IB Bio - Origins of Life

origin of water on earth

many collisions occur with water-rich asteroids

goldilocks zone

habitable zone and refers to the orbital distance from a star that will result in liquid water

the two gases that formed the majority of earth’s early atmosphere

methane and ammonia

when life originated

between 3.5 and 3.9 years ago

temperature on early earth

75 to 95 degrees celsius

LUCA

hypothetical last universal common ancestor

capsid

protein shell of a virus that surrounds and protects the genetic material

virus

small infectious particles

virus traits

• capsid

• dna or rna as genetic material

• few or no enzymes

• 20 to 500 nm

single-stranded RNA

HIV

double-stranded RNA

rotavirus

single-stranded DNA

parvovirus

double-stranded DNA

bacteriophage lambda

viral envelope

membrane made of lipids and proteins that surrounds the capsid

obligate intracellular parasites

living organism that lives in or on a host that’s restricted to a certain function or mode of life and dependent on host cell

endosome

membrane-bound vesicles, formed by the process of endocytosis

receptor-mediated fusion

the process by which a virus binds to a receptor on a host cell membrane to fuse with the host cell membrane and enter the cell

lytic cycle

a viral reproductive cycle involving rapid production of viral progeny which lyse and destroy the cell

viroids

an infectious entity affecting plants that viruses may have evolved from

transposons

sequences of nucleic acid (DNA or RNA) that are able to move position within the genome

convergent evolution

pattern of evolution where distantly related organisms evolved similar traits in response to environmental similarities which viruses are thought to demonstrate

horizontal gene transfer

the process viruses can do that is the exchange of genetic material between individuals that does not involve reproduction

dna replication

copying of dna to create a new dna molecule

transcription

the process in which the dna is used as a template to produce rna

translation

the process in which the transcribed rna is translated by the ribosomes to produce proteins

purine

two ring compound. adenine and guanine

pyrimidine

one ring compound. cytosine, thymine, and uracil

histone

proteins around which eukaryotic dna is wrapped, forming nucleosomes. this organization helps regulate gene expression and protect the structural integrity of dna

nucleosome

structural unit of eukaryotic chromatin, consisting of dna wrapped around a core of histone proteins

what hershey and chase proved

that it was dna, not protein, that made up genetic material

what chargaff proved

that equal amounts of cytosine and guanine and equal amounts of adenine and thymine meant that dna was double helix

directionality

the orientation of polarity of a dna strand, referring to the 5’ (phosphate) to 3’ (hydroxyl) directionality of nucleotide addition during dna synthesis

leading strand

the dna strand that is synthesized continuously in the 5’ to 3’ direction during dna replication

lagging strand

the dna strand that is synthesised discontinuously in short fragments called okazaki fragments during dna replication

replication fork

the y-shaped structure formed during dna replication where the dna double helix is unwound and new strands are synthesised

okazaki fragments

short dna fragments that are synthesised on the lagging strand during dna replication and later joined together

helicase

unwinds and unzips the dna molecule by breaking the hydrogen bonds that hold complementary bases together

single stranded binding proteins

proteins that bind to and stabilize single-stranded dna during dna replication or repair

gyrase

enzyme that moves ahead of helicase to relieve tension created by unzipping the double helix

dna primase

attaches small rna primers to template strand which allows dna polymerase iii to attach

dna polymerase iii

assembles the new strands of dna by placing free nucleotides in the correct sequence. only able to build new strands in the 5’ to 3’ direction

dna polymerase i

removes dna nucleotides of the primers and replaced them with the correct dna nucleotides. also does dna proofreading

dna ligase

catalyses the formation of the phosphodiester bonds between the okazaki fragments

promoter

non-coding region of dna to which rna polymerase binds to initiate transcription

transcription factors

a group of proteins that bind in the correct orientation to the promoter so rna polymerase can bind and begin transcribing dna to rna

regulators of gene expression

non-coding regions that regulate gene expression. include enhancers and silencers

introns

non-coding regions in eukaryotic genes that get removed at the end of transcription

telomeres

non-coding regions that are repetitive sequences that protect the ends of the chromosomes. with every cell division, short stretches of dna are lost from the telomeres

genes for trna and rrna

these genes code for rna molecules that do not get translated into proteins, but instead fold to form trna or rrna

exons

coding regions within a gene that contain the instructions for synthesising a protein and are retained in the mature rna molecule

pre-mrna

initial rna molecule transcribed from dna which contains both introns and exons

5G cap

modified guanine nucleotide added to the 5’ end of pre-mrna during post-transcriptional modification, providing stability and assisting in mrna processing and transport

poly-A tail

multiple adenine nucleotides added to the 3’ end of a mrna transcript to protect and stabilise the molecule

splicing

the process of removing introns from pre-mrna and joining the exons together to produce mature mrna that can be translated into a protein

alternative splicing

a mechanism by which different combinations of exons within a gene can be spliced together to generate multiple mrna isoforms and increase protein diversity

three stages of translation

initiation, elongation, and termination

proteasome

protein complexes that degrade and recycle damages or unwanted proteins

genetic engineering

the process of altering the dna of an organism in order to introduce new characteristics, remove unwanted traits or modify existing ones

gene knockout

a genetic engineering technique in which a specific gene is intentionally made inoperative to study its function

crispr

a specific region of dna that is found in bacteria that contains short, repeated sequences and unique spaced sequences that are incorporated from foreign dna encountered by the bacteria

cas9

an endonuclease enzyme that can be used to cut dna at specific target sites on a chromasome

single guided rnas

a synthetic rna molecule that is used in the crispr-cas9 gene editing system that scientists have adapted for use in genetic engineering

conserved sequences

sequences that remain identical or similar across a species or a group of species over evolutionary time

highly conserved sequences

regions of dna or rna that exhibit an exceptionally high level of similarity across different species

homology

similarity or shared characteristics between different organisms, genes, or proteins due to their common ancestry

gene expression

the process by which genetic information is used to produce rna and proteins

phenotypic plasticity

the ability of an organism to exhibit variations in its physical characteristics or traits in response to environmental influences

stages in gene expression

transcription and translation

rna polymerase

enzymes that use a dna template to synthesise rna

activator proteins

specific types of regulatory proteins that bind enhancers to activating the transcription of nearby genes

operon

a group of genes that share a promoter

repressor proteins

transcription factors that can block the binding of rna polymerase or other transcription factors to a promoter, downregulating gene expression

epigenesis

the process by which cells and organisms differentiate through the interaction between dna and environmental factors

dna methylation

addition of a methyl group to dna

histone modification

addition of chemical groups to histone proteins

heterochromatin

the highly condensed and transcriptionally inactive form of chromatin

euchromatin

the less condensed and transcriptionally active form of chromatin

acetylation

the addition of an acetyl group to a molecule

epigenetic inheritance

the inheritance of non-genetic information that can influence gene expression and phenotypic traits