Nucleotides and Nucleic acid

What do DNA and RNA stand for?

DNA stands for deoxyribonucleic acid; RNA stands for ribonucleic acid.

What is the main function of DNA?

To store genetic information, including the instructions needed to produce proteins and functional RNA molecules.

Which type of RNA carries genetic information from DNA to ribosomes?

Messenger RNA, or mRNA.

What are ribosomes made of?

Ribosomal RNA (rRNA) and proteins.

What are DNA and RNA polymers made from?

Nucleotide monomers.

What are the three components of a nucleotide?

A pentose sugar, a nitrogen-containing organic base and a phosphate group.

What is a pentose sugar?

A sugar containing five carbon atoms.

Which sugar is found in DNA nucleotides?

Deoxyribose.

Which sugar is found in RNA nucleotides?

Ribose.

Which four bases occur in DNA?

Adenine, thymine, cytosine and guanine.

Which four bases occur in RNA?

Adenine, uracil, cytosine and guanine.

Which base in RNA replaces thymine?

Uracil.

What are the components of a DNA nucleotide?

Deoxyribose, a phosphate group and one base: adenine, thymine, cytosine or guanine.

What are the components of an RNA nucleotide?

Ribose, a phosphate group and one base: adenine, uracil, cytosine or guanine.

What type of bond joins adjacent nucleotides in a polynucleotide?

A phosphodiester bond.

What type of reaction forms phosphodiester bonds between nucleotides?

A condensation reaction.

What forms the sugar–phosphate backbone of a polynucleotide?

Alternating sugar and phosphate groups linked by phosphodiester bonds.

Describe the overall structure of DNA.

Two antiparallel polynucleotide strands twisted into a double helix, held together by hydrogen bonds between complementary bases.

What does antiparallel mean in DNA?

The two strands run in opposite directions: one runs 5′ to 3′ and the other runs 3′ to 5′.

Which bases pair together in DNA?

Adenine pairs with thymine; cytosine pairs with guanine.

How many hydrogen bonds form between adenine and thymine?

Two.

How many hydrogen bonds form between cytosine and guanine?

Three.

What holds the two DNA strands together?

Hydrogen bonds between complementary bases.

How does the usual structure of RNA differ from DNA?

RNA is usually a shorter, single polynucleotide strand, whereas DNA consists of two strands forming a double helix.

Can a single RNA strand form hydrogen bonds within itself?

Yes. Complementary bases in different parts of the strand can pair, causing the RNA to fold.

Why is mRNA needed for protein synthesis in eukaryotic cells?

DNA remains in the nucleus, while translation occurs at ribosomes in the cytoplasm; mRNA carries a copy of the genetic instructions to the ribosomes.

Where are the ribosomes used in protein synthesis located?

Free in the cytoplasm or attached to the rough endoplasmic reticulum.

What are the three main types of RNA involved in protein synthesis?

Messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA).

What is the function of mRNA?

To carry a copy of a gene’s genetic information to a ribosome and act as the template for translation.

What is the function of tRNA?

To carry a specific amino acid to a ribosome and match its anticodon to a complementary mRNA codon.

What is the function of rRNA?

To form part of the ribosome’s structure and help catalyse peptide-bond formation.

Why is a sample ground or crushed during DNA extraction?

To break up the tissue and mechanically disrupt cells, including cell walls in plant samples.

Why is detergent added during DNA extraction?

To disrupt the phospholipid membranes of cells and nuclei, releasing the DNA.

Why is protease added during DNA extraction?

To digest proteins associated with DNA, including histones, and help remove protein contamination.

Does protease prevent DNA breakdown by digesting histones alone?

No. Digesting histones frees DNA from associated proteins; protease may also digest protein enzymes such as DNases that could break down DNA.

Why is salt added during DNA extraction?

Positive ions help neutralise the negative charges on DNA’s phosphate groups, allowing DNA molecules to aggregate and precipitate more easily in alcohol.

Why may a controlled warm-water bath be used during DNA extraction?

Depending on the protocol, warming helps cell disruption and can inactivate DNA-degrading enzymes; excessive heating can damage the DNA.

Why is the mixture cooled during DNA extraction?

To slow enzyme activity and help limit DNA breakdown.

Why may the mixture be filtered during DNA extraction?

To remove large pieces of tissue and cell debris while allowing dissolved DNA to pass through.

Why is ice-cold ethanol added during DNA extraction?

DNA is poorly soluble in cold ethanol, especially in the presence of salt, so it precipitates out of solution.

What does extracted DNA look like after adding cold ethanol?

A white, cloudy or stringy precipitate, often appearing at the boundary between the aqueous solution and ethanol.

How many standard amino acids are used to make proteins?

20.

What is the triplet code?

The genetic code in which a sequence of three bases specifies an amino acid or a start/stop signal.

Why are at least three bases needed to code for an amino acid?

There are four possible bases: two-base combinations provide only 16 possibilities, while three-base combinations provide 64, enough to specify 20 amino acids.

What is a codon?

A sequence of three bases on mRNA that specifies an amino acid or a stop signal.

What is an anticodon?

A sequence of three bases on tRNA that is complementary to an mRNA codon.

How many different codons are possible?

64.

What does it mean that the genetic code is degenerate?

More than one codon can specify the same amino acid.

How can the degeneracy of the genetic code reduce the effects of mutations?

Some base substitutions produce a different codon that still specifies the same amino acid, leaving the amino acid sequence unchanged.

Does the degeneracy of the genetic code prevent all mutations from affecting a protein?

No. Some mutations change an amino acid or introduce a stop codon.

What does it mean that the genetic code is non-overlapping?

Within a reading frame, each base belongs to only one codon; adjacent codons do not share bases.

What does it mean that the genetic code is nearly universal?

The same codon specifies the same amino acid in almost all organisms, although a few exceptions exist.

Does “universal genetic code” mean that every organism uses five bases in its DNA?

No. DNA normally uses four bases: A, T, C and G. Universality refers to the meanings of codons, not the number of bases.

What is the usual start codon on mRNA?

AUG, which codes for methionine.

What is the function of a start codon?

To signal where translation begins and establish the reading frame.

What are the three stop codons on mRNA?

UAA, UAG and UGA.

What is the function of a stop codon?

To signal the end of translation; stop codons do not specify amino acids.

What are introns?

Sequences within a gene that are transcribed into pre-mRNA but removed during RNA splicing.

What are exons?

Sequences retained in the mature RNA after splicing; in protein-coding genes, they include the protein-coding sequence and may also include untranslated regions.

Are all non-coding sections of DNA introns?

No. Non-coding DNA also includes regulatory sequences, regions between genes and genes for functional RNAs.

What are the two main stages of protein synthesis?

Transcription and translation.

What is transcription?

The production of an RNA molecule using one DNA strand as a template.

Where does transcription of nuclear genes occur in eukaryotic cells?

In the nucleus.

Which enzyme synthesises RNA during transcription?

RNA polymerase.

What happens to the DNA at the start of transcription?

A small section unwinds and the strands separate as hydrogen bonds between complementary bases are broken.

What is the DNA template strand also called?

The antisense strand.

Are both DNA strands used as templates for the same gene during transcription?

No. Only one strand acts as the template for a particular gene.

How do RNA nucleotides pair with the DNA template during transcription?

By complementary base pairing: DNA A pairs with RNA U; DNA T with RNA A; DNA C with RNA G; and DNA G with RNA C.

What does RNA polymerase do during transcription?

It moves along the template and catalyses phosphodiester-bond formation between adjacent RNA nucleotides.

In which direction is a new RNA strand synthesised?

5′ to 3′.

What happens to the DNA behind RNA polymerase?

The strands rejoin and the double helix reforms.

What is the initial RNA transcript of a typical eukaryotic protein-coding gene called?

Pre-mRNA.

What happens during RNA splicing?

Introns are removed from pre-mRNA and exons are joined together.

How does mature mRNA leave the nucleus?

Through a nuclear pore.

Where does mRNA go after leaving the nucleus?

To a ribosome in the cytoplasm, where translation takes place.

What are the main similarities between DNA replication and transcription?

Both use DNA as a template, involve local separation of DNA strands, use complementary base pairing and involve polymerase enzymes forming phosphodiester bonds.

Which polymerase is used in DNA replication, and which is used in transcription?

DNA polymerase is used in replication; RNA polymerase is used in transcription.

How do the products of DNA replication and transcription differ?

Replication produces DNA, while transcription produces RNA.

How do the nucleotides used in replication and transcription differ?

Replication uses DNA nucleotides containing deoxyribose and thymine; transcription uses RNA nucleotides containing ribose and uracil.

Should you list DNA helicase as a shared enzyme in replication and transcription without qualification?

No. DNA helicase separates strands during replication; transcription involves RNA polymerase and associated proteins, so the same named enzyme should not automatically be listed for both.

What is translation?

The production of a polypeptide using the codon sequence of mRNA.

Where does translation occur?

At ribosomes, either free in the cytoplasm or attached to the rough endoplasmic reticulum.

What components are needed for translation?

mRNA, ribosomes, tRNA molecules, amino acids, enzymes and energy supplied by ATP and GTP.

Describe the structure of tRNA.

A short, single RNA strand folded by internal hydrogen bonding, with an anticodon and an amino acid attachment site.

What holds parts of a tRNA molecule together in its folded shape?

Hydrogen bonds between complementary bases in different parts of the strand.

Where does an amino acid attach to tRNA?

At the 3′ end, which ends in the sequence CCA.

Is the amino acid attachment site the same as the anticodon?

No. The amino acid attaches to the 3′ end; the anticodon is a separate three-base sequence that pairs with an mRNA codon.

How is the correct amino acid attached to a tRNA molecule?

A specific aminoacyl-tRNA synthetase enzyme attaches the amino acid using energy from ATP.

What happens at the start of translation?

A ribosome assembles on the mRNA at the start codon, and a tRNA carrying methionine pairs with it.

How does a tRNA molecule recognise the correct mRNA codon?

Its anticodon forms temporary hydrogen bonds with the complementary codon.

What determines the order of amino acids in a polypeptide?

The sequence of codons on the mRNA.

What type of bond forms between adjacent amino acids during translation?

A peptide bond.

What catalyses peptide-bond formation during translation?

The ribosome, specifically its ribosomal RNA.

How does the ribosome move along the mRNA during translation?

It advances one codon at a time, allowing successive tRNAs to deliver their amino acids.

What happens to a tRNA after it has transferred its amino acid?

It leaves the ribosome and can be reloaded with another molecule of its specific amino acid.

What happens when a stop codon enters the ribosome?

A release factor binds, translation ends and the completed polypeptide is released.

What happens to a polypeptide after translation?

It folds into its specific three-dimensional shape and may undergo further modification or combine with other polypeptides.

Summarise the flow of genetic information in protein synthesis.

DNA is transcribed into RNA; mature mRNA is translated into a polypeptide at a ribosome.