Biology and the origin of life Flashcards
what is science?
Science is an attempt to understand the
world around us with a logical and
structured approach
what is biology?
Biology is a subset of science that aims to
understand the living world, it is also known as “The Science of Life”
what is the scientific method?
Interpret results, Forming hypotheses
make new —-> (tentative explanation;
observations testable, falsifiable)
/ /
Test hypotheses
what is Empiricism
knowledge should be
derived from experience and
sensory evidence, not innate ideas
and traditions
What are the reoccurring themes in the study of life?
- Organisation » Molecule › Cell › Tissue › Organ › Organism › Population › Community › Ecosystem › Biosphere - Information: DNA, the genetic material - Energy and matter » Use of energy, recycling of matter - Interactions » At every level of organisation - Evolution
why is evolution is the core theme of Biology?
Theory of Evolution provides a unifying concept that explains much of the
living world
Details of evolution are often misunderstood, why?
- Evolution is NOT goal oriented
- Natural selection is NOT the only mechanism of change. Mutations, gene flow and genetic drift are also powerful evolutionary forces.
what does theory mean?
A scientific Theory is a general, verifiable principle that explains many observations (“general law”)
how long ago did earth form and what was the first period of the earth?
Earth formed ≈ 4.6 BYA (billion years ago)
First, 0.5 BYA was a period of intense
bombardment
» Moon formed 4.5 BYA
what was the initial atmosphere of earth?
The initial atmosphere of methane, hydrogen,
ammonia and water vapour
When did life first appear?
Life appears ≈ 4.2 BYA
» Simple prokaryotic cells (“proto-cells”), similar
to today’s bacteria
What are the four main organic molecules
Amino acids → protein
» Nucleotides → nucleic acid
» Simple sugars → carbohydrate
» Fatty acids → lipid
What are biological macromolecules?
Biological macromolecules are polymers of
small organic molecules
What is Abiogenesis?
The leading scientific hypothesis
» The conditions of the early Earth made it possible for life to spontaneously form from non-living material
» Inorganic molecules → small organic molecules →
macromolecules → proto-cell
What is Step 1 of Abiogenesis?
Step 1 – Create organic molecules:
- Organic molecules today can only be created by living organisms
- Organic compounds degrade quickly in an oxygen-rich (“oxidising”) environment
- Oparin & Haldane (1920s) - early earth had a reducing
environment: very little oxygen, but plenty of hydrogen (H), methane (CH4), ammonia (NH3) and water vapour (H2O)
what proof is there that life could have formed on early earth?
- Experiment in 1953 by Miller and Urey
- Simulated early Earth conditions
» Hydrogen (H)
» Methane (CH4)
» Ammonia (NH3)
» Water vapour (H2O)
» And energy! - Created several organic molecules,
including amino acids - in just a couple
of days!
What is Step 2 of Abiogenesis?
Step 2 - Polymerisation
- Miller Urey proved organic molecules created
from inorganic compounds in early Earth environment
» Reducing atmosphere, high energy input
- In a liquid environment and with some energy input, this “primordial soup” of organic molecules self-assembles into more complex macromolecules
» Amino acids → proteins
» Nucleotides → nucleic acid, esp. RNA
» Fatty acids → lipid vesicles
what must all living organisms be able to do?
» Organise biological molecules on a higher level » Access and use energy (metabolism) » Grow » Respond to their environment » Reproduce (store and retrieve biological information to create copies)
What was the first genetic material on earth?
RNA, because it is able to encode information and
assume a variety of shapes determined by nucleotide sequence
What is step 3 of Abiogenesis
Step 3 –A protective layer
- Phospholipids (type of fatty acid with phosphate
group) are amphipathic
- In water, they will form micelles and eventually
self-assemble into sacs called vesicles
What is the simple recipe for life?
- Step 1 – Provide enough energy and starting material to create small organic molecules
- Step 2 – Join them into macromolecules
» Pick the one that can self-replicate (eg, RNA) - Step 3 – Wrap it in a flexible package that provides stability (phospholipid membrane)
What is the Panspermia hypothesis?
Panspermia is the evolution theory that Life did not originate on Earth:
» Problem: Creation of single-stranded RNA requires
borate and molybdate, both of which were unlikely to be found on Earth … but were common on Mars
» Observation 1: Plenty of evidence of inter-planetary
exchange (eg meteorites)
» Observation 2: Organic compounds are present in
meteorites (eg Murchison meteorite)
» Hypothesis: Life started on Mars and came to Earth on a rock.
What is a Polymer?
A substance that has a molecular structure built up from a large number of similar units bonded together
How are polymers synthesises and broken down?
Synthesised by dehydration reaction
broken down by hydrolysis
What are Carbohydrates used for?
Fuel and building material
What are Lipids used for?
- (Not true polymers)
- Various functions, mostly structural
- Share a “dislike” for water (“hydrophobic”)
- Various, but most biologically important:
» Fat: glycerol with up to 3 fatty acids
» Phospholipid: component of cell membrane
» Steroids: membrane, hormone precursor
What are proteins used for?
Wide range of structure and functions
What are nucleic acids (DNA, RNA) used for?
Store genetic information
what are the different kinds of proteins?
Enzymatic proteins: selective acceleration of chemical reactions
Defensive proteins: protection against diseases
Storage proteins: storage of amino acids
Transport Protein: transport of substances
Hormonal Protein: coordination of activities of organism
Receptor proteins: response of cell to chemical stimulus
Contractile and motor protein: movement
Structural protein: support
what are ribosomes?
- RNA capable of performing biological function
including self-replication
Why are proteins better than just RNA?
- RNA is only capable of limited shapes and the shape
determines the function!
Proteins (polymers of AA) produce much greater variety of shapes
» Proteins thus replaced RNA over time as they are better at performing a much wider variety of biological functions
what is the typical AA structure and how many AA’s make up all proteins?
R =20 AA’s make up al
H | O proteins
\ | //
N —- C —- C
/ | \
H H OH
what kind of reaction links AA’s?
Dehydration reaction links C in carboxyl
group of one AA to N in amino group of
another
How many AA’s make up a single protein (usually)
Proteins usually made up of 200-300 AA,
but some much smaller, and some larger
» eg titins can be up to ≈ 30,000 AA
What are the four levels of protein structure?
- Primary structure: Linear polypeptide chain
- Secondary structure: α-helix and β-pleated sheets (due to hydrogen bonds)
- Tertiary structure: main 3D shape, formed by interactions b/w side chains
- Quaternary structure: interaction b/w protein sub-units
What is the Primary structure of a protein?
Simply the linear sequence of AA, eg.
» The smallest functional polypeptide
glutathione: Cys-Gly-Glu
» Transthyretin, a transport protein →
What is the secndary structure of a protein?
Segments of the polypeptide chain form coiled or folded patterns
due to hydrogen bonding within the peptide backbone
What is the teriary structure of a protein?
- Main 3D shape of the protein
- Affected by interactions between side chain (the “R-group”)
» Hydrophobic interactions: away from water and towards each other
» Hydrogen bonding: b/w polar R groups
» van der Waal forces: b/w non-polar R groups
» Ionic bonding: b/w + and - charged R groups
» Disulfide bridges: sulfur of cysteine R groups
What are two examples of the tertiary structure of a protein?
- Hemoglobin (alpha sub-unit)
- Proteinase K
What is the Quaternary structure of a protein?
- not all proteins require this
- Assembly of multiple sub-unit polypeptides
What determines the function of a protein?
AA’s determine the primary, secondary and tertiary structures. Therefore, AA sequence of a protein is the primary determinant of its function
What is a key factor in protein structure?
Structure depends on environmental conditions (pH, salt concentration, temperature)
What is protein denaturation?
In extreme conditions, weak chemical bonds can break leading to unravelling of protein:
- Loss of structure = loss of function
- This is why a high fever is dangerous
- Can sometimes be “renatured” when returned in normal condition (not always – eg, egg protein)
What are the Nucleic Acids?
- DNA: Deoxyribonucleic acid
» Encodes all information needed to create life’s diversity - RNA: Ribonucleic acid
» Has several roles, but most basic is to deliver information from DNA to sites of protein synthesis
What are the nucleotide bases?
» DNA: C, T, A, G
» RNA: C, U, A, G
What is polynucleotide?
when nucleic acid molecules bond together and form a chain
Who were Watson and Crick and what did they discover?
Watson and Crick using crystallography by
Rosalin Franklin, determined in 1953 that
DNA is formed by two intertwined strands
of nucleic acids: the DNA double helix
What is the broad structure of a nucleotide?
Phosphate-sugar backbone on the outside, paired nitrogenous bases on the inside (purine-pyrimidine)
What was Chargruff’s rule?
Chargraff’s rule (1950): if you analyse bases in DNA
of an organism, the percent A=T and percent G=C because A always pairs with T & G always pairs with C
What is strand directionality?
- In a double helix, there are two strands, 5’ to 3’ of one strand is opposite to the complementary strand, oriented in 3’ to 5’ direction.
- Two complementary strands run in opposite directions (“antiparallel”)
What is the role of DNA?
DNA carries hereditary information (the genetic code)
- Sequence of bases along DNA (and RNA) is unique for each gene
How does DNA replication work?
Three steps of DNA replication
» Double helix unravels
» Free bases bond complementary bases on original “template” strands
» Polymerisation connects the bases together, forming two new “daughter” strands
What is the difference between DNA & RNA?
RNA exists as single strands
» Pyrimidines: C, U (instead of T); Purines: A, G
How does complimentary base pairing in RNA work?
Occurs either b/w two RNA molecules or b/w two stretches of same RNA molecule → various 3D structures → various functions
What is mRNA?
- DNA serves as a template for RNA synthesis
- RNA copies the message of DNA and transports it to site of protein production
What are some roles of RNA?
- Messenger RNA (mRNA) is linear, and carries message from DNA to protein assembly site
- Protein assembly site: ribosome, a complex protein made up of ribosomal RNA (rRNA) and proteins, accepts the mRNA and produces the protein, with the help of …
- Transfer RNA (tRNA): translate gene language into amino acid sequence
What is a Codon
A nucleotide triplet, linked to specific amino acid
What is the Central Dogma?
Explains the flow of genetic information within biological systems, proposed by Francis Crick in 1958
What are viruses and what do they do?
- Viruses are strands of nucleic acid (RNA or DNA) with a protein coat and lipid envelope
- Viruses have evolved methods to reverse flow of information
» RNA → DNA (“reverse transcription”)
• Retroviruses (eg, HIV)
» RNA → RNA (“RNA replication”)
• Many RNA viruses replicate that way
What are the benefits of biotechnology?
- Understanding gene language can help us design specific proteins
- By introducing specific genes into organisms (GMO), we can:
» Develop high-yielding, disease resistant crops
» Develop new techniques of waste remediation (eg, GM bacteria that consume oil)
» Treat genetic diseases (“gene therapy”)
