Lec 3 slides and reading

Question 1

theory of evolution

Answer 1

accounts for the diversity of life, and explains similarities between different species

Question 2

Similarities between different groups of species

Answer 2

-Systems of biological classifications have been based on easily visible structural characteristics
-Species are essentially groups of similar individuals capable of interbreeding with each other
-Similar species are grouped in the same genus
-Another set of facts that strongly support the theory of evolution is provided by modifications of the same structure in different species
-E.g. bones of bats and birds wings indicate they are modified forelimbs; flippers of whales and fish fins, both well adapted for swimming

Question 3

Embryonic development

Answer 3

-Provides many examples of similarity between different groups of organisms, clearly suggesting descent from common ancestors

-Embryonic forms of different species are similar, even when the adults are different
-E.g. at one stage in mammalian development, structures appear that look like the developing gill slits of fish embryos → makes sense if we descended from fish-like ancestors

Since it’s the adult structures that adapt the organism to its environ, they usually get modified by selection

Question 4

Vestigial organs

Answer 4

remnants of structures that were functional in the ancestors of present day organisms

E.g. human appendix → reduced version of part of the digestive tract that’s bigger in orangutans
E.g. fossils of snakes have been found with hindlegs, showing snakes evolved from lizard-like ancestors

Question 5

Similarities in cells

Answer 5

-Basic feature of all animal, plant and fungal life is that their tissues are made up of cells
-Cells→ basis of bodies of all organisms other than viruses

In eukaryotes (all cellular non-bacterial life) the cells are organized into cytoplasm and nucleus within it that contains genetic material
Cytoplasm → contains complex set of tiny pieces of machinery with many subcellular structures
Mitochondria → generate cell’s energy
Chloroplasts → photosynthesis in green plants’ cells occurs

It’s now known that both of these are descended from bacteria that colonized cells and became integrated into them as essential components

Question 6

prokaryotes

Answer 6

bacteria that are cells but simpler with no nucleus or organelles

Question 7

viruses

Answer 7

viruses are the only non-cellular forms of life and are parasites that reproduce inside the cells of other organisms, and consist of a protein coat surrounding genetic material

Question 8

proteins

Answer 8

Proteins are enzymes that take a chemical and carry out a procedure for it (like chemical scissors)
-Also have storage or transport functions (haemoglobin in RBCs transports oxygen)
-Structural proteins (keratin) forms skin, hair and nails
-Communication proteins (hormones, signal to control cell behaviour during development)

Question 9

effect of mutations in the myosin protein gene

Answer 9

deafness

Question 10

how are enzymes categorized

Answer 10

Enzymes categorized by the jobs they perform (digestive enzymes snip molecules into pieces)

Question 11

process by which cells generate energy from food sources

Answer 11

In process by which energy generated by cells from food sources, there’s an energy source (sugar or fats) and goes thru chemical steps, some release energy

Metabolic pathway organized like an assembly line and enzymes carry out the different steps
Cells have pathways to make chemicals and to generate energy from foods

Question 12

what does the functioning of each chemical pathway depend on

Answer 12

Functioning of each biochemical pathway depends on enzymes
If any enzyme in pathway stops working → end product will not be produced
E.g. albino mutations result from lack of an enzyme necessary for production of pigment melanin

Question 13

what is stopping a pathway useful for

Answer 13

Stopping a step in a pathway is useful to control the output of cell machinery (cells contain inhibitors to carry out control functions - e.g. control of melanin production)

Question 14

dna structure

Answer 14

Sugar phosphate backbone (structure of DNA- sugars connected to nucleotides)
Nucleotides: adenine, guanine, cytosine and thymine: A&T, G&C
When DNA replicates during cell division, the 2 strands unwind and a complementary daughter strand is combined from each parent strand

Question 15

genes

Answer 15

Inheritance is the control of individuals’ characteristics by physical entities called genes (Gregor Mendel)

The genes that control the production of metabolic enzymes and other proteins(and thus determine individuals’ characteristics) are stretches of DNA carried in the chromosomes of each cell

Discovery that chromosomes carry genes in a linear arrangement was made in the fruitfly (Drosophila melanogaster)

Question 16

true or false: order of genes on a chromosome can be rearranged during evolution

Answer 16

true

Chromosome is a long DNA molecule encoding hundreds of genes DNA of a chromosome is combined with protein molecules that help package it in neat coils inside the cells nucleus

Each gene encodes a different protein
Chromosomes carry the info needed to specify the amino acid sequences of an organism’s proteins, together with the controlling DNA sequences that determine which proteins will be produced by organism’s cells

Question 17

What is a gene, and how does it determine the structure of a protein?

Answer 17

Gene is sequence of four chemical letters of the genetic code, in which sets of 3 adjacent letters (codons) correspond to each AA in the the protein for which the gene is responsible

Gene sequence is translated into the sequence of a protein chain (has triplets marking the end of the AA chain)

Change in sequence of a gene causes mutation (some mutation don’t change the protein sequence)

Across living organisms, the genetic code differs slightly, suggesting that all life on Earth has a common ancestor

Question 18

In order to produce its protein product, DNA…

Answer 18

DNA sequence of a gene is first copied into a ‘message’ made of RNA, whose sequence of letters is copied from the gene by a copying enzyme
RNA message interacts with proteins and other RNA molecules, to translate the message and produce the protein specified by the gene (occurs in all cells - in eukaryotes occurs in cytoplasm & message has to move outside of nucleus first)

Question 19

non coding DNA

Answer 19

In between genes on chromosomes are stretches of DNA that don’t code for proteins
Non-coding DNA acts as binding proteins that turn production of RNA messages of genes on or off as needed

E.g genes for hemoglobin are turned on in cells developing into RBCs but off in brain cells

Question 20

cell division

Answer 20

Single-celled organisms(amoeba or yeast) can reproduce by division into 2 daughter cells

Fertilized egg of a multicellular organism, produced by fusion of egg and sperm, divides into 2 daughter cells as well

Genes are turned on and off to ensure that the right kind of cell is produced in the right place at the right time

When a cell divides, the DNA of the chromosomes is first replicated, so that there are 2 copies of each chromosome
-Cell division is a process with tight controls to ensure that the newly copied DNA sequence undergoes ‘proof-reading’ for errors

Question 21

proof reading in RNA

Answer 21

Proof-reading that occurs in DNA replication does not happen when RNA is copied → viruses have high mutation rates and can evolve rapidly in host’s body

Question 22

mutations and their effects

Answer 22

If a mutation results in a change in the amino acid sequence of a protein, the protein may malfunction (not fold up correctly/unable to do its job)
If it’s an enzyme→causes metabolic pathway to run slowly or not at all
In structural or communication proteins→ impairs cell functions or organism’s development
Many diseases in humans are caused by mutations
E.g mutations in genes involved in controlling cell division →cause cancer
Can lower survival or fertility of affected individuals

Question 23

Gene sequence that leads to non-functional enzyme…

Answer 23

will be under-represented in next gen and will eventually be eliminated from population

Question 24

Mutations causing loss of function…

Answer 24

can contribute to evolution when selection no longer acts to eliminate them

Question 25

______ is the essential raw material on which NS acts to produce evolutionary changes

Answer 25

Genetic variability

Question 26

sources of evidence for evolution

Answer 26

geology, homology, biogeography, domestication

Question 27

endemism

Answer 27

things found somewhere that aren't found anywhere else

Question 28

endemism in Australia

Answer 28

isolated land mass has species there that aren't found anywhere else with unique adaptations

Question 29

convergent evolution

Answer 29

two organisms look or behave in a very similar way, even though they're only distantly related. This means they've independently evolved those similarities rather than inheriting them from a common ancestor. '

Question 30

how many different lines of evidence can we make sense of only by invoking evolution

Answer 30

Fossil Record: Fossils show a timeline of life on Earth and reveal the progression of species through transitional forms, such as fossils of early hominids that show the gradual evolution of humans from apelike ancestors. Comparative Anatomy: The study of similarities and differences in the anatomy of different species. Homologous structures (e.g., the limb bones of humans, birds, and whales) indicate a common ancestor, while analogous structures (e.g., wings of bats and insects) result from convergent evolution. Biogeography: The distribution of species around the world makes sense in the context of evolution. For example, species on islands often resemble those on nearby continents, reflecting shared ancestry, while isolated ecosystems develop unique species. Molecular Biology: DNA sequence comparisons across species show clear patterns of relatedness, with more closely related species sharing more genetic similarities. This molecular evidence aligns with evolutionary theory and allows scientists to trace common ancestry. Embryology: The study of embryos reveals that many organisms go through similar stages of development, even when their adult forms are quite different. This suggests that they share a common developmental pathway inherited from a distant ancestor. Direct Observation of Evolutionary Changes: We can observe evolution in action, such as the development of antibiotic resistance in bacteria or changes in the size of beaks in finches on the Galápagos Islands in response to environmental pressures. Vestigial Structures: These are remnants of structures that served important functions in ancestors but are now reduced or functionless in modern species. Examples include the human appendix or whale pelvic bones. Genomic Evidence: Genome-wide studies show patterns of genetic variation that can only be explained by descent with modification. Gene duplications, mutations, and non-functional "junk" DNA provide evidence of evolutionary processes over time.

Question 31

how does new evidence about genetics and DNA evidence connect to Darwin

Answer 31

New Evidence: Darwin didn’t know about DNA, genes, or how traits were inherited, which left a gap in his understanding of the mechanism of evolution. With the discovery of DNA and the development of genetics, scientists found that traits are passed from generation to generation through genes, and random mutations in DNA can introduce new traits into a population. How It Fits: Genetics provides the mechanistic basis for Darwin’s theory of evolution. Mutation creates genetic variation, which natural selection can act upon. The concept of heredity that Darwin speculated on is now fully explained through our understanding of genes. No Inconsistencies: Genetics reinforces Darwin’s ideas by showing how traits are inherited and how new variations arise, perfectly fitting the theory of natural selection.

Question 32

how does new evidence about molecular biology connect to darwin

Answer 32

New Evidence: DNA sequencing has allowed scientists to compare the genetic makeup of different species. This has led to the discovery of homologous genes (genes shared between species) and molecular clocks (the rate at which mutations accumulate), which provide precise data on the evolutionary relationships and the timing of divergence between species. How It Fits: Molecular biology has allowed for greater precision in mapping evolutionary lineages and divergence times. The genetic similarities between species (such as humans and chimpanzees) confirm common ancestry, which Darwin proposed based on anatomical similarities. No Inconsistencies: The genetic evidence aligns closely with Darwin’s concept of common descent, supporting the evolutionary tree he envisioned.

Question 33

how does new evidence about the molecular clock connect to darwin

Answer 33

New Evidence: By measuring the rate at which mutations accumulate in DNA, scientists can estimate the time when two species last shared a common ancestor. This concept, called the molecular clock, wasn’t available in Darwin’s time. How It Fits: The molecular clock has allowed scientists to date evolutionary events more precisely, offering a timeline that complements fossil evidence. No Inconsistencies: Molecular clocks provide a timeline that aligns well with the fossil record, confirming the ages of divergence Darwin could only estimate roughly.

Question 34

how does new evidence from the fossil record connect to darwin

Answer 34

New Evidence: Since Darwin’s time, many new transitional fossils have been discovered (e.g., Tiktaalik as a transitional form between fish and amphibians, or feathered dinosaurs that bridge the gap between reptiles and birds). How It Fits: These fossils provide concrete evidence of the gradual changes Darwin proposed. Transitional forms show how one species evolved into another, illustrating the gradual process of evolution. No Inconsistencies: The new fossil discoveries provide physical evidence of the “missing links” Darwin predicted, further validating his theory.

Question 35

how does new evidence of genomics and comparative genomics connect to darwin

Answer 35

New Evidence: Whole-genome comparisons across species have revealed deep genetic relationships, with even distantly related organisms sharing significant portions of their DNA. The study of non-coding DNA and shared endogenous retroviruses (ERVs) also provide evidence of common ancestry. How It Fits: Genomics has provided fine-scale data on how closely related species are and has uncovered patterns of evolutionary history encoded in the genome itself. This allows us to trace ancestry and evolutionary events with great precision. No Inconsistencies: Genomic evidence consistently supports Darwin’s tree of life and deepens our understanding of the genetic relationships between species.

Question 36

how does new evidence of developmental biology connect to darwin

Answer 36

New Evidence: The field of evolutionary developmental biology has revealed that small changes in the timing, location, or expression of genes during development can lead to major changes in an organism’s form. Genes that control development (such as Hox genes) are shared by many organisms and have evolved to produce a diversity of forms. How It Fits: Shows that evolution can occur by modifying existing developmental pathways, rather than by creating new structures from scratch, which fits with Darwin’s idea of modification of existing traits. No Inconsistencies: This field reinforces Darwin’s principle of descent with modification by explaining how complex forms can evolve from simpler ancestors through changes in gene regulation.

Question 37

how does new evidence of direct observations of evolution relate to darwin

Answer 37

New Evidence: Darwin didn’t have direct experimental evidence of evolution happening in real-time, but today, we can observe it. For example, we’ve seen bacteria evolve resistance to antibiotics and finch beaks change size in response to environmental pressures in the Galápagos. How It Fits: These real-time observations confirm Darwin’s ideas about how natural selection operates. We can directly see evolution in action, such as mutations providing advantages and becoming more common in a population. No Inconsistencies: These observations provide real-world examples of Darwin’s mechanisms at work.

Question 38

evidence of evolution in fossils

Answer 38

fossils in younger strata increasingly resemble modern species in same region -older strata show increasing differences (descent with modification)

Question 39

homology

Answer 39

similarity of traits in 2 or more species that is due to inheritance from a common ancestor (shared ancestry) -same structure, different function

Question 40

vestigial structures

Answer 40

-features inherited from an ancestor, but reduced in morphology and function -homologous to functional structures in related species -not required for survival

Question 41

vestigial traits relating to evolution

Answer 41

provide evidence of the evolutionary past -have no function (or reduced function) in surviving organisms -can only be explained by the presence of functional traits in ancestors followed by evolutionary degradation

Question 42

evidence from biogeography - galapagos

Answer 42

-flora and fauna colonized from mainland South America -species capable of long-distance dispersal -distinct forms on different islands provide evidence of early stages of speciation

Question 43

speciation

Answer 43

one species splits into 2 -factors cause them to become too different to mate = considered diff. species

Question 44

species vary locally

Answer 44

appearance depends on environ and evolved adaptations

Question 45

how does australia demonstrate high endemism

Answer 45

has many species found nowhere else in the world -isolated from other land masses

Question 46

biogeographically isolated regions

Answer 46

-have species adapted to niches unusual for their group -harbor endemic radiations of species that are convergent(evolved independently, look similar) with radiations elsewhere