Biology Unit 3: The Nucleus

Podcast

Play an AI-generated podcast conversation about this lesson

Questions and Answers

What is the primary role of the centromere during mitosis?

To condense the chromosome structure

To ensure correct distribution of duplicated chromosomes (correct)

To protect chromosomes from degradation

To create telomeres at the ends of chromosomes

How many chromosomes do human gametes contain?

46 chromosomes

22 chromosomes

44 chromosomes

23 chromosomes (correct)

What distinguishes the X and Y sex chromosomes from autosomes?

They are both homologous and identical

They have the same information, shape, and size

They behave as homologues but differ in information, shape, or size (correct)

They have more chromosomes than autosomes

What is the structure of human telomeres primarily composed of?

Repeats of a DNA sequence with G residues Signup and view all the answers

Which of the following best describes females in terms of gametic chromosomes?

They are homogametic with two X chromosomes Signup and view all the answers

What function do telomeres serve in chromosomes?

They ensure that chromosomes can replicate DNA completely Signup and view all the answers

What is the role of shelterin in telomeric structure?

To protect telomeres from degradation Signup and view all the answers

What feature characterizes sister chromatids?

They are joined by the centromere Signup and view all the answers

What is the primary role of telomerase in DNA replication?

It replicates telomeric DNA at chromosomal endings. Signup and view all the answers

Which of the following statements about introns is true?

Introns do not contribute functionally to protein synthesis. Signup and view all the answers

How many different proteins can the 21,000 human protein coding genes potentially produce due to alternative splicing?

Approximately 85,000 different proteins. Signup and view all the answers

What is one of the main functions of regulatory sequences in the genome?

They are involved in the transcriptional regulation of genes. Signup and view all the answers

Which type of DNA is known for not encoding any protein, but may have regulatory functions?

Extragenic DNA. Signup and view all the answers

What is the typical nucleotide length of micro RNA (miRNA)?

Approximately 22 nucleotides. Signup and view all the answers

Which of the following best describes the concept of gene duplication?

It is the increase in the number of genes due to errors in DNA replication. Signup and view all the answers

What defines a genome in the context of an organism?

The complete set of genetic material present in an organism. Signup and view all the answers

What is the main function of microRNAs (miRNAs) in the RNA-induced silencing complex (RISC)?

They direct RISC to target mRNAs for inhibition or degradation. Signup and view all the answers

How many different mRNAs can a single microRNA target?

Up to 100 Signup and view all the answers

What is the role of long non-coding RNAs (lncRNAs) in gene expression?

They regulate gene expression without being translated into proteins. Signup and view all the answers

What is the primary structural component of the nuclear envelope?

Two nuclear membranes Signup and view all the answers

What is the main purpose of the nuclear pore complex?

To serve as the sole communication channels between nucleus and cytoplasm. Signup and view all the answers

What is a characteristic of repetitive DNA sequences such as satellite DNA?

They are important for the structure of chromosomes. Signup and view all the answers

What is the function of the nuclear lamina?

It underlies the inner nuclear membrane and supports nuclear structure. Signup and view all the answers

Which statement about the composition of genomic DNA in humans is accurate?

Repetitive DNA sequences make up approximately 10% of the human genome. Signup and view all the answers

Which DNA polymerases are involved in the replication of nuclear DNA in eukaryotes?

DNA polymerase α, δ, and ε Signup and view all the answers

What is the direction of DNA synthesis by polymerases?

5' to 3' Signup and view all the answers

Why do eukaryotes require multiple origins of replication?

To replicate the long chromosomes in a timely manner Signup and view all the answers

What initiates the process of DNA replication at the origins?

Initiator proteins recognizing specific sequences Signup and view all the answers

How does the replication of the E. coli genome differ from mammalian genomes?

E. coli has a single origin of replication. Signup and view all the answers

Which of the following statements is true regarding the forces involved in DNA replication?

Hydrogen bonds between bases are broken to open the DNA. Signup and view all the answers

What role do single-stranded DNA-binding proteins play in DNA replication?

They stabilize the unwound DNA strands. Signup and view all the answers

Which DNA polymerase is responsible for the replication of mitochondrial DNA?

DNA polymerase γ Signup and view all the answers

Where are chromosomes rich in genes typically located within the nucleus?

In the center of the nucleus Signup and view all the answers

What effect does histone acetylation have on chromatin structure?

It relaxes the chromatin structure. Signup and view all the answers

What is the role of histone acetyltransferase (HAT) in histone acetylation?

To add acetyl groups to histones. Signup and view all the answers

How does DNA methylation affect gene expression?

It serves as a primary mechanism for transcriptional repression. Signup and view all the answers

Which component plays a significant role in genomic imprinting?

DNA methylation Signup and view all the answers

What is the primary function of miRNAs in gene regulation?

To inhibit translation or induce degradation of target mRNAs. Signup and view all the answers

What is a characteristic of long noncoding RNAs (lncRNAs)?

They can modify or recruit chromatin-modifying proteins. Signup and view all the answers

Which process explains why bacterial mRNAs can be used for protein synthesis while still being transcribed?

Bacterial mRNAs do not require processing. Signup and view all the answers

What is the role of snRNAs in the nucleus?

They are involved in the splicing of pre-mRNAs. Signup and view all the answers

Which nuclear structure is known for modifying snRNAs?

Cajal Bodies Signup and view all the answers

Where do snoRNAs primarily function within the cell?

In the nucleus for processing rRNA. Signup and view all the answers

What characterizes nuclear bodies such as speckles and Cajal bodies?

They are dynamic structures that do not have membranes. Signup and view all the answers

What is the primary function of the nucleolus?

Ribosome biogenesis. Signup and view all the answers

Which protein mediates the transport of snRNAs from the cytoplasm to the nucleus?

Importin snuportin Signup and view all the answers

How are splicing factors organized within the nucleus?

They are concentrated in structures called speckles. Signup and view all the answers

What process do speckles facilitate in gene expression?

Pre-mRNA splicing. Signup and view all the answers

Study Notes

Unit 3: The Nucleus

The nucleus serves as a storehouse for genetic information
DNA replication occurs at the genomic level
RNA transcription and processing are regulated
Regulates gene expression, by controlling the transport of transcription factors from the cytoplasm to the nucleus.

Index

The cell nucleus and the DNA
Nuclear envelope
DNA replication
DNA transcription
Traffic between the nucleus and the cytoplasm
Nuclear bodies

3.1 The cell nucleus and the DNA

Functions: serves as a storehouse for genetic information
At the genomic level: DNA replication takes place
RNA transcription and processing
Regulates gene expression, by controlling the transport of transcription factors from the cytoplasm to the nucleus.

Chromosomes and chromatin

Eukaryotic genomes are more complex than prokaryotic genomes, organized into multiple linear chromosomes. Instead of a single DNA molecule, the DNA is organized into multiple linear molecules
DNA is organized into smaller packages (chromatin).
Human DNA is 2 meters long but fits into a 5-10 micrometer nucleus
DNA binds tightly to small proteins (histones) to form chromatin
Chromatin exists in two forms:
Chromatin: unwound and active in RNA synthesis
Chromosomes: tightly wound and found during cell division and inactive for RNA synthesis

Heterochromatin and euchromatin

Heterochromatin: condensed chromatin structure, inactive for transcription
Euchromatin: loose chromatin structure, active for transcription
Euchromatin is distributed throughout the nucleus, while heterochromatin is located around the periphery of the nucleus.

Chromatin structure

Chromatin is a complex structure of DNA and proteins whose degree of condensation can vary depending on the cell cycle and chromosomal activity
Levels of DNA packaging:
2nm fiber (double-stranded DNA)
11nm fiber ("beads-on-a-string" structure)
30nm fiber (solenoid structure)
300nm fiber (chromatin loops)
700nm fiber (condensed sections)
1400nm fiber (entire mitotic chromosome).

Histone modifications and DNA

Histones have an amino-terminal tail that can be modified (acetylated, methylated, phosphorylated).
These modifications constitute a "histone code" that influences DNA replication or expression
Histone acetylation is associated with transcriptional activity
Methylation can be associated with both active and repressed chromatin.

Chromosomes

Each eukaryotic species has a characteristic chromosome number (e.g., humans have 46 chromosomes).
Most cells are diploid (2n), having two sets of chromosomes (one from each parent).
Gametes (sex cells) are haploid (n), having one set of chromosomes.
22 pairs of chromosomes are homologous (autosomes)
Two sex chromosomes are either homologous or heterologous (XX for females and XY for males)
Chromosomes have a centromere, dividing the chromosome into two arms (p-arm and q-arm).
The ends of the chromatids are called telomeres
Telomeres maintain structural integrity, position, ensure complete DNA replication of the chromosomes.

Telomerase

Telomerase is a type of DNA polymerase involved in telomere formation
It replicates telomeric DNA
Telomeric DNA forms a loop structure protected by the protein complex shelterin
Telomeres have specific sequences (TTAGGG in humans).

Genes and genomes

Genome: the complete set of genetic material in an organism
Gene: a segment of DNA that codes for a gene product (typically a protein).
Contains structural and regulatory DNA
Extragenic DNA (non-coding DNA) has various functions including regulation of gene expression.

DNA quantity paradox

The amount of DNA in an organism does not directly correlate with the complexity or number of genes present in that organism.
More complex organisms do not have more DNA than prokaryotes, due to a large percentage of repetitive DNA.

Gene structure

Genes consist of exons (coding sequences) and introns (non-coding sequences).
Introns are removed during RNA processing (splicing).
Exons are spliced together to form mature mRNA.
Alternative splicing allows a single gene to produce multiple protein isoforms.

Alternative splicing

Alternative splicing generates a variety of mRNA transcripts from a single gene, which causes diversity in the proteins an organism can produce
This results in many more different proteins than expected based on the number of genes.

Complexity in human DNA

Human genomes contain 21000 genes, but also non-coding DNA (regulatory sequences, repetitive sequences).
Regulatory sequences: promoters, silencers, enhancers
Repetitive DNA sequences: tandem repeats (satellite DNA), sparse repeats (LINES, SINES, LTR, transposons), gene duplication and pseudogenes
The human genome contains more non-coding sequence than coding sequence

Non-coding RNA

ncRNA: RNA molecules that do not encode proteins. Examples include tRNA, rRNA, miRNA and long ncRNA (lncRNA).
miRNAs: small non-coding RNAs that regulate gene expression via RNA interference
IncRNAs: long non-coding RNA molecules involved in gene regulation.

RNA processing

Bacterial mRNAs are used immediately for protein synthesis while still being transcribed
Ribosomal, Transfer, and eukaryotic mRNAs must be processed
5' capping, 3' polyadenylation, splicing of introns are examples of RNA processing steps carried out on pre-mRNAs

3.2 Nuclear envelope

Structure of the nuclear envelope
Nuclear pore complex

Nuclear envelope

It is a selective barrier that prevents the free traffic of molecules between the nucleus and the cytoplasm; only nuclear pore complexes allow communication between both compartments.
Key role in regulation of gene expression, maintaining the internal composition of the nucleus, and keeping the two compartments metabolically independent.

Nuclear envelope structure

2 nuclear membranes: outer and inner membrane
Nuclear lamina
Nuclear pore complex

Outer nuclear membrane

Connected to the endoplasmic reticulum membrane.
Ribosomes are frequently attached to the outer membrane.
Membrane proteins bind to the cytoskeleton.

Inner nuclear membrane

Contains specific membrane proteins that bind the nuclear lamina.

Nuclear pore complex

Junction of inner and outer membranes.
The only channels that allow molecules and larger macromolecules to pass through.
Involved in selective trafficking of proteins and RNA between the nucleus and cytoplasm.

Nuclear lamina

Fiber network that provides structural support to the nucleus.
Made up of proteins lamin A, B, and C.
All lamins are fibrous proteins between 60-80 kDa.
Lamins are joined together to form filaments.

3.3 DNA replication

Semi-conservative mechanism: the two strands separate to form templates for producing new strands, thus producing an identical copy.
DNA polymerases are essential enzymes; they catalyse the addition of dNTPs onto the 3'OH group of the growing strand, continuously in the 5' → 3' direction.
Replication begins at origins of replication, where initiator proteins separate the DNA strands to form replication forks.
Replication proceeds in both directions from the origin of replication, creating replication bubbles or forks
Prokaryotes have a single origin, whereas eukaryotes have multiple.

DNA polymerase

Various in eukaryotes and prokaryotes with specific roles in replication and repair
Bacteria use DNA polymerase III mostly for replication
Eukaryotes use α, δ, ε polymerases for nuclear DNA and γ for mitochondrial DNA.

Origin of replication

DNA molecule opens like a zipper by breaking hydrogen bonds between complementary bases.
Initiator proteins recognize specific nucleotide sequences (origins of replication) on DNA, and stimulate the separation of strands and connection of other proteins needed for replication.
A large number of enzymes and proteins are involved in replication forming a complex called replisome
Replication in prokaryotes starts at a single origin.
Replication in eukaryotes begins at multiple origins.

Replication fork

The place where the parental DNA strands separate, allowing new strands to be synthesized.
Replication proceeds in both directions from the origin of replication.
Leading strand is synthesized continuously
Lagging strand is synthesized discontinuously in small fragments (Okazaki fragments).
Enzmyes and proteins like DNA polymerase, helicase, primase, and ligase are involved.

DNA maintenance

The accuracy of DNA replication is critical for cell reproduction.
Error frequency is less than one incorrect base for every 10^9 incorporated nucleotides.
Mechanisms by which DNA polymerase achieves high accuracy:
Correct base selection.
Double-reading capability (exonuclease activity in 3'→5' direction).

3.4 DNA transcription

The process of synthesizing an RNA molecule from a DNA template.
DNA strands have different functions in transcription
The antisense strand acts as the template for RNA synthesis.
The RNA transcript is complementary to the antisense strand and identical to the sense strand, except for uracil in place of thymine
RNA polymerase is the main enzyme involved; it adds ribonucleotides to the 3' end of the growing RNA chain, in 5'→3' direction.

RNA polymerase

RNA polymerase is the main enzyme involved in RNA synthesis
Catalysed reaction: (NMP)n + NTP → (NMP)n+1 + PPi
NMP: nucleotide monophosphate
NTP: nucleotide triphosphate
PPi: pyrophosphate

Initiation of transcription

Transcription begins with the binding of RNA polymerase to the promoter
The promoter region extends for tens or hundreds of bases before the transcription start site, containing consensus sequences that are repeated in different genes
DNA unwinds and RNA polymerase undergoes conformational and chemical changes (phosphorylation) that induce the initiation of transcription

Elongation of transcription

Most of the transcription factors are released at the beginning of the elongation.
RNA polymerase moves in 5ʹ → 3ʹ direction by adding nucleotides to the 3′ end of the growing RNA molecule
DNA strand that is being transcribed unwinds and rewinds during the polymerase movement, so that the DNA-RNA hybrid region remains relatively short.

Termination of transcription

RNA polymerase recognizes certain DNA sequences that lie at the end of genes.
This ends RNA synthesis, followed by the release of the transcription machinery

3.5 Traffic between the nucleus and the cytoplasm

Selective transport of proteins to and from the nucleus
Regulation of protein transport to the nucleus
RNA Transport
Proteins necessary for nuclear functions must enter the nucleus from synthesis sites in the cytoplasm
Importins recognize the NLS ('Nuclear localization signal') of the cargo protein and transport it from the cytoplasm to the nucleus
Ran proteins:
Guanosine di/triphosphate binding protein
High concentration of GTP in the nucleus determines directionality of nuclear transport
Enzymes that stimulate the exchange of GDP for GTP on Ran - are located on the nuclear side of the envelope.
Exportins: recognize NES ('Nuclear export signal') responsible for proteins leaving the nucleus.
Regulation of transport: some cytoplasmic proteins mask the NLS, preventing proteins from entering the nucleus; proteins also regulated by phosphorylation

3.6 Nuclear bodies

Differentiated organelles in the nucleus
Compartmentalize the nucleus for RNA and protein concentration that functions in certain processes
Dynamic structures without membranes, maintain integrity via interactions with proteins and RNA.

Nuclear bodies summary

Nucleolus: rRNA transcription, processing, ribosome assembly
Cajal body: snRNP assembly, modification of snRNAs
Clastosome: proteasomal activity, histone pre-mRNA processing
Histone locus body: storage of histone pre-mRNAs
Speckle: transcriptional regulation, DNA repair
PML body: transcriptional regulation, DNA repair
Polycomb body: gene silencing

Studying That Suits You

Use AI to generate personalized quizzes and flashcards to suit your learning preferences.

Description

Explore the intricate functions of the cell nucleus in this quiz. Learn about its role as a storehouse for genetic information, the processes of DNA replication and RNA transcription, and the regulation of gene expression. Test your understanding of nuclear components and their significance in eukaryotic organisms.