IB Biology- Lessons 7 - 12

Light microscopy:

• colours?

• Living or dead?

• how to increase clarity?

natural colour

live specimen

fluorescent labelling

synthetic dyes

Electron microscopy

• colours?

• living or dead?

monochromatic

dead

Types of electron microscopy

Transmission electron microscopy

Scanning electron microscopy

Transmission electron microscopy

• pass electrons through a specimen to generate a cross-section image

Scanning electron microscopy

Scatter electrons over a surface to differentiate depth and map in 3D

Cryogenic electron microscopy

• what is it

• how is the resolution

• How to see internal cellular structures?

• freezing samples before viewing to generate images of comparable quality to x-ray crystallography

• near-atomic resolution

• freeze fracturing → cracking along a place and studying internal cellular structures (this was used to find integral membrane proteins)

Magnification formula

Image size = Actual size X Magnification

Characteristics of a prokaryotic cell when drawing

• plasma membrane

• capsule

• cytosol

• genophore

• 70S ribosomes

• plasmid

• flagellum

• pili

Characteristics of an animal cell when drawing

• cell membrane

• cytosol

• nucleus with pores

• nucleolus 

• golgi apparatus

• rough endoplasmic reticulum 

• smooth endoplasmic reticulum

• mitochondria

• lysosome

• 80S ribosomes

Characteristics of an animal cell when drawing

• cell membrane

• cytosol

• cell wall

• nucleus with pores

• nucleolus 

• large vacuole

• chloroplasts

• golgi apparatus

• rough endoplasmic reticulum 

• smooth endoplasmic reticulum

• mitochondria

• lysosome

• 80S ribosomes

Cells with many mitochondria…

• use energy

• eg: muscle cells, neurons

Cells with lots of ER

• secretory activity

• eg: Plasma cells

Cells with lysosomes

digestive processes

eg: phagocytes

cells with chloroplasts

photosynthesise

Endosymbiosis

• what is the theory

• evidence for the theory in mitochondria and chloroplasts

Eukaryota:

• endosymbiotic origin

• one cell engulf another

• prokaryotic characteristics in mitochondria and chloroplasts

Membrane – Double membrane (hints at vesicle)

Antibiotics – susceptible to antibiotics targeting prokaryotic characteristics

DNA - naked, circular DNA

Division- Divide in a similar fashion to binary fission

Ribosomes- 70S ribosomes

Benefits of multicellularity

one challenge of multiceelularity

• exceeding limits of surface area to volume ratios

• allows for cell differentiation

• cancer is bad

Sources of biological variation

• mutations in genetic code

• recombination during rearrangement in sexual reproduction

Discrete variation vs. continuous variation

Discrete = distinct categories

Continuous = exists on a continuum.

When species are defined as group of organisms with shared traits, they are classified into…

ranking units (taxa)

Binomial system format

Genus + species

Biological species concept

Organisms which can breed to produce fertile, viable offspring belong to the same species

Different species reproduce to make..

Hybrids

How can speciation occur from the biological species concept

Over time, a new species can form if members of a single species become reproductively isolated and begin to genetically diverge.

Limitations to biological species concept

• asexual reproduction in some organisms

  • eg: binary fission

• Horizontal gene transfer (plasmid exchange in bacteria)

• physically impossible for some populations to breed

• Geographical distance can make it so members of different populations cannot interact to breed.

• fossils

• Interlinked populations, where ends cannot breed

  • eg: species A can breed with species B, and species B with species C, but species A cannot breed with species C

Population definition

members of the same species in a specific area at the same time

Why is it hard to differentiate between populations and species?

• Genetic differences accumulate in different populations due to different environments.

How are bacteria classified into species?

• morphologically

• metabolic processes (aerobic; anaerobic)

• structures (gram positive or gram negative)

Asexual reproduction types

1. Parthenogenesis

   1. development of a mostly female gamete takes place without fertilisation

2. Vegetative propagation

   1. taking plant stems and growing them

      1. plant cutting

3. Binary Fission

   1. used by prokaryotic cells

Jumping genes are…

humans have sections of what DNA in them?

sections of DNA that can move around

viral DNA

Shared genomic trait within species

• chromosome number

• biological species concept requires organisms of the same species to have the same chromosome number

Why does chromosome number have to be the same according to the biological species concept?

• different number of chromosomes = cannot have fertile offspring

• hybrids are possible → but infertile

How must genetic information be organised for organisms to have fertile offspring?

• same chromosome numbers

• comparible sizes and gene loci patterns

chromosome fusion event between humans and chimpanzees

• which chromosomes

• evidence

• human chromosome 2 and chimpanzee chromosomes 12 and 13

• evidence:

  • length of 12 + 13 = that of 2

  • centromere position in 2 is where it it would be at 12

  • banding pattern of 12 matches that of p arm of 2

  • banding pattern of 13 matches that of q arm of 2

  • telomeric DNA at fusion site

  • ncDNA in 2 where 13’s centromere would’ve been

Karyotyping

• what is it

• how is it done

• the process of pairing and ordering the complete set of chromosomes within a cell to provide a snapshot of the organism’s genetic profile

• chemical inhibitor introduced (usually in metaphase) to arrest mitosis and see the condensed chromosomes / sister chromatids

What is the order of ranking in karyotyping

Largest chromosomes to smallest

Centromere position

Karyogram

an photograph that generates a visual representation of the chromosomes

Why is karyotyping useful?

• type of species

• chromosomal anomalies

• sex of organism

How are chromosomes identified?

• length

• banding patterns

• centromere position

Single nucleotide polymorphism

A mutation to a single nucleotide base in >1% of the population

Diversity in genome sizes

• eukaryotes vs prokaryotes

• plants vs animals

• relation to genomic complexity

• eukaryotes have larger genomes

• plant genomes can vary dramatically due to self-fertilisation and polyploidy.

• genome size is not an indication of genome complexity

genome size and chromosome relations

more genome size does not mean more chromosomes, or vice versa

Definition of genome

what does this include specifically?

All genetic information in an organism

• coding DNA

• ncDNA

• non-nuclear sequences 

  • eg: plasmids, organelle DNA

Whole genome sequencing purpose

• provides geneaological information

Benefits of whole genome sequencing

• identifying mutations that can cause health problems

• predicting genetic predispositions to diseases

• public health responses for epidemiological interventions for population groups

• evolutionary origin analysis

Why do we classify organisms?

• seeing if a new species has been discovered

• observing similarities with other species

• deducing common ancestry

• predicting features that undiscovered but related species should have

why is it hard to classify hybrids in traditional taxa?

• hybrids form over generations

• don’t have same amounts of DNA from each species

• hard to put into heirarchies

Ideal classification system should..

• follow evolutionary relationships

• group organisms with common ancestors

• be able to be used for predicting characteristics

Why is evolutionary classification good?

• natural relationships

• evolutionary history

• prediction of undiscovered species’ traits

Clade

group of organisms with common ancestry and shared characteristics / ancestral organism and its descendants

primitive traits

characteristics that have similar structure and function

were found in common ancestor

found in most members of the taxonomic group

derived trait

newly evolved trait

Parts of a clade

root - origin

node- speciation event

terminal branch- end of clade

Molecular clock

• comparing genetic material for the smae molecule across species

  • hybridisation of DNA

• finding number of mutations

• more mutations = more time

common issue with non-phylogenetic grouping

common characteristics from convergent evolution misinterpreted as common ancestry

evolution

change in heritable characteristics of a population / change in ratio of alleles in a population

heritable traits

passed down

acquired traits

environmental

evolution is facilitated by..

natural selection

Which molecules’ sequences are used for comparison to find mutations? Why / when?

ncDNA→ where most mutations happen. best means of compariosn

Amino acid sequences- change slowly, used for distantly related organisms

DNA or RNA→ used for closely related organisms

Evidence for evolution

• commonalities in DNA, RNA, or AA sequences

• selective breeding

What is selective breeding and how does it work?

• aritfiical selection for desired traits

• trait becomes more common over generations

• this is evidence of evolution

two examples of selective breeding

cows→ bigger backs, longer legs, better milk, more muscular

horses- lighter, faster, thinner

What are homologous structures + one example

structures similar in traits but can be different in function.

eg: human hands and bat wings

divergent evolution

development of different traits in species that have a common ancestor

Example of divergent evolution

Pentadactyl limbs for mammals, bird, amphibians, and reptiles. 

yet, different modes of locomotion. 

birds→ fly

horses→ gallop

whales→ swim

humans→ tool manipulation

Evidence for divergent evolution

adaptive radiation

adaptive radiation

new species rapidly diversify from an ancestral source, with each species adapted to utilise a specific niche

this is evidence for divergent evolution

convergent evolution

similar enviornmental pressures lead to the development of similar traits in species without common ancestry

shared traits with similar function from convergent evolution are called…

analogous traits

example of an analogous trait

wings in bird and insects

atypical cells

cells that do not follow the typical cell patterns

2 examples of atypical cells and how were they made

• red blood cells

  • no nucleus

  • during late stage of development in bone marrow, the part of the RBC with the nucleus is pinched off and destroyed by a phagocyte

• Phloem sieve tube elements

  • large pores in the dividing walls between adjacent cells

  • during sieve tube development the nucelus and most other cell contents break down, though the membrane stays

  • sieve tube elements are dependent to their adjacent companion cells to carry out their function (companion cells have the mitochondria and nuclei)

2 more examples of atypical cells

• skeletal muscle

  • groups of cells fuse together

  • nuceli stay. long columns of cells

• Aseptate fungi hyphae

  • large multinucleate structures formed by nucleus duplicating without cell division

Benefits of new evolution based classification methods

• Accuracy

• Morphology + convergent

• Direct comparison

• Reclassification

• New species

• Phylogenetic trees

• Homologous and analogous characteristics