biology

The seven pillars of life

Program

Innovation

Compartmentalisation

Energy

Regeneration

Adaptability

Seclusion

Program

Living things must have a program in order to make copies of themselves from generation to generation

• E.g. DNA, heredity

Innovation

Ability of living organisms to adapt and evolve in step with external changes in environment

• Allows for optimisation for gradual changes in the environment

Compartmentalisation

Chemicals found within their bodies are synthesised through metabolic processes into structures that have specific purposes

• E.g. cells

Energy

Living things have ability to take energy from environment and change it from one form to another

• To facilitate growth and reproduction (metabolism)

Regeneration

Ability to replace parts of themselves that are subject to wear and tear, and all organisms degrade into a final non-functioning state; death

Adaptable

Ability to respond to environmental stimuli through feedback mechanisms

• React through behaviour, metabolism and physiological change

• Increases chance for survival

Seclusion

Ability to maintain metabolic reactions even in a single instance in time

2 step process in evolution

1. Variability

2. Ordering variability via natural selection

Darwin’s 3 observations

1. Individuals in a population vary - fitness

2. Pass on traits (fitness) to offspring - heredity

3. Never enough resources - competition for survival and reproduction

Variability definition and examples

Tendency of individual genetic characteristics in a population to vary from one another

• Size, colour, speed, camouflage, fecundity, aggressiveness, guile, strength

Heredity definition

Biological process of transmitting most physical and genetic traits from parents to offspring

Species definition

No universal agreement, most go with the ‘biological species definition’ (individuals of the same species can breed successfully)

Difficulties with biological specifies definition example

Bananas are unable to breed as they are grown from cutting; is each plant a separate species?

Flies example of speciation

• Flies fed either maltose food or starch food

• After many generations, two types of flies were released to each other

• Flies who ate the same food were more attracted to each other

Evidence of evolution (3)

• Speciation

• Fossil records

• Unity biochemical processes

Homology definition

Derived from a common ancestral feature

Central dogma of biology definition

One-way flow of genetic information within a biological system

DNA language letters and words

4 letter - 64 three letter words

Protein language letters and words

20 letters - infinite words of any length

What letter does protein always start with?

M

What are the letters of protein language?

Amino acids

Transcription definition

First step of protein synthesis where a gene is copied into messenger RNA (mRNA) by the enzyme RNA polymerase in the nucleus

Transcription process

1. Initiation (polymerase binds to a promoter)

2. Elongation (building the RNA strand)

3. Termination (releasing the mRNA)

Mutations definition

Mistakes or changes during DNA replication, loss or gain in DNA

Cells definition

A closed domain wherein the chemical reactions required for life are carried out

Cell division process

1. Copying program

2. Dividing into 2 cells

3. Giving them program

What are membranes composed of?

Phospholipids - schizoid molecules with opposite chemical properties at each end

Hydrophilic vs hydrophobic

Loves water - hates water

Virus definition

An infectious agent

Groups in amino acids

• R group

• Acid

• Proton

• Amine

• Bonded to a carbon

What makes amino acids hydrophilic?

• Polar but uncharged

• Charged

What makes amino acids hydrophobic?

Non-polar

Shape of chain on amino acids

Linear

Ribosomes definition

Small machines composed of numerous proteins and several RNAs, taking the mRNA sequence to translate it into a protein sequence

Enzyme specificity definition

Ability for enzyme to catalyse only one specific reaction or act upon a specific substrate, or a small group of closely related substrates

• Seclusion

Enzymes definition

Catalysts, typically proteins, that speed up chemical reactions within living organisms without being consumed in the process

Before gene sequencing, study of cell morphology produced a tree of life with which two types of cells?

Prokarotes and eukaryotes

Does prokaryote or eukaroyte cell have a nucleus

Eukaryote

What cell is found in fermeted foods; yoghurt, cheese, beer?

Prokaryotes

Facts about prokaryotic cells (4)

• Usually microscopic

• DNA is single, circular chromosome

• No proteins attached to DNA (bacteria)

• Proteins (histones) attached DNA (archaea)

Name of the wall that typically surrounds prokaryotic cells

Peptidoglycan

Gram + bacteria definition

One surrounding membrane around the peptidoglycan

Gram - bacteria definition

Two surrounding membranes around the peptidoglyfcan

Cyanobacteria definition

Cell envelope

Prokaryotic flagellum definition

A motility appendage, which is a long thin filament composed of flagellin protein, and is extracellular

How do prokaryotic cells divide?

Binary fission

Prokaryotic division process (4)

1. Bacterial chromosome is attached to the plasma membrane

2. Chromosomal DNA replicates, and attachment points separate

3. Cell beings to divide

4. Fission is completed

Archaea definition

Prokaryotes that inhabit extreme environments, with some features in common with eukaryotes

Halophiles definition

A type of archaea that loves salt

Thermophiles definition

A type of archaea that loves heat

Hadearchaea definition

A type of archaea that metabolises carbon dioxide and hydrogen

Hydrothermal vents definition

Cracks in ocean floor where lots of archaea live

Lokiarchaeota (Asgards) definition

Type of archaea that has a cytoskeleton and an endomembrane system (features previously thought to be restricted to Domain Eukarya)

Which came first, prokaryotes or eukaryotes?

Prokaryotes

What do stromatolites tell us about cyanobacteria?

It existed 3.5 billion years ago

How old are prokaryotes?

At least 3.5 billion years old

How old are eukaryotes?

Less than 2 billion years old

Eukaryotes definition

Cells with a nucleus, endomembrane system and linear chromosomes

Genome definition

A complete set of DNA

Histones definition

Small balls that the DNA wraps around to keep it from getting tangled

Nuclear envelope definition

Double-membrane barrier that separates the nucleus from the cytoplasm in eukaryotic cells

What can ribosomes do to the endoplasmic reticulum?

Insert proteins into it as it is translating

Golgi apparatus definition

Membrane-bound organelle in eukaryotic cells that is connected to the ER and acts as a processing, sorting, and packaging factory

Endomembrane system function

Plumbing system to deploy proteins within and to the outside of large cells

How does a nucleus arise?

Internalisation of plasma membrane and enveloping of DNA by membrane sacs

Origin of nuclear envelope

• During nuclear division the envelope disintegrates

• Chromosomes divide and separate

• ER clusters around the chromosomes and forms a new envelope

Reasons for the nuclear envelope (3)

• Shields excessively long DNA during cell division

• In combination with endomembrane system, it allowed for larger cells

• Separates processes of transcription and translation

Why do prokaryotes have one circular chromosome and eukaryotes multiple linear chromosomes? (2)

• DNA ends are vulnerable and needs protection from fraying (telomeres)

• DNA continuously loses its ends because DNA synthesis must start with a little piece of RNA; a primer

How do telomeres solve the end problem?

Keeps adding DNA to the end of the chromosome to compensate for it being shortened each time

What does a circular bacterial chromosome restrict?

Replication time

How to speed up the DNA copy time and its issues? (2 and 2)

• Convert from circular to linear

• Add more origin points

BUT

• Linear DNA is vulnerable

• Ends get frayed

Number of origins in prokaryotic chromosome vs linear eukaryotic chromosomes

Single origin in P, multiple origins in LE

What did linear chromosomes allow?

Cells to have large amounts of DNA yet still replicate rapidly and thus be competitive

Parasitic DNA definition

Introns/junk DNA that interrupts the DNA words in a gene

Where are introns excised?

Nucleus, but nuclear envelope partitions the process of intron removal

Why was the nuclear envelope necessary

Separate the two steps of central dogma so that introns could be removed before translation began

Panspermia definition

Theory that life arrived from another planet

Macromolecules definition

Polymers of monomers

Oparin/Haldane theory

Theory that life arose gradually from non-living matter through chemical evolution

Why is life based on carbon? (3)

• Carbon has a valence of 4, many options

• Forms strong covalent bonds

• Abundant

Carbon v silicon (3)

• Same valence

• Abundant

• Silicon forms slightly weaker covalent bonds

Phospholipids function

A perfect molecule for a membrane

Selfish gene hypothesis

Theory that the body is merely a gene’s way of making more genes

Why can’t proteins replicate themselves?

They lack a program

RNA forms

Both a software (contains info) and a hardware (catalyse reactions), and it can be an enzyme

Paradox of RNA being a replicator

It needs a 3D structure to be an enzyme but needs to unfold to ‘read’ itself for copying

RNA world hypothesis conclusion

RNA can be an enzyme, catalyses its own cleavage, rejoining of cleaved RNA and peptide bond formation (protein synthesis)

What happened after RNA? (4)

• Proteins offer more R groups to catalyse reactions

• Proteins make more versatile hardware (does more jobs)

• RNA learnt to template protein synthesis to get the job done

• Fitter replicators, selective advantage

Why is DNA a safe storage of program (2)

• Preserved for thousands of years

• Double stranded

Why couldn’t silica clays be the ‘crucible’ of life? (2)

• Lacks energy system

• Lacks boundary membrane

Why is RNA at the middle of everything? (6)

• mRNA contains all info to make a protein

• RNA is catalytic and can self-replicate

• rRNA catalyst that controls protein synthesis in ribosome

• tRNA fetches amino acids to ribosome for protein synthesis

• Primer RNA required to kick off copying of DNA

• RNA recruited proteins as hardware to make it a better replicator then recruited DNA to back up its info

Potential energy definition

Stored energy

Kinetic energy definition

Moving energy

Cellular respiration equation

c6h12o6+6o2→6co2+6h2o

What do cells use to set up proton gradients?

Light or chemical energy

What does the gateway do?

Allows protons to diffuse back until equillibrium is reached

What do cells use to hold the energy in a useful form?

ATP

ATP definition

Universal currency for energy metabolism

Process for making ATP from food (4)

• Glucose burned to release energy from bonds between carbon

• Electrons transferred to NAD+

• Electrons used to pump protons to set up potential difference

• Potential difference harvested to attach phosphate to ADP to make ATP —> respiration