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1
Q

carbohydrates

A

Chemical compounds that contain carbon (C),
hydrogen (H) and oxygen (O) usually with a H:O ratio
of 2:1, and the empirical formula Cm(H2O)n

  • monosaccharides
    (Glucose, Fructose,Galactose)
  • disacharides
    (sucrose, lactose, maltose)
  • oligosacharides
    (raffinose, stachyose)
  • polysacharides
    (starch, glycogen, cellulose)
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2
Q

lipids

A
  • Heterogeneous group of organic
    compounds that are insoluble in
    water and soluble in non-polar
    organic solvents.
  • Part of cell membranes
  • Help control what goes in and out
    of cells.
  • Help with moving and storing
    energy, absorbing vitamins and
    making hormones
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3
Q

nucleic acids

A
  • Principle information molecules of the cell
    (genetic machinery of the cell)
  • Two main types:
    DNA: Deoxyribonucleic acid
    RNA: Ribonucleic acid
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4
Q

proteins

A
  • The ‘doers’ of the cell
  • Execute the tasks assigned by the genetic
    information.
  • Most diverse macromolecules in the cell.
  • Proteins direct virtually all activities of the cell.
  • Amino acids
  • Peptides
  • Polypeptides
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5
Q

what gave rise to the first cell?

A

Theory: Enclosure of self-replicating
RNA in a phospholipid membrane gave rise to the first cell.

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6
Q

def: genes

A

Genes: segments of DNA that encode RNA (or proteins) – functional
units of inheritance

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7
Q

def: transcription

A

Transcription: Process by which nucleotide gene sequence is copied
into RNA

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8
Q

def: translation

A

Translation: Nucleotide sequence of RNA is used to specify the
order of amino acids in a protein

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9
Q

def: archaea

A

Archaea: Found in the ocean and also extreme environments
(E.g. Extreme thermophiles, halophiles, acidophiles etc.) Cell
walls lack peptidoglycan.

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10
Q

def: bacteria

A

Bacteria: Wide range of environments (soil, water, other
organisms) Cell walls usually present and contain peptidoglycan

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11
Q

def: cyanobacteria

A

Cyanobacteria: Largest/most complex prokaryotes; bacteria in
which photosynthesis evolved

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12
Q

Escherichia coli (E. coli)

A

Rod-shaped (bacillus)

Rigid cell wall: polysaccharide and peptides;
maintains shape and provides some protection
against osmotic stress; porous

Plasma membrane: phospholipid bilayer and
associated proteins

DNA: single circular chromosome in nucleoid (not
membrane-enclosed)

Ribosomes: sites of protein synthesis, ~30,000 found
in the cytoplasm

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13
Q

def: nucleus

A

Nucleus: Largest organelle; Contains linear DNA molecules; Site
of DNA replication, RNA synthesis

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14
Q

def: mitochondria

A

Mitochondria: Sites of oxidative phosphorylation; generate ATP

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15
Q

def: chloroplasts

A

Chloroplasts: Sites of photosynthesis, only found in plants/some
algae

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16
Q

def: lysosomes

A

Digestion of macromolecules

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17
Q

def: peroxisomes

A

various oxidative reactions

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18
Q

def: vacuoles

A

-Plant cells; digestion of macromolecules, storage (waste products and
nutrients)

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19
Q

def: endoplasmic reticulum (ER)

A

Membrane network extending from the nuclear envelope; Protein
processing and transport; Lipid synthesis

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20
Q

def: golgi apparatus

A

Receives proteins from the ER; Protein processing and sorting; Lipid
synthesis (plants), cell wall polysaccharide synthesis

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21
Q

def: cytoskeleton

A
  • Network of protein filaments
    extending throughout the cytoplasm
  • Provides structural framework
  • Determines cell shape and
    organization
  • Involved in movement of whole cells,
    organelles, and chromosomes during
    cell division
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22
Q

Endosymbiotic Theory

A

Eukaryotic cells may have arisen from a fusion of genomes from Bacteria and the Archaea

EVIDENCE:
Mitochondria and Chloroplasts:
— Similar to bacteria in size;
— Reproduce by dividing in two;
— Contain their own genetic systems (DNA ,RNA and ribosomes);
— Double membranes

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23
Q

what are the 3 main tissue systems in plants?

A
  1. Ground tissue:
    Parenchyma cells – site of
    metabolic reactions, including photosynthesis.
    Collenchyma and sclerenchyma – have thick cell
    walls and provide structural support
  2. Dermal tissue:
    Covers the plant surface;
    Protective coat; Allows absorption of nutrients
  3. Vascular tissue:
    Xylem and Phloem – elongated
    cells that transport water and nutrients throughout
    the plant
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24
Q

what are the 5 main tissue types in animals?

A

More Diverse than plants with 5 main tissue types:

1.Epithelial cells: form sheets that
cover the surface of the body and
line internal organs

  1. Connective tissues: Include
    bone, cartilage, and adipose
    tissue. Loose connective tissue is
    formed by fibroblasts
  2. Blood: Several cell types
    * Red blood cells (erythrocytes) for oxygen transport
    * White blood cells (granulocytes, monocytes, macrophages, and lymphocytes) for
    inflammatory reactions/immune response
  3. Nervous tissue: Composed of supporting cells and nerve cells (neurons), and
    various types of sensory cells
  4. Muscle cells: Production of force and movement
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25
Q

yeasts

A
  • Simple Eukaryotes
  • Model for fundamental studies of
    eukaryote biology

S. cerevisiae (most commonly studied yeast):
12 million bp DNA (6,000 genes)

Distinct eukaryotic features:
- membrane-enclosed nucleus,
- genomic DNA arranged in 16 linear
chromosomes,
- subcellular organelles in cytoplasm

Fast doubling time

Mutants have expanded understanding of:
- DNA replication
- Transcription
- RNA processing
- Protein sorting
- Regulation of cell division

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26
Q

C. elegans (nematode)

A
  • Relatively simple, multicellular eukaryote
  • 100 million bp DNA (19,000 genes)
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27
Q

Drosophila melanogaster

A

The fruit fly D. melanogaster has been a crucial model organism
in developmental biology

180 million bp DNA (14,000 genes)

Easily maintained and bred in the laboratory

Short reproductive cycle (2 weeks) – genetic experiments

Embryos develop outside

Short lifespan (monitor development)

Advances in understanding the
molecular mechanisms in animal
development – body plan of complex
organisms

Parallels between genes in Drosophilia
and vertebrates

Wound healing, tissue regeneration,
drug discovery, genetic disease,
Parkinson’s disease research,
neurodevelopment

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28
Q

Arabidopsis thaliana

A
  • Relatively simple organism: suitable
    model organism for study of plant
    molecular biology and development
  • 125 million bp DNA (26,000 genes,
    unique 15,000)
  • Easily grown and genetically
    manipulated in the laboratory
  • Used to elucidate mechanisms such
    as flower development in higher
    plants
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29
Q

Induced Pluripotent
Stem Cells (iPSCs)

A

■ Take adult skin biopsy
■ Grow cells in tissue culture
■ Treat with special cocktail of
chemicals to reprogram
■ Cells forget they were skin
cells and revert to basic stem
cells
■ Can be programmed into any
cell type

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30
Q

HeLa cells

A

■ First immortalised human cell
line.
■ The oldest and most commonly
used human cell line in scientific
research.
■ Derived from cervical cancer
cells taken on February 8, 1951,
from named Henrietta Lacks, a
31-year-old African-American
mother of five, who died of
cancer on October 4, 1951
■ HeLa cells have an active version of
telomerase during cell division, which copies telomeres over and over again
■ Prevents the incremental shortening of telomeres that is implicated in aging and eventual cell death
■ Results in unlimited cell division and immortality

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31
Q

how many elements are essential for life?

A
  • About 26 of the 92 elements are
    considered essential for life
  • Carbon, hydrogen, oxygen and
    nitrogen make up 96% of living
    matter
  • Most of the remaining 4% consists
    of calcium, phosphorus, potassium
    and sulfur
  • Implications for amino acids and
    thus protein composition
32
Q

hydrogen bonds

A

Weak intermolecular interactions between partial
charges on polar molecules

Collectively forms a strong bond; individually can
form and break easily as they are individually
relatively weak bonds

Often represented as dashed or dotted lines

e.g. H-bonds between certain amino acid side chains and between C=O and N-H of amino acids in alpha helices and beta sheets

33
Q

van der waals’ forces

A
  • Interactions between non-polar amino acid side
    chains.
  • Allow even non-polar groups to form favourable
    electrostatic interactions with one another.
  • Non-polar bonds can have a transient polarity and
    induce a transient polarity on a neighboring non-polar
    bond.
  • VdW forces are especially important in the
    hydrophobic interior of a protein.
34
Q

Hydrophobic effect

A
  • Not a force per se, however considered the major
    driving force for the folding of globular proteins.
  • Hydrophobic interactions cluster hydrophobic groups
    away from water (think of oil and water not mixing).
  • Non-polar amino acids have a strong tendency to
    cluster together, away from water, allowing very
    favourable H-bonds to form between water and
    hydrophilic amino acid residues
35
Q

how are units of macromolecules grouped together?

A

Single units = Monomers

A few units joined together = Oligomers

A large number of monomers joined = Polymers

36
Q

nucleic acids

A
  • Principle information molecules of the cell
  • Two main types: DNA and RNA

DNA: Deoxyribonucleic acid
- The genetic material of all life (except some viruses)

RNA: Ribonucleic acids
- Messenger RNA (mRNA) carries information from DNA to the ribosomes
- Ribosomal RNA (rRNA) and transfer RNA (tRNA) are involved in protein
synthesis
- Other RNAs involved in regulating gene expression and processing transport of
RNAs and proteins (miRNA, lncRNAs, etc)
- RNA can also catalyse some chemical reactions

37
Q

The chemical structure of nucleic acids

A

Nucleotides:
■ 5 - carbon sugar
- DNA = deoxyribose
- RNA = ribose
■ Nitrogenous base
■ 1 or more phosphate groups linked to the 5’ carbon of the sugar

DNA and RNA are polymers of nucleotides

38
Q

Nucleic Acids: Nitrogenous bases

A

Purines: Adenine and Guanine
Pyrimidines: Cytosine, Thymine (DNA only) and Uracil (RNA only)

Base pairing:
Occurs between pyrimidines and purines

DNA
A = T
G ≡ C

RNA
A = U
G ≡ C

39
Q

Nucleic Acids: Phosphate group

A
  • Attached to the 5’ carbon on the 5-C-sugar
  • 1 or more phosphates attached

Example:
ATP (Adenosine triphosphate) the principal form of
chemical energy within cells.

40
Q

Other Nucleotides:

A

■ Nucleotides are not exclusively
found in DNA or RNA
■ Can be involved in other
biochemical processes and
pathways within the cell.
■ e.g. ATP, AMP, dAMP, cAMP

41
Q

Nucleic Acids : Polymerization & Directionality

A
  • Polymerisation of nucleotides involves phosphodiester bonds between the 5’
    phosphate of one nucleotide and the 3’ hydroxyl of another
  • Gives polynucleotide chains a sense direction: polynucleotides are always
    synthesized in the 5’ to 3’ direction
  • Dehydration synthesis: production of a H20 molecule during the reaction
  • Oligonucleotides are polymers of only few nucleotides
  • RNA and DNA are polynucleotides and may contain thousands or millions of
    nucleotides
  • RNA mainly single stranded
  • DNA double stranded
42
Q

3D structure of DNA

A
  • Double helix
  • Polynucleotides formed by phosphodiester
    bonds
  • Strands run anti-parallel * H-bonds pair the bases on opposite strands,
    which run antiparallel
  • Bases are on the inside * Inert sugar-phosphate backbone on outside * Structure stabilized by Hydrogen bonds
43
Q

Nucleic Acids: Complementarity / Double Helix

A
  • Information in DNA and RNA is always conveyed by the order of the bases
  • DNA is made up of 2 polynucleotide chains that run anti-parallel to each other
  • Complementary base pairing allows one strand of DNA (or RNA) to act as a
    template for synthesis of a complementary strand
  • Nucleic acids are thus capable of self-replication
  • The information carried by DNA and RNA directs synthesis of specific proteins,
    which control most cellular activities
  • While DNA was first discovered and isolated by Friedrich Miescher in 1869, it
    would take another 75 years before it was shown to hold the genetic blueprint
    of life…
44
Q

DNA is the genetic material and the
‘transforming principle’

A

Griffith’s experiment (1928):
There is a substance (transforming principle) in cell extracts that is
capable of transforming a non-pathogenic bacterial strain into a
pathogenic form

Avery, MacLeod and McCarthy Experiment (1944):
Digestion of cell extracts with proteases, carbohydrates and RNAse
did not destroy the transforming principle but treatment with DNAse
did -> DNA is the transforming principle

Hersey-Chase Experiment (1952):
Radio-labelled DNA (but not protein) from bacteriophages entered
bacterial cells upon infection -> DNA is the genetic material

45
Q

The role of messenger
RNA

A

While DNA had been shown to determine the
order of amino acids in a protein sequence, it
did not infer/prove that DNA itself directs
protein synthesis

Experiment by Brenner, Jacob and Meselson
determined that RNA and not ribosomes are
the intermediate messenger molecule
between DNA and proteins

– identified messenger RNA (mRNA)

In addition to mRNA, two other types of RNA molecules are involved in
protein synthesis: transfer RNA (tRNA) and ribosomal RNA (rRNA)

46
Q

the genetic code

A

64 different codons:
61 specify amino acids
3 are used as stop signals

— Universal: used by all
organisms

and

— Redundant: multiple
codons for most amino
acids

47
Q

Expression of Genetic Information

A

The order of the bases (A, T, G and C) must specify the genetic
information but how exactly does this determine protein
structure?
1957 Sickle-cell anaemia studies:
First link between genetic variation and an alteration to the
amino acid sequence (Glutamic acid (charged)->Valine
(hydrophobic))
Patients with this inherited disease had altered haemoglobin
molecules resulting from a single amino acid substitution.
Indicates that possibly some variation in the DNA sequence
correlated to a change in the amino acid sequence (GAG-
>GTG)
i.e. order of DNA nucleotides determines the order of amino acids
■ With few exceptions (some viruses contain RNA instead of DNA), all
organisms utilize the same genetic code—strong support for the
conclusion that all present-day cells evolved from a common ancestor.
■ The mode of replication of viral RNA was determined by studies of RNA
bacteriophages of E. coli.
■ These viruses encode an enzyme that catalyzes synthesis of RNA from
an RNA template (RNA-directed RNA synthesis).
■ Most animal viruses replicate in this way, but one group (RNA tumor
viruses) requires DNA synthesis in infected cells.
■ These viruses (now called retroviruses) replicate via synthesis of a DNA
intermediate, a DNA provirus.
■ Reverse transcriptase can be used experimentally to
generate DNA copies of any RNA molecule.
■ This has allowed mRNAs of eukaryotic cells to be
studied using the molecular approaches currently
applied to the manipulation of DNA.

48
Q

Reverse transcription

A

■ This hypothesis was initially met with disbelief
because it reverses the central dogma.
■ Later, an enzyme that catalyzes synthesis of DNA from
an RNA template (reverse transcription) was
discovered (reverse transcriptase enzyme).
■ Reverse transcription has other broad implications.
■ It also occurs in cells and is frequently responsible for
transposition of DNA from one chromosomal location
to another

49
Q

Unicellular Genomes

A
  • In bacteria, most of the DNA encodes proteins (little non-coding DNA), often arranged in operons (groups of genes with related function expressed together)
  • The E.coli genome is twice the size of H. influenzae: contains 4.6 Mb
    and 4,000 genes (90% of DNA is protein-coding)
  • Simplest eukaryotic genome is Saccharomyces cerevisiae (yeast):
    contains 12 Mb and 6,000 genes (70% of DNA is protein-coding; only
    4% of its genes have introns)
50
Q

the human genome

A

Number of protein-coding genes: 21,000 (1.2 % of genome)
Very unexpected result (Estimated 100,000)
40% of human proteins are related to proteins in simpler
eukaryotes; most involved in basic cellular processes
Most unique proteins have similar domains to other species
but arranged in different combinations
Mice, rats, and humans have 90% of their genes in common
Humans and chimpanzees share ~ 98.8% DNA similarity

51
Q

Human Accelerated regions (HARs)

A

■ HARs represent conserved genomic loci with elevated divergence in humans.
■ ~ 3,000 of human accelerated regions: enriched in genes related to DNA
interaction, transcriptional regulation and neuronal development.
■ If some HARs regulate human-specific social and behavioral traits, then
mutations would likely impact cognitive and social disorders.
■ NPAS3 (neuronal PAS domain-containing protein) gene contains 14 HARs.
■ NPAS3: Brain-enriched transcription factor
(Maria V. Suntsova & Anton A. Buzdin, BMC Genomics, 2020)

52
Q

Introns

A
  • Found in most, but not all eukaryotic genes (not found in histone genes)
  • Rarely found in prokaryotic genes (90% of DNA is protein-coding)
  • Found in both plants and animals
  • Present in low numbers in yeast (70% of DNA is protein-coding)
  • Intermediate number in C. elegans, Drosophila and Arabidopsis

Introns and Exons
Similar observations soon made on cloned eukaryotic genes

Sequencing of cloned DNAs and cDNAs (complementary DNAs) indicated that the coding region of the mouse β-globin gene is interrupted by two
introns that are removed from the mRNA by splicing

53
Q

The amount of DNA in Introns can be greater than Exons

A

Average human gene has 56,000 base pairs (56 kilobases, kb);
contains about 10 exons with 4.3 kilobases-kb

Introns make up >90% of the average human gene

Additional 3’ or 5’ untranslated regions (UTRs) within the exons

54
Q

Roles of Introns

A

Many introns encode functional (non-coding) RNAs and a very small
amount encode proteins (nested genes)

Others contain regulatory sequences that control transcription and
mRNA processing
- regulatory sequences very important for expression of
different genes in different cell types in a complex organism.

Allow exons of a gene to be joined in different combinations –
alternative splicing; this gives rise to different proteins from the
same gene

Alternative splicing is common in complex organisms

Human genes: Alternative splicing can yield between 2 and several
thousand different mRNAs per gene; Average 6 alternatively spliced
mRNAs; Average 4 different proteins per gene

55
Q

Non-coding Sequences
ENCODE Project (2003 - present)

A
  • Investigation of function in the
    human genome
  • Non-coding regions don’t encode
    protein; but they are not ‘junk DNA’
  • Roles in: - gene regulation
  • structure and replication of eukaryotic chromosomes
  • evolution of eukaryotic genome
  • Undiscovered roles? Hot bed of research – are there keys to disease
    mechanisms and novel therapies in this DNA (eg. MiRavirsen for Hep C)
56
Q

What is in non-coding sequences?

A

ENCODE project (2003-present)
Discovered that 75% of the human genome is transcribed
This cannot all be accounted for by protein-coding genes

Includes:
* Some non-coding RNA molecules produced (tRNAs, rRNAs, long noncoding RNAs and others)
* Pseudogenes

!!! Many of the genetic alterations responsible for inherited
diseases may be due to mutations in non-coding regions,
rather than in the protein-coding region itself !!!

57
Q

Repetitive Sequences

A

Highly repeated DNA sequences account for a large proportion of
complex eukaryotic genomes (100s-1000s of copies per cell)

Include: Simple-sequence repeats and LINEs or SINEs

58
Q

Repetitive Sequences: Simple-sequence Repeats

A

Up to thousands of copies (repeats) of short sequences (1-500
nucleotides) arranged in tandem along a section of the chromosome

Can be separated on a density gradient based on their GC:AT ratio

Repeat sequence DNAs band as “satellites”, separate from main DNA
band (satellite DNAs)

Simple-sequence repeats are not transcribed (40% of Drosophila
genome, 10% of human genome)

Role in chromosome structure

59
Q

Repetitive Sequences: SINEs and LINES

A

Other repetitive DNA sequences are scattered (interspersed) throughout the genome as opposed to being arranged in tandem repeats on a chromosome

Their transpositions into random sites, introducing mutations; expected to be harmful to the cell (eg. Cystic fibrosis, muscular dystrophy, inherited cancers)

Short-interspersed elements (SINEs): 100-300 bp; 13% of genome; transcribed; unknown function

Long-interspersed elements (LINEs): 4-6 kb; 21% of the genome; transcribed; some encode proteins (e.g. reverse transcriptase) but unknown function

Both SINEs and LINEs are examples of transposable elements
(capable of moving to different sites in genomic DNA)

SINEs and LINEs are retrotransposons as their movement to other parts of the genome involves reverse transcription (RNA ® DNA)

60
Q

Repetitive Sequences:
Movement of Retrotransposons

A

Retrotransposons (e.g. LINEs and SINEs) account for at least 34% of
human genome

Function/Effect on the Genome:
Depends on their new integration location:
- May disrupt the expression of a gene and lead to some inheritable
disorders (cystic fibrosis, hemophilia etc.) or cause some cancers
- Contributes to genetic diversity as can regulate the expression of
nearby genes following transposition

61
Q

Other Repetitive Sequences

A

Retrovirus-like elements also move within the genome by reverse transcription; 2-10kb; 8% of human genome

DNA transposons move through the
genome by being copied and reinserted as
DNA sequences; no reverse transcription;
80-3,000 bp; 3% of human DNA

62
Q

Gene Duplications: Gene Families and Pseudogenes

A

Genomes can contain multiple copies of many genes (some are
non-functional). Why?

May be required to produce large amounts of certain proteins or
RNAs (e.g. histones, rRNAs)

Members of a group of related genes (a gene family) with altered
functionality and may be transcribed in different tissues or at
different stages of development

Other members will have undergone mutations that result in loss
of function; non-functional gene copies called pseudogenes
-> evolutionary relics; increase genome size (~11,000 in humans)

Example: Hemoglobin – α and β subunits are both encoded by gene families in the genome, with different members being expressed in embryonic, fetal
and adult tissues

Gene duplication can arise by:
1. Duplication of a segment of DNA resulting in the transfer of a
block of DNA to a new location in the genome, or
2. Duplication by reverse transcription of an mRNA, followed by integration of the cDNA copy into a new site on a chromosome
(retrotransposition) – similar mechanism to that used in
transfer of repetitive elements; this can lead to an inactive gene
copy (processed pseudogene) with no introns or chromosomal
sequences that direct transcription

63
Q

Eukaryotic genomes

A

■ Autosomes: Any chromosome that is not a sex chromosome (X or Y chromosome). Humans have 22 pairs of autosomes.
■ Most eukaryotic cells (somatic cells) are diploidand have two copies of each autosomal chromosome and two sex chromosomes.
■ Sex cells (gametes) are haploid (one copy of each chromosome and one sex chromosome.

64
Q

Diploid vs Haploid cells

A

Chromosomes were proposed as carriers of genes

Most cells of higher plants and animals are diploid (2n)

Meiosis gives rise to haploid cells (n)

Fertilisation gives a diploid organism (2n)

Experiments carried out with Drosophila melanogaster demonstrated that while some
traits are independent of each, other traits are inherited together (genetic linkage).

65
Q

def: karyotype

A

A photograph of the complete diploid set of chromosomes groups in homologouspairs and arranged in order of decreasing size

66
Q

Chromosome painting

A

Different staining techniques can be
used to distinguish chromosomes and have been used to map chromosome regions and genes.

G-banding: By staining with Giemsa
heterochromatin (AT-rich) stains darkly forming G-bands, while less densely packed euchromatin (GCrich) stains more lightly forming R bands.
Q-banding: Quinacrine banding.
C-banding: constitutive heterochromatin.

67
Q

Chromosomes (Mitosis)

A
  • As cells enter mitosis, chromosomes become highly condensed for distribution to the daughter cells
  • Loops within interphase chromatin fold upon themselves and condense
    10,000 fold to highly compact
    metaphase chromosomes
  • No longer transcriptionally active
  • Exact folding has not been defined but it appears to be highly reproducible
68
Q

Centromeres (Mitosis)

A

Centromere:
Specialised region of the chromosome that plays an integral role in ensuring the correct distribution of duplicated chromosomes to daughter cells during mitosis
Interphase: DNA is replicated – 2 copies of each chromosome
(humans: 46 chromosomes become 46 pairs of sister
chromatids)

69
Q

Centromeres

A

Centromere is a constricted chromosomal region:
- Site where sister chromatids are joined
- Attachment site for microtubules of the mitotic spindle fibers

Kinetochore:
Specialized structure formed by proteins at the centromere; Proteins form attachment between chromatid and microtubule, and also act as
motors to move chromatid along spindle fibers to poles of cell

Aside from yeast, specific eukaryotic DNA sequences that mediate centromere function have not been identified.

Centromeres do have a unique chromatin structure

In centromeres:
- Histone H3 is replaced by a H3-like variant (CENPA/Centromere Protein A)
- CENP-A is found in all studied eukaryotic centromeres
- CENP-A containing nucleosomes are required to assemble other kinetochore proteins

70
Q

Assay of a centromere in yeast
(Saccharomyces cerevisiae)

A

DNA sequences of centromere
regions were first defined in yeast
Followed the segregation of plasmids
during mitosis
* Functional centromeres: equal
plasmid distribution among
daughter cells
* Non-functional centromeres:
many daughter cells fail to inherit
plasmid DNA
Identified sequences important for
centromere function

71
Q

Epigenetic inheritance of CENP-A

A

Unique chromatin structure allows
centromeres to be stably maintained at cell division

Example of epigenetic inheritance

Epigenetic inheritance is the transfer of information to progeny that is not based on DNA sequences. The information is carried on the histones

When chromosomal DNA replicates, the parental nucleosomes are distributed to the 2
progeny strands

These CENP-A-containing nucleosomes direct
the assembly of new CENP-A-containing nucleosomes into chromatin

72
Q

Telomeres

A

Telomeres are the sequences at the ends of eukaryotic chromosomes

Critical roles in chromosome replication and maintenance

Identified after it was noted that broken chromosomes were
highly unstable in eukaryotic cells – must be some specific sequences needed at the ends (termini) of chromosomes to confer stability

Tetrahymena (protozoan)
-Telomeres from Tetrahymena were added to the ends of linearised yeast plasmid DNA
-Plasmids gained the ability to replicate in a linear form
-Conclusion: Telomeric DNA sequences are required
for the replication of linear DNA molecules

-DNA sequences of telomeres from
various eukaryotes are similar
-Repeats of simple-sequence DNA;
clusters of G residues on one strand
-Repeated 100s-1000s of times

Telomere maintenance may be
important in determining the
lifespan and reproductive capacity
of the cell

73
Q

Telomerase

A

The ends of linear chromosomes cannot be replicated by DNA
polymerase

DNA polymerase extends a growing DNA chain (Lecture 5) but it cannot start replicating from the end (terminus) of a linear DNA
molecule

Telomerase plays a critical role in replicating the ends of linear DNA
molecules

Telomerase: Reverse transcriptase enzyme that replicates telomeric
DNA sequences

Because of their importance in reproductive capacity and cellular
lifespan, telomeres and telomerase are the subject of many aging
and cancer studies

74
Q

Chromatin

A

Chromatin: complexes between eukaryotic DNA and proteins

Experiments using nuclease (an enzyme that breaks down
DNA (DNAse)) to digest chromatin yielded nucleosome core
particles (beads on electron microscopy):

Nucleosome:
- 147 base pairs; 1.67 turns around a histone core
- Histone core: 2 molecules of H2A, H2B, H3 and H4 (core histones)
-Basic structural unit of chromatin
-DNA wrapped around a histone core
-Described by Roger Kornberg (1974)

Chromatosome:
- 166 base pairs; 2 full turns around the histone core
- held in place by one molecule of histone H1 (linker histone)

  • Chromatin condensation has an important role in regulating gene
    expression
  • Two forms of chromatin: Euchromatin and Heterochromatin
  • Euchromatin: chromatin is less condensed and distributed throughout the nucleus; most interphase chromatin exists in this form (cells are not dividing); transcription is active; DNA can be replicated ahead of cell division
  • Heterochromatin: chromatin is in a highly condensed state; 10 % of
    interphase chromatin is heterochromatin; transcriptionally inactive; can contain highly repeated DNA sequences or genes that are not expressed in those specific cells
75
Q

Histones

A

Major proteins of chromatin
- Small, basic proteins (high arginine/lysine content)
- Facilitates binding to negatively charged DNA
- Five major types (H1, H2A, H2B, H3, H4)
- Highly conserved among eukaryotes

76
Q

Fluorescence in situ hybridization
(FISH):

A

a kind of cytogenetic technique which uses fluorescent probes to bind parts of the chromosome that show a high degree of sequence complementarity. Fluorescence microscopy can be used to find out where the fluorescent probe bound to the chromosome

77
Q

Non-coding DNA and gene regulation

A

■ Looping of DNA to bring long-range
regulatory elements close together.
■ Local (cis) gene regulation
■ Cross-chromosome (trans) gene
regulation

molecular biology of the cell (1 decks)

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