Biology Study Blog

This is my study blog for BIOL10005 at the University of Melbourne. I google image or screen shot from my lectures all the pictures on this page and do not claim to own any of them. If you find my blog helpful thats great :) I love science!

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Summary of Protists (because I hate them)

Eukaryotes not belonging to plant, animal or fungal kingdoms and have a variety of ways of gaining nutrition

Can be uni/multicellular or colonial and have many cellular forms including flagellates and plasmodia

Majority are aquatic and have flagella or cilia

Gain nutrition by photosynthesis, parasitism, predation and absorption

First eukaryotic organisms were probably similar to modern day protists

The nuclear membrane and endomembrane system probably evolved from infolding of the bacterial cell membrance that enveloped the nucleoid. Plastids and mitochondria are derived from endosymbiotic bacteria that have become organelles in eukaryotic cells.

Major eukaryotic lineages, such as animals and fungi, arose from different protist lineages, but many more independent protist lineages exist

choanoflagellates - animals

slime moulds - fungi

Photosynthetic protists, commonly called algae, are diverse and not all related.  Primary plastids arose in the 'green lineage' which includes glaucophytes, red algae and green algae

Glaucophytes - photosynthetic flagellates with primitive chloroplast that have a peptidoglycan wall like bacteria

Red Algae - multicullular and lack flagella, contain chlorophyll a ad phycobilin pigments

green algae - unicellular, colonial and multicellular forms, contain chlorophyll a and b

Secondary plastid acquisitions created an enormously diverse new array of protists, some which abandoned photosynthesis to become heterotrophic or parasitic

Chromists (cryptomonads, coccolithophorids, diatoms, brown algae, oomycetes) 

characterized by flagellar architecture and secondary plastids, typically have one smooth posterior flagellum and one hairy anterior flagellum

most photosynthetic with chlorophyll a and c

oomycetes absorb food through hypae

cryptomonads clearly ingested eukaryotic cells, nucleomorph is relict nucleus of engulfed cell

Alveolates are unicells with distinctive vesicles, cortical alveoli, beneath the cell membrane

Dinoflagellates - 2 flagella, many photosynthetic containing chlorophyll a and c, some predatory

Apicomplexans - intracellular parasites of animals, cause diseases such as malaria, apical complex used to penetrate host cells

Ciliates - predatory unicells characterized by 2 types of nuclei and a covering of cilia

Euglenoids are closely related to flagellates that all have an anterior depression from which the flagella emerge

euglenoids are freeliving, some have cloroplasts and some engulf prey through anterior depression (gullet)

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Evolution of the Eukaryotic Cell

What do we know about the origin of the Eukaryotic cell?

1.3 - 2 billion years before the present

mechanism of evolution is not known

There is good evidence for the origin of mitochondria and chloroplasts from primary endosymbiosis

The first Eukaryotic cells to evolve were protists and they are an extremely diverse group of organisms.

When do Eukaryotic cells first appear in the fossil record?

Precambrian acritarch fossils are the first known of eukaryotic cells – about 1.3 – 2 billion years old.

Multicellular (filamentous), eukaryotic organisms appear about 1.4 billion years ago

Early seaweed fossils – from 635 million years ago

Where did Eukaryotic cells come from?

It is generally thought that eukaryotes eveolved from prokaryotic organisms.

The nuclear membrane and endomembrane system of eukaryotes probably evolved from a prokaryote where invaginations of the bacterial cell membrane enveloped the nucleoid.

Mitochondria and plastids (or choloroplasts, but choloroplast usually refers to 'green plastids' reseverved for plants or green algae) of eukaryotes arose by endosymbiosis, which refers to an organism living inside another.

Plastids derive from cyanobacteria and mitochondria are descended from purple bacteria. Plastids and mitochondria are derived from endosymbiotic bacteria that have become organelles in eukaryotic cells.

Mitochondria --> animals & fungi

Chloroplasts (Plastids) --> green algae and plants 

What is the Key Evidence for the Endosymbiotic Origin of Mitochondria and Chloroplasts?

Mitochondria and chloroplasts are semiautonomous, retaining their own genome (DNA, RNA). Their genomes resemble those of prokaryotes (i.e., purple bacteria, cyanobacteria)

They also retain their own machinery for synthesizing proteins, including ribosomes.

Their metabolism is like existing prokaryotic organisms (e.g., a cyanobacteria for chloroplast).

ftsZ protein involved in division of prokaryotes and organelles

Some chloroplasts still have the bacterial peptidoglycan wall between the inner and outer membranes.

Protists with primary chloroplasts have 3 genomes, while all protists with secondary chloroplasts have either 3 or 4 genomes.

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Cyanobacteria

Green and purple bacteria lack PSII, do not use H20 as a source of electrons and, therefore do not produce oxygen. With the evolution of cyanobacteria came PSII, which provided the mechanism for using H20 as a source of electrons and provided the earth with an atmosphere that includes oxygen.

Cyanobacteria contain chlorophyll a and water soluble pigments called phycobilins. Blue phycobilins, present in most species give them a blue-green appearance.

Cyanobacteria have specialised cells such as akinetes and heterocysts. An akinete is a spore that develops from a cell which becomes enlarged and filled with food reserves. The spore can remain dormant and then germinate to produce a new filament. A heterocyst is relatively colourless, has a thick, transparent cell wall, may be involved in asexual reproduction and is a sige of nitrogen fixation.

What characteristics do Cyanobacteria share with chloroplasts?

Their photosynthetic thylakoids contain chlorophyll A, as do all chloroplasts.

Their accessory pigments, phycocyanin and phycoerythrin, are found in the chloroplasts of several protists.

Chloroplast genomes show they are related to Cyanobacteria

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Classification

TAXONOMY: description and naming of organisms, which leads to

CLASSIFICATION: recognizing groups of related organisms and naming the groups, which leads to…

PHYLOGENY: the evolutionary history of an organism.

Ultimately, we hope that our classifications reflect phylogeny.

Carl Linnaeus (1707-1778) formalized use of the “binomial”, where each individual organism is known by a Genus and species name.

Order of classification

Kingdom

Phylum

Class

Order

Family

Genus

Species

There are often intermediate taxa such as subclass, subgenus etc.

The 6 kingdoms

Bacteria

Archaea

Protista

Plantae

Fungi

Animalia

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Earth History and the Evolution of Life

Three super kingdoms: Bacteria, Eukarya and Archaea.

Earth is approximately 4.5 billion years old with fossil records having bacteria between 3-3.5 billion years ago.

Cellular life must have originated in the first 1 billion years of earth history.#

The Origin of Life in Primitive Oceans

Primitive Oceans - a dilute, hot, smelly soup of ammonia, formaldehyde, formic acid, cyanide, methane, hydrogen sulfide and organic hydrocarbons.

UV light contributed to organic synthesis, yet UV light also destroys organic molecules.

Therefore, life evolved in the oceans, protected by water that filters out the UV.

A cooler early earth means more time for the evolution of the first cells via chemical evolution.

What do we know about the First Cells?

were prokaryotic

were heterotrophs

are not in the fossil record

First fossils reveal photosynthetic Cyanobacteria, which eventually changed the earth’s atmosphere forever by generating oxygen.

Snowball earth possibly could have arisen 2 billion years ago and and just over half a billion years ago.

The cambrian explosion occured around 500 million years ago and saw a rapid movement in evolution especially large animals.

Evidence for Evolution

Palaeontology and the fossil record

Comparative anatomy of cells and organisms

Embryology

Comparative biochemistry and molecular biology

Structure of DNA, gene sequences

Comparing Molecules

Understanding the role of DNA in protein synthesis gave rise to the idea that the sequence of amino acids in a polypeptide chain is a molecular record of the gentic information and evolutionary history of an organism. 

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Detecting Variation

Variation can be at the phenotypic level through to the molecular level.

look for visible differences in the phenotype

chromosome differences eg., length of long arm of Y

immunological markers eg., blood groups

protein gel electrophoresis eg., esterases in Drosophila

SSLPs (Simple sequence length polymorphisms) or VNTR (variable number of tandem repeats)

STR or (short tandem repeats)

Single nucleotide polymorphisms (SNP)

Discontinuous Variation

mid digital hair present or absent

blue or green budgerigar

black or brown dog

Variable regions often in non-coding regions

Minisatellites 15 -100b (eg., tandem repeat of 18 bases) total length from 1-5kb.

Microsatellite short tandem repeats (STR): 2 - 9 bases – can have several alleles according to how many repeats

Single nucleotide polymorphism (SNP) 1 base – can only have two alleles at a locus

VNTR (variable number of tandem repeats)  Minisatellites

In non coding regions of the genome

Repeat sequence between 15bp -100bp long

But number of repeats varies from person to person so VNTR can be from 1 - 20kbs in length

Multilocus probe (found in more than one location)

–  minisatellites –  eg., tandem repeat of 18 bases total length from 1-5kb.

Single locus probe – minisatellites (as above) – microsatellite - short tandem repeats (STR) - 2 - 4 bases

Application Identification

Paternity

Forensic analysis – Crime

Matching after a disaster

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Epigenetics

Changes in gene expression that do not involve a change in DNA sequence.

Epigenetic modifications alter chromatin structure in a variety of ways without changing the DNA including:

DNA methylation

Histone acetylation

RNA interference

Methylation

In tissue-specific genes or time-specific genes the enzyme DNA methyltransferase adds a methyl (CH3) group to the 5’ carbon of cytosine

When the CpG islands are methylated a gene is switched off

DNA methylation is reversible

Methylation and Gene Expression

CpG islands are approx 1000-2000bp in length and a series of these CG dinucleotides are found in the ‘island'

CpG = dinucleotide of G and C, p = phosphodiester link between them

In housekeeping genes (switched on all the time) the CpG islands are unmethylated so the gene is continuously expressed

Chromatin modification of histones Amino acids at the N terminal of the histone can be modified by:

Methylation (Me)

Acetylation (Ac)

P phosphate groups (phosphorylation) 

Histone modification is reversible

Unmethylated and Acetylated histones allow genes to be expressed. Methylated and de-aceylated histones stop genes from being expressed. 

Example include

X-inactivation

genomic imprinting

Genomic Imprinting

some genes are affected by whom you inherit the gene from, mother or father

sex of transmitting parent produces observable differences in the phenotype

specific genes are differentially marked during parental gametogenesis

Reversible and reverses in gametogenesis

Evidence for genomic imprinting

Triploids (3N) with: 2N paternal + 1N maternal are different from

2N maternal and 1N paternal

Prader willi syndrome and Angelmann Syndrome

deletion of paternal 15q11-q13 causes PWS

deletion of maternal 15q11-q13 causes AS

same region but different outcome! (genomic imprinting)

Some genes in this region of chromosome 15 are only expressed only from the maternal or paternal chromosome. Described as monoallelic expression.

Other causes

Uniparental disomy (UPD)

chromosomes of a pair come from the same parent.

In PWS, the two chromosome 15s are maternal (missing a paternal copy of chromosome 15)

In AS, the two chromosome 15s are paternal (missing a maternal copy of chromosome 15)

A. Heterodisomy - non disjunction meiosis I

B. Isodisomy - non disjunction meiosis II

Imprinting

Due to methylation

 If a male inherits a maternal imprint but passes to his daughter the imprint changes (therefore not inherited)

Wiped in primordial germ cells but re-established according to the sex of the parent

so new methylation pattern according to the sex of the parent (may be different from what parent had)

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Examples of Gene Mutations

Cystic Fibrosis ΔF508 mutation accounts for 70% of mutations in Caucasian populations, mutation is deletion of 3 bases in DNA coding There are currently 1913 mutations listed for CF in the database including: nonsense, missense, frameshift, insertion/deletion, splicing 

beta-Thalassaemia Missense mutants – changes amino acid Nonsense mutants - introduces stop codon Frameshift mutants - e.g. deletion of 2 bases at codon 8  Splicing mutants - Single nucleotide changes create new splice site, extended exon 2 

Huntington Disease

Defect in gene is a triplet (3 base) repeat (CAG) <35 repeats normal (most 17-20)

27-35 rare but unstable when transmitted via a male

36 - 41 indeterminate (reduced penetrance)

40-50 most adult cases

>50 generally juvenile onset

Earlier onset and more severe if inherited from father 

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Reading Frame Mutations

Mutations are any alteration in DNA sequence from a single base pair substitution, deletion, insertion or several base pairs or a major alteration in the structure of a chromosome

Mutations can occur in coding and non-coding regions of the genome.

Coding mutations can affect the gene product

Non-coding mutations can affect the expression of the gene

Coding regions of genes

Three types of base substitution mutation, defined by the effect on the gene product  

Silent: No change in the gene product

Missense: Amino acid substitution in the gene product

Nonsense: Premature termination of translation (chain termination)

Silent mutations: A change in the third base of a codon may not alter the

expression or the functioning of a gene or a gene product because of the wobble of the code.

UCA

UCG

UCC

UCU

All code for serine

Missense mutation: A mutation that changes the nucleotide sequence of a codon so that it encodes a different amino acid.

Nonsense mutation: A mutation the nucleotide sequence of a codon so that it becomes a stop codon and causes premature termination of translation.

Frameshift mutation: A mutation that removes or adds a number of nucleotides not equal to multiples of 3 (i.e mutations that disrupt the normal sequence of codons). The code is out of phase after the mutation, therefore almost all the amino acids are altered downstream.

Mutations can also include deletion or insertion where whole nucleotide can be deleted or inserted.

Illustration of concept:

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Difference between Eukaryote and Prokaryote RNA processing

Eukaryote

Prokaryote

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The Genetic Code

Read in threes from a fixed starting point - triplet code

Each three bases in mRNA = codon

20 amino acids therefore the code is degenerate

The genetic code is non-overlapping 

Synonymous codons are groups of codons which all code for the same amino acid

There are stop codons (UAA UAG and UGA) There is a start codon (AUG) (occasionally another codon GUG or UUG)

DNA sequences may be transcribed but not translated. mRNA is the only RNA to be translated into a polypeptide.

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RNA processing in Eukaryotes

In prokaryotes the primary transcript is mRNA.

In eukaryotes the primary transcript is modified and processed into mRNA.

The ends of the transcript are treated for stability and binding to the ribosome

The mRNA is commonly spliced , the introns are removed and the exons (expressed sequences) joined up to make the final transcript 

Naming of Strands

Template strand is transcribed into a complementary mRNA sequence but the sequence on the mRNA is similar to the non template strand except U instead of A

The non template strand is called the coding strand and is often used when showing a sequence because it represents the mRNA sequence

Non template strand is referred to as the coding strand

Depending on which exons are cut out during splicing can produce different effects.

Alternative splicing of the same primary transcript can lead to different polypeptides from the same DNA sequence.

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Transcription

DNA repliction --transcription/processing--> mRNA --translation--> Polypeptide

Transcription

A gene consists of the coding sequence and regulatory sequences

Only one strand of the DNA double helix in a given gene codes for the polypeptide = template strand

only 1 strand is a template strand from which the mRNA is manufactured

Either strand may be a template but transcription to form new RNA occurs in a 5’ to 3’ direction

For a particular gene, it is always the same strand which is the template, and it depends on which way the mRNA is produced

Initiation - promoter recognition RNA polymerase binds to promoter regions and this determines where RNA synthesis begins 

RNA polymerase binds and DNA is denatured in this region

DNA strands separate

First RNA nucleoside triphosphate is placed at the site

Elongation Addition of complementary nucleotides 

RNA moves along DNA template strand adding bases 5’ 3’ to growing RNA strand

Bases are complementary to the DNA template

Termination RNA polymerase reaches a chain termination sequence. This is a sequence which can form a loop.

RNA polymerase and mRNA are released

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Ribonucleic Acid

RNA is a usually single stranded, nucleic acid, composed of nucleotides. Its sugar is ribose and its bases are: adenine, uracil, cytosine & guanine.

Types of RNA

messenger RNA (mRNA): formed during transcription from a DNA template

ribosomal RNA (rRNA): rRNA and protein combine to form ribosomes

transfer RNA (tRNA): carries amino acids to the ribosome in translation, anticodon matches with codon of mRNA, specific amino acid for each anticodon attached to 3’ end

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DNA Manipulation

Denaturing DNA DNA can be made single stranded by:

heating to 80 degrees +

adding a strong alkali 

Once single stranded (ss) DNA will hybridise (join) with other complementary ss DNA or RNA.

e.g RNA probe AAAGCTTGCCCA will find and hybridise with TTTCGAACGGGT

Restriction enzymes Bacteria have DNA which cleave (cut up) DNA of the virus so it can't take over, protecting its own DNA.

Type II restriction enzymes cut DNA within a specific sequence of bases called a recognition sequence which hydrolizes the phosphodiester bonds.

If the enzymes cut zigzag or diagonally through DNA it will produce 'sticky ends', if the enzymes cut straight through it will produce 'blunt ends'.

Gel Electrophoresis The gel can be used to separate DNA fragments of different sizes 

Smaller fragments move further

fragments move towards either positive/negative end

Transformation Plasmids are self-replicating, circles of DNA, which occur naturally in bacteria cells. 

They can be transformed by being cut by an enzyme and a new fragment of DNA re-joining the ends together, so the plasmid now incorporated the new piece of DNA.

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Pedigrees and Inheritance

Rules

Can't be Y-linked if: - a female affected - father to son inheritance not 100%   

Can't be dominant if: - trait skips a generation - e.g normal parents have an affected child

Can't be recessive if: - both affected parents have an unaffected child

Can't be X-linked recessive if:  - affected mother has a normal son - normal father has an affected daughter

Can't be X-linked dominant if: - affected father has normal daughter - normal mother has an affected son 

Unlikely to be autosomal recessive if it is a rare disease and it appears frequently in the pedigree.

X-linked recessive generally more males than females affected (e.g colour blindness)

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Polygenes

Multi-factorial traits with discontinuous distribution of phenotypes (result of many factors, genes and environment but phenotype is either present or not e.g blood group either A, B, AB or O)

e.g spina bifida

usually a threshold between a combination of genetic predisposition and accumulating environmental factors which once reached the trait shows

can have different threshold for males and females so more common in the sex with the lower threshold

  Quantitative traits with continuous distribution of phenotypes e.g height, volume of milk, thickness of wool etc

Polygenic inheritance

many gene loci contributing to the phenotype of the quantitative trait

each locus has two alleles eg., A1 & A2

no dominant phenotype

alleles are inherited in a similar way to any other trait

allele A1 adds to trait contributor

allele A2 does not add to trait non contributor

the effect of the alleles is cumulative

eg., If A1 adds 1cm to height then A1A1 = 2cms

looks like incomplete dominance from F1 but F2 shows difference  

As the number of genes controlling a phenotypic character increases the differences between phenotypic classes becomes less distinct.

To calculate number of polygenes: (1/4)^n = proportion of F2 that resemble the parents, where n = no. polygenes.  NB: Only use one of the groups that resembles the parents 

Heritability: A statistical measure of how strongly the phenotype of the offspring will resemble the phenotype of the parents.

To measure heritability in humans we look at twins and if only one twin has a trait, non concordance, if both have the trait, concordance.