Lecture 6

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Questions and Answers

What is the main function of the telomerase RNP?

Adds telomeres to the ends of chromosomes (correct)

Formation of the 5’ end of mature tRNA molecules

Synthesis of polypeptides

Removal of introns from pre-mRNA

Which of the following RNPs is involved in RNA maturation?

Reverse Transcriptase

Spliceosome (correct)

Telomerase

Ribosome

Which RNP is responsible for the formation of the 5' end of mature tRNA molecules?

RNase P (correct)

Spliceosome

Ribosome

Telomerase

What is the primary role of the ribosome?

Synthesizing peptides, polypeptides, and proteins Signup and view all the answers

Which of the following does RNA not directly do in RNA catalyzed reactions?

Catalyzes the synthesis of polypeptides Signup and view all the answers

What type of bond links the nitrogenous base to the sugar residue in a nucleotide?

N-glycosidic bond Signup and view all the answers

Which carbon atom of the deoxyribose sugar is involved in forming the phosphodiester bond with the phosphate group in a nucleotide?

5' carbon Signup and view all the answers

What is the name given to the structure formed by eight histones?

Octamer Signup and view all the answers

In a DNA double helix, how are the two strands oriented relative to each other?

Antiparallel, one 5' → 3' and the other 3' → 5' Signup and view all the answers

Which nitrogenous bases form base pairs through hydrogen bonding in DNA?

A with T and G with C Signup and view all the answers

What is the distance between consecutive base pairs in the DNA helix?

0.34 nm Signup and view all the answers

Which carbon of the deoxyribose sugar is involved in the phosphodiester linkage that form the backbone of the DNA molecule?

3' and 5' carbons Signup and view all the answers

What is the primary role of linker histones H1 and H5 in DNA structure?

To hold the DNA strands together Signup and view all the answers

Which of these is a correct representation of a deoxycytidine 5'-monophosphate?

dCMP Signup and view all the answers

The sequence of bases in DNA is read in which direction?

5' → 3' Signup and view all the answers

What is the primary role of histones H1/H5 in chromatin structure?

Stabilizing the chromatosome structure. Signup and view all the answers

Approximately how much shorter is the DNA in the 30-nm fiber compared to its extended form?

What type of bond links the nitrogenous base to the sugar residue in ribonucleosides?

N-glycosidic bond Signup and view all the answers

Which carbon of the ribose sugar is involved in the phosphodiester bond formation in RNA nucleotides?

5' carbon Signup and view all the answers

What structural feature distinguishes an A-form helix in RNA from a B-form helix typically found in DNA?

The -OH group on the 2' carbon of the ribose Signup and view all the answers

Which groove do proteins typically bind to in double-stranded RNA?

The minor groove. Signup and view all the answers

Which of the following is NOT a type of non-canonical pairing found in RNA helices?

Watson-Crick base pairs. Signup and view all the answers

Which type of RNA primarily functions as a carrier of amino acids during protein synthesis?

tRNA Signup and view all the answers

Which loop of tRNA is involved in the recognition of ribosomes and the binding of tRNA to the ribosome?

The T-loop (TψC) Signup and view all the answers

What is the function of aminoacyl-tRNA synthetases in the context of tRNA structure?

Attaching amino acids to tRNA molecules Signup and view all the answers

Which arm of the tRNA molecule contains the anticodon loop?

Anticodon arm Signup and view all the answers

What is a unique feature of the 3' end of the tRNA acceptor arm?

It always ends with a CCA sequence. Signup and view all the answers

Which of these is the main component of the ribosome?

rRNA Signup and view all the answers

What is the catalytic role of rRNA within the ribosome?

Catalyzing protein synthesis. Signup and view all the answers

What term is used to describe RNA molecules with catalytic activity?

Ribozymes Signup and view all the answers

What is the primary function of the nuclear lamina?

To provide structural support to the nucleus and organize chromatin. Signup and view all the answers

Which of the following is NOT a component of the nuclear envelope?

The nuclear matrix. Signup and view all the answers

What is the function of nuclear pores?

To control the selective transport of macromolecules between the nucleus and the cytoplasm. Signup and view all the answers

What are the main components of the nucleolus?

RNA and proteins. Signup and view all the answers

During interphase, what percentage of the genome is typically comprised of euchromatin?

Approximately 92% Signup and view all the answers

Which of the following is a characteristic feature of heterochromatin?

It's always in a condensed state and stains dark. Signup and view all the answers

Which statement best describes the difference between constitutive and facultative heterochromatin?

Constitutive heterochromatin is always condensed, whereas facultative heterochromatin can decondense under certain conditions. Signup and view all the answers

What are the three components of a nucleotide?

A nitrogenous base, a five-carbon sugar, and a phosphate group. Signup and view all the answers

Which of the following nitrogenous bases is NOT found in DNA?

Uracil. Signup and view all the answers

What is the key difference between the pentose sugars found in DNA and RNA?

Deoxyribose lacks a hydroxyl group at the 2' carbon, which is present in ribose. Signup and view all the answers

What are the structural components of a nuclear pore complex?

Three rings made of eight elements each; cytoplasmic, central pore, and nuclear. Signup and view all the answers

During DNA packing, what is the approximate reduction in length of a DNA molecule when it is organized into a metaphase chromosome?

10,000 times shorter. Signup and view all the answers

What is the name for the DNA organization in the nucleus, where it anchors to the nuclear lamina?

Lamina-associated domain (LAD). Signup and view all the answers

Which of the following best describes the function of the nuclear matrix?

It plays a role in regulating DNA replication, gene expression, and RNA processing. Signup and view all the answers

How does the packing of DNA change when euchromatin transforms into inactive chromatin?

DNA strands become condensed. Signup and view all the answers

Besides guiding the protein enzyme to the right place, what is another direct role of RNA in RNA-catalyzed reactions?

It permits the binding of the enzyme to the substrate. Signup and view all the answers

Which RNP is responsible for adding telomeres to the ends of chromosomes?

Telomerase Signup and view all the answers

Which RNP complex is responsible for splicing introns from pre-mRNA?

Spliceosome Signup and view all the answers

Which of the following RNP complexes is directly involved in the maturation of tRNA molecules?

RNase P Signup and view all the answers

Which of the following options correctly pairs a RNP with its main function?

Spliceosome - RNA maturation Signup and view all the answers

What gives nucleic acid molecules their acidic property?

The phosphoric acid residue Signup and view all the answers

In a pyrimidine base, what nitrogen atom is linked to the C1 carbon of the sugar?

The N1 nitrogen Signup and view all the answers

What type of bond connects the phosphate group to the 5' carbon in the sugar ring of a deoxynucleotide?

Phosphodiester bond Signup and view all the answers

In DNA, what is the linkage between two adjacent nucleotides?

Phosphodiester linkage between 5’ and 3’ carbons of neighboring deoxyribose sugars Signup and view all the answers

What is the directionality (polarity) of a DNA molecule primarily determined by?

The chemical differences in the phosphodiester bonds at the 5’ and 3’ carbons Signup and view all the answers

In the double helix of DNA, how are the base pairs arranged?

A pairs with T and G pairs with C Signup and view all the answers

Which of the following best describes the orientation of the two strands in a DNA double helix?

One strand runs 5’ to 3’, and the other runs 3’ to 5’ Signup and view all the answers

Approximately how many base pairs are present in one complete twist of the DNA helix?

10 Signup and view all the answers

Which histones are known as the core histones?

H2A, H2B, H3, and H4 Signup and view all the answers

What is the basic structural unit of DNA packing in eukaryotes?

Nucleosome Signup and view all the answers

Which of the following is a primary function of the nuclear lamina?

Providing structural support to the nucleus and organization of chromatin. Signup and view all the answers

What is the main function of the nuclear basket structure associated with nuclear pores?

Facilitating the selective passage of macromolecules through the nuclear pore. Signup and view all the answers

In which phase of the cell cycle does the nucleolus disappear?

Late Prophase Signup and view all the answers

What is the approximate percentage of histone proteins in nuclear chromatin?

37.5% Signup and view all the answers

During metaphase, how much shorter is the DNA molecule in a packed chromosome compared to its extended form?

10,000 times shorter Signup and view all the answers

What distinguishes euchromatin from heterochromatin?

Euchromatin is genetically active and less condensed, while heterochromatin is generally inactive and more condensed. Signup and view all the answers

Which statement best describes facultative heterochromatin?

It is formed by the reversible condensation of euchromatin and contains genes used when necessary. Signup and view all the answers

What is the fundamental monomer unit of a nucleic acid chain?

Nucleotide Signup and view all the answers

How many carbon atoms are in a pyrimidine ring structure?

4 Signup and view all the answers

Which of the following nitrogenous bases is a purine?

Guanine Signup and view all the answers

What is the key structural difference between ribose and deoxyribose?

Ribose contains a hydroxyl group at the 2' carbon, but deoxyribose does not contain this. Signup and view all the answers

Which type of chromatin is primarily found within the confines of the nuclear envelope?

Heterochromatin Signup and view all the answers

What is the role of the nuclear matrix in terms of gene expression?

It regulates the spatial organization of chromatin and has a role in gene expression. Signup and view all the answers

Which of the following best describes the physical location of intercalary heterochromatin within a chromosome?

Located within some parts the chromosomes. Signup and view all the answers

Considering all the nitrogenous bases in DNA, how many have a double-ring structure?

2 Signup and view all the answers

What is the primary structural feature that stabilizes a chromatosome?

The binding of linker histones H1/H5. Signup and view all the answers

What is the approximate reduction in DNA length when it is packed into the 30-nm fiber?

What component facilitates the formation of chromosome loops by creating a clamp at the base of each loop?

Non-histone proteins Signup and view all the answers

What is the approximate diameter of a nucleosome?

11 nm Signup and view all the answers

Which nitrogenous base is unique to RNA compared to DNA?

Uracil Signup and view all the answers

Which carbon atom of the ribose sugar is involved in the formation of the phosphodiester bond that links adjacent nucleotides in RNA?

3' Signup and view all the answers

What prevents the formation of a B-form double-stranded helix in RNA?

The presence of a hydroxyl (-OH) group on the 2' carbon of the ribose. Signup and view all the answers

Which type of RNA is produced in the nucleus and contains both exons and introns before maturation?

mRNA Signup and view all the answers

What percentage of the total RNA in a cell does tRNA typically constitute?

10-15% Signup and view all the answers

Which specific loop of tRNA is directly involved in the recognition of aminoacyl-tRNA synthetases?

The D loop Signup and view all the answers

How many base pairs typically form the T stem within the secondary structure of tRNA?

5 base pairs Signup and view all the answers

What is the function of the CCA sequence located at the 3' end of the tRNA molecule?

It is the site where an amino acid is attached. Signup and view all the answers

In what cellular structure are most ribosomal RNA molecules synthesized and stored?

Nucleolus Signup and view all the answers

Which catalytic function is performed by RNA molecules known as ribozymes?

Catalysis of various chemical reactions Signup and view all the answers

What is a common characteristic of ribozymes?

They exhibit autocatalytic activity. Signup and view all the answers

Study Notes

DNA Structure, Genome Organization, and RNA Structure

DNA structure is a double helix composed of two complementary chains.
Nitrogenous bases are oriented inwards, forming base pairs (A=T, G=C) linked by hydrogen bonds.
Sugar-phosphate backbones are on the outside of the chain.
DNA molecules in human cells are 2 meters long (5.3 x 10⁹ base pairs).
In metaphase, DNA is compacted 10,000 times shorter, forming chromosomes.
The packing of DNA is a result of its specific structural organisation in space and the participation of histone and non-histone proteins.

The Nucleus

The nucleus is enclosed by a nuclear envelope.
The nuclear envelope is made up of the outer (cytoplasmic) nuclear membrane, inner nuclear membrane, perinuclear space, and nuclear lamina which adheres to the inner membrane.
Nuclear pores allow the exchange of molecules with the cytoplasm.
Chromatin is located within the nucleus.
The nucleolus is a structure within the nucleus that occupies 25% of the nuclear volume during interphase.
The nucleolus disappears in late prophase and reassembles in telophase.
The main components of the nucleolus are RNA and proteins.

Nuclear Lamina

The nuclear lamina is a network of protein filaments (lamins).
The structure and amino acid composition of lamins are similar to intermediate filaments.
The nuclear lamina gives shape to the nucleus and participates in organizing chromatin by providing a site of attachment for chromatin domains (LADs).
Lamins are involved in the fragmentation and reconstruction of the nuclear envelope during mitosis.

Nuclear Pores

A nuclear pore consists of three rings: a cytoplasmic ring, a central pore, and a nuclear ring.
Each ring is made of eight elements.
Eight nuclear filaments are anchored to both rings.
Nuclear pore filaments form a nuclear basket structure.
Nuclear pores facilitate two-way, selective transport of macromolecules between the nucleus and cytoplasm.

The Nuclear Matrix

The nuclear matrix is a network of fibers within the nucleus.
It participates in DNA replication, gene expression, and pre-RNA transcription and maturation.
It facilitates the transport of ribosome precursors into the cytoplasm.

Nuclear Chromatin

Nuclear chromatin is the form of chromosomes during interphase.
Chromatin composition includes DNA (36.5%), histone proteins (37.5%), non-histone proteins (10.5%), RNA (9.5%), and water, calcium, and magnesium ions.
DNA molecules are 2 meters long in human cells.
They are compacted 10,000 times during metaphase for chromosome formation.
This compaction is due to the specific DNA organisation in space and the participation of histone and non-histone proteins.
Interphase chromosomes occupy distinct spaces within the nucleus.
Chromatin types include euchromatin and heterochromatin.

Chromatin Types

Euchromatin is partially or completely relaxed chromatin that stains bright in microscopy.
It is genetically active and contains DNA that can be transcribed.
Euchromatin constitutes approximately 92% of interphase genomes.
It can condense into inactive chromatin.
Heterochromatin is condensed chromatin that stains dark in microscopy.
It is genetically inactive and contains DNA generally not transcribed.
Heterochromatin occurs at telomeres and centromeres of chromosomes (constitutive) and in other regions of chromosomes (facultative).

Nucleic Acids

Nucleic acids are composed of: heterocyclic nitrogenous bases, a five-carbon sugar, and a phosphate group
A base-sugar unit is called a nucleoside.
A base-sugar-phosphate unit is called a nucleotide.
Deoxyribonucleotides are the basic building blocks of DNA.

Nitrogenous Bases

Nitrogenous bases are heterocyclic aromatic compounds.
They contain carbon and nitrogen atoms within the ring structures.
They are classified as purines (double-ring) or pyrimidines (single-ring).
Purines include adenine (A) and guanine (G).
Pyrimidines include cytosine (C), thymine (T), and uracil (U).

Pentose Sugars

In RNA, the sugar component is ribose.
In DNA, the sugar component is deoxyribose (lacking an oxygen at the 2' carbon).
Both contain oxygen within the ring and the 5' carbon is outside the ring.

Phosphate Group

Phosphate groups give nucleic acids their acidic properties.
They carry a negative charge from cleaved hydrogen cations.

DNA Structure (Details)

A deoxyribonucleoside is a nitrogenous base attached to deoxyribose.
N-glycosidic bonds connect the base to deoxyribose (C1 carbon).
Phosphodiester bonds connect nucleotides via the 5' carbon of the sugar.

Nucleosides and Nucleotides

This table lists the corresponding nucleoside and nucleotide names for relevant bases. (Table from the original notes should be used)

DNA Primary Structure

Information in DNA is encoded in the order of nitrogenous bases.
DNA polynucleotide chain is formed by connecting 5' and 3' deoxyribose carbons.

DNA Secondary Structure

DNA exists as a double-stranded helix.
The two strands run anti-parallel (5' to 3' and 3' to 5').
Base pairs are held together by hydrogen bonds (A-T and G-C).
Sugar-phosphate backbones are on the outside of the helix.
The distance between consecutive nucleotides is 0.34 nm.
10 base pairs occur per twist of the helix.

Histones

Two types of histones are involved in DNA packaging: core histones (H2A, H2B, H3, H4) and linker histones (H1, H5).
Core histones form an octamer.
Core histones contain amino acid "tails" extending beyond the core.
Linker histones hold DNA strands together within chromatin.

Nucleosome

Nucleosomes are the basic structural units of DNA packaging.
Each nucleosome consists of eight histones and a section of DNA (approximately 200 base pairs) wound around the core.

Chromatosome

Chromatosomes are structural units of chromatin consisting of a nucleosome and linker histones (H1/H5).
Linker histones stabilize the chromatosome.

30-nm Fiber

The 30-nm fiber is a higher-order structure formed by interactions between nucleosomes, requiring histones H1/H5.

Chromosome Loops and Domains

Chromosome loops are formed by non-histone proteins binding to specific DNA sequences.
Loops fold into looped domains.

DNA Packaging in Chromosomes

DNA undergoes progressively higher levels of packaging within chromosomes: double helix, nucleosome, 30-nm fiber, loops, domains, mitotic chromosome.
A metaphase chromosome is much shorter than an extended DNA helix.

RNA Structure

RNA is a single-stranded molecule.
RNA molecules include ribonucleotides.
Ribose is the sugar component of RNA.
In RNA, a nitrogenous base is linked to a carbon atom of ribose via an N-glycosidic bond.
RNA has a 5' phosphate end and a 3' hydroxyl end.
Phosphodiester bonds form the RNA backbone.
RNA is less stable than DNA.

RNA Types

Ribonucleic acids can be classified as coding or non-coding.
Coding RNA types are messenger RNA (mRNA), pre-mRNA (hnRNA), which contains exons and introns.
Non-coding RNA types are transfer RNA (tRNA), ribosomal RNA (rRNA), short non-coding RNA (sncRNA) and long non-coding RNA (lncRNA)

mRNA

mRNA is produced in the nucleus from pre-mRNA.
Pre-mRNA contains exons (coding sequences) and introns (non-coding sequences).
Pre-mRNA undergoes a multi-stage maturation process to become mRNA.
mRNA migrates to ribosomes in the cytoplasm for protein synthesis.

tRNA

tRNA is a small RNA molecule (63-94 base pairs) primarily found in the cytoplasm.
tRNA constitutes 10-15% of total RNA in eukaryotic cells.
tRNA recognizes the appropriate amino acid, then transfers it to a growing polypeptide chain on a ribosome.
Primary tRNA structure contains canonical and modified bases.
Secondary tRNA structure includes 3 loops and 3 stems.

rRNA

rRNA is the major component of ribosomes (80% total RNA).
rRNA is synthesized and stored in the nucleolus.
rRNA consists of single-stranded chains and double-stranded helices.
rRNA facilitates protein synthesis in ribosomes.
rRNA is found in large (28S, 5.8S, 5S rRNA) and small (18S rRNA) ribosomal subunits.

Ribosomes

Ribosomes are RNA-protein complexes that facilitate protein synthesis.

Catalytic Properties of RNA

Some RNA molecules, known as ribozymes, catalyze reactions, often autocatalytically modifying themselves.
In some RNA-protein complexes (RNPs), the catalytic function is performed by the RNA or the protein.

Roles of RNPs

RNPs play various roles in gene expression pathways (e.g., telomerase, spliceosome, RNase P, ribosome).
Telomerase adds telomeres to chromosome ends during DNA replication.
Spliceosomes remove introns from pre-mRNA in the nucleus.
RNase P forms the 5' end of mature tRNA molecules.
Ribosomes synthesize peptides, polypeptides, and proteins.

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Explore the fascinating structures of DNA and the nucleus in this quiz. Learn about the components of DNA, including its double helix configuration and the organization of the nucleus, including the nuclear envelope and nucleolus. Test your knowledge on these fundamental aspects of cellular biology.