BS101: Lecture 4 - Ultrastructure of DNA and Chromatin folding

How do Ribosomes make proteins?

Use info from DNA to make proteins via DNA

How is mRNA made?

Transcription uses DNA to make mRNA

Where does Translation occur?

Ribosomes

How does Transaltion happen?

mRNA used to make peptides/proteins

What is the function of the Nucleus relating to separation of DNA?

Separates DNA from cytosol

What is the function of the Nucleus relating to Transcription & Translation?

Separates Transcription & Translation

What is the function of the Nucleus relating to gene storage?

Stores genes on chromosomes

What is the function of the Nucleus relating to gene organisation?

Organises genes into chromosomes, allowing cell division

What is the function of the Nucleus relating to gene replication?

Organises uncoiling of DNA to replicate key genes

What is the function of the Nucleus relating to transport?

Transports regulatory factors & gene products via nuclear pores

What is the function of the Nucleus relating to mRNA production?

Produce mRNA that code for proteins

What is the function of the Nucleus relating to rRNA production?

Produce rRNA in nucleolus?

What is the function of the Nuclear Pores?

Regulate entry/exit of molecules from nucleus

Describe the Nuclear Lamina

Composed of protein filaments to maintain its shape

Describe the Nuclear Matrix

Consists of a framework of fibres

What is a function of the Nuclear Lamina relating to chromosomes?

Provides structural support for chromosomes

What is a function of the Nuclear Lamina relating to mitosis?

Essential in disintegration of nuclear envelope during mitosis

What happens to the Lamina when the nuclear envelope disintegrates in mitosis?

Depolymerised

What is LMNA?

Gene that codes for lamina

What happens if there is a mutation in the LMNA gene?

Progeria

What is Progeria?

Premature aging disorder

Describe what happens in LMNA mutation

Changes in the shape of cell nuclei

How can the effects of Progeria worsen?

Gets worse w/ age + affects cell’s ability to divide correctly

What is the Nucleoplasm?

Non-staining liquid/semi-liquid of the interphase nucleus which fills the space around chromosomes + nucleoli

Describe the composition of the Nucleoplasm

Primarily water, dissolved ions + complex mixture of molecules (nucleotides, enzymes)

What is a function of the Nucleoplasm relating to the Nucleus’ Organelles?

Acts as a suspension medium for nucleus’ organelles

What is a function of the Nucleoplasm relating to the Nucleus’ structure?

Maintains nuclear shape/structure

What is a function of the Nucleoplasm relating to transport?

Transports ions, molecules + substances important to cell metabolism & function

What are the Nuclear Pores?

Regulate entry/exit of molecules from the nucleus (eg proteins, RNA)

What can diffuse through Nuclear Pores?

Small proteins & ions

How are Large Proteins transported through the Nuclear Pore Complex?

Actively transported via transporter molecules

How do Transporter Molecules transport large proteins?

Bind to proteins + interact w/ nucleoporins as they pass through

What is the shape of the NPC?

Octagonal made from membrane-embedded proteins

What proteins are on the cytoplasmic surface?

Nucleoporins, extend into cytoplasm

What proteins are on the nuclear surface?

Protein filaments, extend inwards into nucleus forming nuclear basket

What is the Nucleolus?

Region where rRNA is transcribed and processed

What happens to the Nucleoli during Mitosis?

Disappear and reappear in new daughter cells

What are the identifiable compartments in the Nucleolus?

• FC

• DFC

• GC

Fibrillar centre, Dense fibrillar component, Granular component

What happens in the Nucleolus?

• Fibrillar Centre

• Dense Fibrillar Component

• Granular Component

• Protein + DNA complexes found in FC

• Ribosomal subunits made in DFC

• Ribosomes assembled in GC

What is Chromatin?

Complex of DNA and protein, found in nucleus

What are Histones?

Proteins responsible for 1st level of DNA packing in chromatin

Amino Acids in Histones

Lots of positively charged amino acids so bind easily to negatively charged DNA

How does DNA exist in non-dixiding cells?

As chromatin

Describe Chromatin in non-dividing cells

Uncoiled and randomly dispersed

How does DNA prepare for cell division?

• What phase?

• What happens?

• S phase

• DNA replicates then chromatin condenses into chromsomes

What is the makeup of Chromatin?

50% DNA + 50% Proteins (mainly histones)

What is the Eukaryote Genome packaged into?

Chromatin

Why is the Eukaryote Genome packaged?

Allows long DNA molecules fit into nucleus’ small volume

What is the Nucleosome?

Basic structural unit of chromatin

What is the result of further folding of the chromosome?

Produces visible metaphase chromosomes during cell division

What is the further folding of chromosomes caused by?

Interactions between H1 histone tails and DNA

What is the end product of the further folding of chromosomes?

30nm fibres

What do 30nm fibres form?

Loops

What do the 30nm Loops do when packing DNA?

Looped domains attach to chromosome scaffold proteins to make 300nm fibre

What happens to the 300nm loop domains when packing DNA?

Coil further to result in metaphase chromosomes, width 700nm

How do Chromosomes fold?

Always the same way so specific genes always in same region of chromosome

What is a Chromosome?

Discrete unit of the genome carrying many genes

What is the Chromosome comprised of?

Highly compacted chromatin

When do Chromosomes form?

During cell division to ensure all DNA is divided correctly/completely

What is the Karotype?

Complete set of chromosomes

What is a Chromatid?

Half of a chromatin

What state do Chromatin exist in?

Nucleosome state - histones are bound

What state are Chromosomes in when ready for mitosis?

Fully compacted

Which has a larger diameter, Chromosomes or Chromatin?

Chromosomes

Which has a larger folding magnitude, Chromosomes or Chromatin?

Chromosomes

What are the 2 types of Chromatin?

Heterochromatin and Euchromatin

What state are Chromosomes usually in?

Heterochromatin

What kind of process is the transition between active and inactive chromatin?

Dynamic

What converts chromatin between active and inactive?

Chromatin Remodelling Factors

How do Chromatin Remodelling Factors do their job?

Addition/removal of acetyl/methyl groups

What happens in Histone Acetylation?

Larger acetyl groups attach to positive lysines in histone tails

What is the effect of Histone Acetylation?

Loosens chromatin structure, promoting transcription

What is Methylation?

Addition of CH3 groups

What can methylation do?

Condense chromosomes, found in inactive heterochromatin

Describe Euchromatin

• Colour

• Condensing

• Packing

• Light colour, active

• Less condensed - transcriptionally active

• Lightly packed

What is the modification of Histones in Euchromatin?

More acetylated so looser packing

How does Euchromatin relate to interphase (Mitosis)?

Characteristic for interphase chromosomes - not condensed

Describe Heterochromatin

• Colour

• Condensing, packing - intertness

• Dark colour, inactive

• Highly condensed, tightly packed - transcriptionally inert

Modifications of Heterochromatin Histones

Methylated - tighter packing

Where is DNA usually found in chromosomes?

Centromere

How can Gene Expression be regulated?

Switching between the 2 types of chromatin

What does dense packing of heterochromatin mean for the cell?

Makes it difficult to express genetic info coded

What Nucleotide Base is this?

Cytosine

What Nucleotide Base is this?

Guanine

What Nucleotide Base is this?

Adenine

What Nucleotide Base is this?

Thymine

Termination of translation happens when…

Ribosome hits a stop codon on the mRNA.

Initiation of translation always happens at the…

start codon of the mRNA

Translation

Process by ribosome of reading mRNA and synthesizing a protein

Amino acids are attached to tRNA by enzymes called…

aminoacyl-tRNA synthetase

The RNA that has an amino acid attached to it, and that binds to the codon on the mRNA, is called a…

tRNA

If a DNA double helix is 100 nucleotide pairs long and contains 25 adenine bases, how many guanine bases does it contain?

• 200 total nucleotides

• A = T, 25 × 2 = 50

• 200 - 50 = 150, 150 / 2 = 75

Short segments of newly synthesized DNA are joined into a continuous strand by...

DNA ligase

The action of helicase creates…

Replication forks/bubbles

Why is the new DNA strand complementary to the 3' to 5' strands assembled in short segments?

DNA polymerase can assemble DNA only in the 3' to 5' direction

The synthesis of a new strand begins with the synthesis of a(n)…

RNA primer complementary to a pre-existing DNA strand

Label

• A = DNA ahead of the fork

• B = helicase

• C = primase

• D = DNA polymerase

• E = RNA prime

Beginning within the nucleus, the first step leading to the synthesis of a polypeptide is _____.    

transferring of information from DNA to messenger RNA

D - Prokaryotes lack membrane-bound organelles (like nucleus, ER, Golgi), while eukaryotes have them.

Sort these organelles into Prokaryotoes, Eukaryotes or both

Nucleoid, Ribosomes, Mitochondria, Nucleolus, Plasma Membrane, Flagella, Lysosome

P - Nucleoid, Flagella

Both - Ribosomes, Plasma Membrane

E - Mitochondria, nucleolus, lysosome