Building Life: The Evolution of Diversity

Question 1

two domains of classification

Answer 1

Classified as plants and animals
Then realised plants and animals were more similar to each other than bacteria
Became bacteria and eukaryotes in 1962

Question 2

three domains of classification

Answer 2

1977 - Archaea (used DNA sequence of ribosomes)

Now it kind of looks like archaea and bacteria are the two groups and eukaryotes evolved from archaea

Question 3

bacteria - history, age, numbers

Answer 3

Used to be seen as primitive
4 billion years of evolution
Outnumber eukaryotic cells massively

Question 4

bacteria features - DNA, membranes, processes, structure

Answer 4

DNA in single circular chromosome
Many have additional DNA in plasmids that replicate independently to the circular chromosomes
Plasmid DNA is not essential to survival but may have genes of adaptive value in particular environments
No membrane around DNA so transcribed mRNA is translated into proteins immediately
Lack membrane bound organelles
Cell processes are carried out by proteins in the cytoplasm or in membrane
Some (like photosynthetic bacteria) have internal membranes like mitochondria and chloroplasts
Cell walls made of peptidoglycan (polymer of sugars and amino acids) - thick or thin (with outer layer of lipids)
Internal scaffolding of proteins that determine shape, polarity and spatial properties

Question 5

diffusion limits size of bacteria

Answer 5

200 nm - 2 micrometers long
Small cells have more surface area
Less distance for molecules to travel through the cell
Some bacteria are multicellular, forming filaments or sheets
Myoxybacteria aggregate to form multicellular reproductive structures composed of several cell types

Question 6

horizontal gene transfer promotes gene diversity

Answer 6

Bacteria genomes are usually smaller than eukaryotes
Can replicate quickly when conditions are right
Replicate their DNA from only one or a few sites so genome size can influence rate of reproduction
Do not undergo cell division and cell fusion
Populations have genetic diversity

Question 7

how does variation arise in bacteria?

Answer 7

Horizontal gene transfer
Synthesis thin strands of membrane-bound cytoplasm called pili that connect with other bacteria
The cells are pulled close
A pore-like opening forms between them
DNA is transferred (conjugation)
Plasmids are often moved
DNA can be released into environment by cell breakdown and are taken up by other cells (transformation)
Can be brought by viruses that accidentally got a bit of bacteria DNA in them when infecting (transduction)

Question 8

archaea

Answer 8

Second domain

Question 9

archaea features

Answer 9

No membrane bound nucleus
Cells are prokaryotic
Small for diffusion
Genetic diversity by horizontal gene transfer
Membranes are made from lipids different from the fatty acids in bacteria and eukaryotic membranes
Different molecules in cell walls
Nothing like peptidoglycan or cellulose or chitin
DNA transcription employs RNA polymerase and ribosomes
Antibiotics that target protein synthesis in bacteria do not work (functional differences)
Can inhabit extreme environments
May be the most abundant organisms in the oceans

Question 10

shared characteristics between prokaryotes and eukaryotes

Answer 10

DNA
Ribosomes
Cytoplasm
Plasma membrane

Question 11

cytoplasm

Answer 11

the collection of organic and inorganic molecules that are collected and produced by the cell and kept within the plasma membrane.
Needs to be at a certain pH and have the correct concentration of ions and materials for reactions
Temperature must kept within an ideal range - interactions are changed, pH levels can change due to increased dissociation of H+ and OH- ions from water at higher temps

Question 12

homeostasis

Answer 12

when everything is at the correct level. The cell must establish and maintain homeostasis.

Question 13

cells must be able to replicate

Answer 13

RNA polymerase - makes transcripts from the genes encoded in DNA
Ribosomes - translate transcripts into protein
DNA polymerase - makes an accurate copy of the genome for cell division

Question 14

characteristic of life shared between prokaryotes and eukaryotes

Answer 14

comprised of a contained space that separates self from non-self (uses plasma membrane).

Question 15

what do cell membranes do? what are they made of?

Answer 15

Seperate extracellular and intracellular environments
Allow cells to carry out functions
Lipids are the main component
Minor components: proteins, carbohydrates (glycolipids and glycoproteins)

Question 16

phospholipids - structure, descriptor, what do they do, what can they form?

Answer 16

Glycerol backbone attached to a phosphate group and two fatty acids
Phosphate head is hydrophilic, polar, forms hydrogen bonds with water
Fatty acids tails are hydrophobic, non-polar and don’t form hydrogen bonds

Amphipathic: have hydrophilic and hydrophobic regions in one molecule

Arrange themselves with polar head out and non polar tails together
Can form liposomes

Micelles: spherical structure forms by phospholipids with bulky heads, single fatty acid tails (wedge-shaped).

Bilayer: two layers of phospholipids formed by lipids with less bulky head groups and two hydrophobic tails.

Bilayers form closed structures with an inner space
Plasma membranes are self-healing because of water’s tendency to exclude non polar molecules

Question 17

life’s first membranes?

Answer 17

Forms spontaneously so long as concentration of phospholipids is high enough and the pH is similar to that of a cell
pH ensures that heads are ionised and more hydrophilic
So will naturally form liposomes and may capture some macromolecules present in solution
Life may have developed this way - liposomes can grow with more lipids, can capture nucleic acids
Early membranes may have been leaky or almost impervious and evolved to limit traffic
Overtime lipids were sources internally (from proteins) not externally
Don’t know how switch to protein mediated synthesis occurred

Question 18

cell membranes are dynamic - fluidity and lipid rafts

Answer 18

Fluid: Continually moving, forming and reforming

Van der Waals forces between phospholipids are weak so allow them to move around
In a single layer of a bilayer, fluidity depends on length of fatty acid tails (longer = more interactions) and double CC bonds (bond = kink = less packed together = more fluid)
Hard for lipids to change sides of the membrane (lipid flip-flop) so each bilayer may be quite different

Lipid rafts: areas of lipids such as sphingolipids (cholesterol and other components tend to accumulate here)
Not a uniform bilayer

Question 19

cholesterol (helps with dynamic nature)

Answer 19

About 30% of animal membranes
Amphipathic
Hydrophilic hydroxyl
Hydrophobic - 4 interconnected carbon rings with a hydrocarbon Chaim
Hydrophilic bit interacts with head of phospholipids and hydrophobic bit participates in van der Waals with fatty acids
Helps maintain fluidity:
normal temp: decreases fluidity by interactions with fatty tails
Decreased temp: increases fluidity to prevent phospholipids packing together

Question 20

types of membrane proteins

Answer 20

Transporters: move molecules across the membrane
Receptors: allow the cell to receive signals
Enzymes: catalyse reactions
Anchors: attach to other proteins and help maintain cell shape.

Question 21

integral membrane proteins

Answer 21

Integral membrane proteins: permanently in the membrane and cannot be removed without damaging the cell.
Most are transmembrane - two hydrophilic regions and one hydrophobic region (can preform different functions at each side)

Question 22

peripheral membrane proteins

Answer 22

Peripheral membrane proteins: temporarily associated with membranes of integral proteins through weak non-covalent interactions such as hydrogen bonds. Can be removed without damage.
Internal or external sides of membrane
Interact with lipid heads
Can be involved in transmitting info from signals
Some limit transmembrane protein’s ability to move and assist proteins in clustering in lipid rafts

Question 23

fluorescence recovery after photobleaching

Answer 23

Proteins move in the membrane
Proteins in membrane are are labelled with fluorescent dye
Dye can be seen under a fluorescence microscope
Bleach an area of the cell so there is no dye
Bleached area does not remain so

Question 24

fluid mosaic model

Answer 24

Fluid mosaic model: the lipid bilayer is a fluid structure within which molecules move laterally and is a mosaic of two types of molecules (lipids and proteins).

Question 25

what is the plasma membrane and what does it do? what does it allow through?

Answer 25

Defining feature of all cells
Separates internal and external
Maintains intracellular conditions - maintains homeostasis

Homeostasis: constant internal environment in the face of a changing external environment.

Selective permeability allows cell to maintain homeostasis
Hydrophobic interior perverts ions, charged molecules or polar molecules from diffusing easily
Large molecules like some macromolecules can’t get across
Gases, lipids and small polar molecules can move freely
Protein transporters allow some things through that can’t diffuse through the membrane
Identity and abundance of membrane proteins varies from cell to cell depending on specific needs

Question 26

passive transport

Answer 26

Diffusion: means of passive transport which is the random movement of molecules.
Molecules always move
Diffusion leads to net movement of a substance
Net movement down a concentration gradient from high to low concentration
Diffuse through the membrane or membrane protein

Facilitated diffusion: when molecules move through a membrane protein.

Question 27

membrane transporters (involved in passive transport)

Answer 27

Channel: opening in the membrane that molecules of particular shape and charge can go through.
May be gated (open after some signal)

Carrier: binds to and then transports specific molecules.
Open to outside or inside
Binding causes a conformational change in the protein which allows transport

Question 28

water and diffusion

Answer 28

Small enough to diffuse

Aquaporins: specific protein channels that make water diffusion easier.

Osmosis: net movement of a solvent such as water across a selectively permeable membrane.
High concentration to low concentration

Question 29

primary active transport

Answer 29

Moving molecules up a concentration gradient
Requires energy
Most energy of a cell goes into the membrane
Some proteins act as pumps, using energy to directly move the substance (sodium-potassium pump)
sodium out, potassium in
Energy stored in ATP

Primary active energy directly uses energy

Question 30

secondary active transport

Answer 30

Driven by an electrochemical gradient
Secondary active transport uses the potential energy of an electrochemical gradient to drive movement of molecules
Sodium potassium pump is used to move glucose and animo acids into cells

Example:
Protons pumped across the membrane by primary active transport
Proton pump generates electrochemical gradient with higher concentration of proteins outside the cell (when one side is more positive than the other)
An antiporter uses the proton electrochemical gradient to move a different molecule out of the cell against its concentration gradient.
Movement is driven by coupling moving protons down gradient and molecules up
So ATP is not used directly (thus secondary)

Electrical gradient: when there is a difference in charges on both sides of a membrane

Electrochemical gradient: when charge and chemical components are involved.

Question 31

hypertonic, hypotonic and isotonic

Answer 31

Hypertonic: higher solute concentration than inside the cell - water leaves the cell and it shrinks

Hypotonic: lower solute concentration than inside the cell - water moves into the cell and it swells or lyses

Isotonic: concentration of solute is same as in cell - cell does not change

Question 32

do cells attempt to stay the same size and composition?

Answer 32

yes - Cells try to stay isotonic - use active transport of ions and the sodium-potassium pump

Contractile vacuoles: compartments that take up excess water from inside the cell and then by contraction, expel it into the environment.
Some single celled organisms use this so they don’t burst
Some take in water with aquaporins
Others take in protons through proton pumps and then water by osmosis

Question 33

cell wall - what does it do?

Answer 33

External to plasma membrane
Maintains shape and size of cells
Plants, fungi and bacteria
Water enters cells by osmosis until pressure created by the cell wall’s resistance to expansion opposes the driving force of the water entering

Turgor pressure: force exerted by water pressing against an object (also hydrostatic pressure).
Pressure can act as structural support
Plants wilt when dehydrated

Vacuole: present in plants and fungi, absorb water and increase turgor pressure.
Conspicuous feature of plants (why plant cells are larger than animal cells)
Store nutrients, ions and wastes

Question 34

components of cell walls

Answer 34

Carbohydrates and proteins
Plants: polysaccharides such as cellulose
Algae have cell wells of cellulose or silicon or calcium carbonate
Fungi: polymer of sugars called chitin
Bacteria: peptidoglycan (mix of amino acids and sugars)

Question 35

microbe adaptation and carrying capacity

Answer 35

Grow in an environment until they reach the carrying capacity
If there is a change in environmental conditions, microbes may die or not grow as well
Occasional errors in genetic replication (1 in 300 cell divisions in bacteria)
Fewer than half of these errors affect the organism but is more likely to cause harm than good
But occasionally the mutation is beneficial
Microbes live in high radiation environments (because of humans) and have mutated to have two copies of genetic info instead of one. Radiation causes genetic info to shatter and cannot be repaired. Mutant cell can use the extra copy as a template repair DNA
Mutant is more likely to survive and pass on this trait

Carrying capacity: maximum population that can be sustained with the available resources.

Question 36

measuring ion concentration in a cell

Answer 36

Concentration of ions against change in cell volume (+/-)

Can plot a relationship between ion concentration and volume

Question 37

if a cell is put in a solution and it does not increase or decrease

Answer 37

The concentration of ions in the cell is equal to that outside the cell (isotonic)
Can work out the concentration of ions within the cell by seeing the point on the graph where the cell does not increase or decrease in volume

Question 38

why would a cell not keep its equilibrium the same as a really salty external environment?

Answer 38

If there was no gradient, it could not bring other things like glucose in
Sodium ions can also be toxic at high concentration

Question 39

what is a positive ion?

Answer 39

potassium

Question 40

deleting genes to study gene essentiality of function

Answer 40

Y axis on population size of the cells you are growing
x axis time
Growth curve
In a growth media (contains all nutrients required)
But take out a nutrient such as carbon - growth curve is now flat (cell cannot grow at all)
Then take away gene x (consider wild type group) - might see reduced growth, growth as good as control or no growth and can determine if it is an essential gene or not
By putting the cells in different conditions, you can see what the gene is involved in eg. In glucose only the cells do not grow as well and it must be involved in glucose utilisation

Question 41

growth curves

Answer 41

Robust growth curves - wild type like growth
Partial growth curves
No growth curves

*know how to interpret such a table for quiz

If two genes are both removed and then there is absolutely no growth - potential that A and B are redundant (cover each others roles a bit if one is absent). Essential together