure that nucleotides remain securely attached during replication.

What are similarities and differences between RNA and DNA?

Both RNA and DNA are nucleic acids that store genetic information, but DNA is double-stranded while RNA is typically single-stranded. RNA contains uracil instead of thymine and has ribose sugar instead of deoxyribose.

What are the different types of RNA?

• pre-mRNA

• mRNA

• tRNA

mRNA

Messenger RNA that carries genetic information from DNA to the ribosome for protein synthesis.

tRNA

is a type of RNA that transports amino acids to the ribosome during protein synthesis, matching them to the appropriate codons in mRNA.

pre-mRNA

A form of messenger RNA that is synthesized from the DNA template during transcription and undergoes processing (including splicing) before becoming mature mRNA.

Final Location of mRNA in the cell

is the cytoplasm, where it is translated by ribosomes into proteins.

Final Location of tRNA in the cell

typically at the ribosome, where it assists in translating the mRNA into a polypeptide chain.

Final Location of rRNA in the cell

Primarily located in the ribosomes, where it plays a crucial role in protein synthesis.

In all DNA, regardless of source, length, etc. A%=T% and G%=C%.  Why, in RNA, does A% ≠ U% and G% ≠ C%%?

Because of complementary base pairing

Where in the cell does transcription occur? 

Transcription occurs in the nucleus of eukaryotic cells, while in prokaryotes, it takes place in the cytoplasm.

What are the key stages of Transcription?

Initiation, Elongation, and Termination.

• During initiation, RNA polymerase binds to the promoter region of the DNA

• In Elongation, the RNA strand is synthesized

• In Termination, the RNA polymerase reaches a termination signal

Initiation Process In Transcription

The first stage of transcription where RNA polymerase binds to the promoter region of DNA to begin synthesis of the RNA strand.

• RNA polymerase identifies the promoter sequence for the gene

• RNA polymerase attaches to the DNA at the promoter sequence and opens up the DNA

• RNA polymerase adds first two RNA nucleotides down and temporarily hydrogen bonds are formed

• RNA polymerase forms a covalent bond between the 2 RNA nucleotides

Elongation Process In Transcription

The stage of transcription where the RNA strand is synthesized as RNA polymerase moves along the DNA template strand, adding complementary RNA nucleotides to the growing RNA molecule.

• RNA polymerase moves down the DNA template strand adding new RNA nucleotides in 5’-3’ direction

• As RNA polymerase moves down the DNA template strand, the DNA molecule reforms and it closes, growing the pre-mRNA single stranded molecule

Termination Process In Transcription

The stage of transcription where RNA polymerase reaches a termination signal in the DNA, resulting in the release of the newly synthesized RNA strand and detachment from the DNA template.

• RNA polymerase hits the terminator sequence

• RNA polymerase disassociates from the DNA

• RNA polymerase releases the “pre-mRNA” which will be modified to mRNA in translation

What happens if a particular step of transcription is prevented/stopped?

The transcription process would be halted, resulting in no RNA synthesis for that gene. This could lead to a lack of protein expression and potentially affect cellular functions and responses.

What portions of the DNA does a cell use for transcription to make an RNA molecule?

The cell uses the coding regions, or genes, of the DNA as templates for transcription, producing complementary RNA molecules.

Describe the importance of hydrogen bonds in transcription

Plays a crucial role because they facilitate the base pairing between DNA and RNA nucleotides. They allow the RNA strand to anneal to the DNA template when synthesizing RNA, ensuring accurate transcription of the genetic code.

Describe the importance of covalent bonds in transcription

Plays a crucial role in connecting the sugar and phosphate groups of the RNA nucleotides, forming a stable and continuous RNA strand during synthesis. This ensures the integrity and stability of the newly formed RNA molecule.

Describe role of complementary base pairing in transcription

Ensures that the correct RNA nucleotides are added to the growing RNA strand by matching their bases with the corresponding DNA template, maintaining the accuracy of the transcribed genetic information.

Different types of modifications that need to occur to the RNA

5’ capping, 3’ polyAtail, and splicing. These modifications enhance RNA stability, facilitate nuclear export, and ensure proper translation of the genetic code.

What are the functions of exons?

C5’oding sequences of RNA that are retained in the final mRNA molecule and translated into protein

What are the functions of introns?

Non-coding sequences that are removed during RNA splicing. This distinction is crucial for gene expression and producing functional proteins.

5’ Cap

A modified guanine nucleotide added to the 5' end of mRNA, which protects it from degradation and assists in ribosome binding during translation.

3’ PolyAtail

A series of adenine nucleotides added to the 3' end of mRNA, which enhances stability and facilitates export from the nucleus.

5’ Cap vs 3’ PolyAtail

Both are modifications added to the ends of mRNA transcripts; the 5’ Cap protects the mRNA from degradation and helps with ribosome binding, while the 3’ PolyAtail increases mRNA stability and aids in nuclear export.

Once the cell has produced a new pre-mRNA molecule, what does it do with it?

The pre-mRNA molecule undergoes RNA modification processing, which includes the addition of a 5' cap and a 3' poly-A tail, before being transported from the nucleus to the cytoplasm for translation.

 How does the sequence of nucleotides in mRNA code for the sequence of amino acids in a protein? 

The sequence of nucleotides in mRNA is read in groups of three called codons, each of which specifies a particular amino acid. During translation, ribosomes read these codons, enabling the assembly of amino acids into a polypeptide chain that forms a protein.

Why is the RNA code for the amino acids called a ‘triplet code’?

Because it is composed of sequences of three nucleotides, known as codons, that each correspond to a specific amino acid during protein synthesis.

What is the meaning of the word ‘codon’? 

A codon is a sequence of three nucleotides in mRNA that corresponds to a specific amino acid or a stop signal during protein synthesis.

How many different codons are there? 

There are 64 different codons, consisting of combinations of the four nucleotides in mRNA (adenine, uracil, cytosine, and guanine), which include 61 codons that code for amino acids and 3 stop codons.

What type of molecule contains codons?

Codons are found in messenger RNA (mRNA), which carries the genetic information from DNA to the ribosome for protein synthesis.

tRNA Role in Translation

Plays a crucial role in translation by transporting the appropriate amino acids to the ribosome, matching them with the corresponding codons on the mRNA during protein synthesis.

rRNA Role in Translation

A key component of ribosomes, facilitating the assembly of amino acids into protein chains and ensuring accurate translation of mRNA codons into polypeptide sequences.

mRNA Role in Translation

Serves as the template for translation, carrying the encoded genetic information from DNA to the ribosome, where it dictates the order of amino acids in a protein.

What is the meaning of the word ‘anticodon’?

A sequence of three nucleotides in tRNA that pairs with the corresponding codon on mRNA during translation, ensuring the correct amino acid is added to the growing polypeptide chain.

What type of molecule contains anticodons? 

tRNA molecules carry anticodons.

How do codons and anticodons interact during translation? 

Codons on mRNA specify amino acids, while anticodons on tRNA bind to these codons, facilitating accurate protein synthesis.

What is the start codon for protein synthesis? 

AUG, which codes for the amino acid methionine and signals the beginning of translation.

Describe the function of the A(aminoacyl) site in translation

Serves as the entry point for incoming aminoacyl-tRNAs carrying the next amino acid for the growing polypeptide chain, ensuring the correct amino acid is added by binding its anticodon to the corresponding mRNA codon

Describe the function of the P(peptidyl) site in translation

Holds the tRNA carrying the growing polypeptide chain during translation

Translation Purpose

To produce polypeptides (proteins) to carry out cellular functions which uses mRNA as a template to guide the sequence of amino acids.