Bio 1000 September 7, 2012
Pigment absorbs light
Photoreceptor a light sensor made of protein and associated pigment, light hits pigment and makes
conformational change in pigment which makes a change in protein (signal transduction cascade)
Negative phototaxis- move away from light stimulus
Compound eye- hexagons (ommatidium)
Third diagram Light passes through cornea and back lens the retina
Blind spot on the retina, allows optic nerve to be sent through retina to the brain
September 10, 2012
Circadian rhythm- you use light to set your biological clock, not necessarily if its dark you sleep. Also, its
controlled by an internal (endogenous) organism-based clock
How do circadian rhythms work?
Melatonin production may be low in some people
Blind animals still have photoreceptors so they’re able to set a biological clock
Coevolution- adaptations make 2 or more populations evolve, and they interact with each other
Is there a dark side of light?
Light can damage biological molecules (including dna)
How can we be protected from sun damage? Melanin absorbs uv rays
Vitamin D3 (cholecalciferol)- made in skin
Some vertebrates (organisms with a backbone) don’t see the sun
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Light is the visible region of the electromagnetic spectrum
It is a source of energy and information
It plays a role in the behaviour and ecology of all organisms (circadian rhythms)
It can also damage biological molecules (UV radiation)
September 12, 2012- biodiversity of life
Species- a group of organisms that are capable of interbreeding and producing fertile offspring of both
genders, dna similarity, habitat
Heterotrophs: obtain organic carbon and energy by consuming other organisms
Autotrophs: synthesize organic carbon molecules using inorganic carbon, CO2
Photoautotrophs: Use light as source of energy for photosynthesis
Chemoautotrophs: use reduced chemicals rich in electrons as an energy source
Archaea and bacteria produce through binary fission
Eukarya goes through sexual reproduction
Similiarities between archaea, bacteria and eukarya: dna, cell membrane, translation and transcription
machinery and have a way to get energy
Selection-how does it relate to biodiversity?
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When some force or phenomenon affects the survival and reproduction of individual organisms
Selection directed by different circumstances
September 14, 2012
Community- 2 or more populations living in the same area
Evolution- A change in inherited traits/characteristics over time
Population- group of individuals from same species that live in same area and regularly interbreed
Evolution is valid science
Theory of evolution- explains the unity and diversity of life
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Highly fertile
Food resources
Genetic variation
Evolution of life on our planet may have been an inevitable outcome of initial physical and chemical
conditions established by Earth’s origins
Anoxygenic- photosynthesis not producing oxygen, influenced by sulphur
Oxygenic- photosynthesis bacteria appears oxygen produced, influenced by oxygen
Bacteria could go under evolution as well (horizontal gene transfer)
Hydrogen bonds hold A-T and C-G together
Adenine and Thyamine have a weaker bond
Linked by phosphor diesther bond
September 17, 2012
Once protein starts translating with (n terminal) when its done translating we end up at the c terminal
(carboxyl)
Primary- amino acids in a sequence
Secondary- linking between primary amino acids
Tertiary- folding in amino acids
Quaternary- structure of protein starts forming
Redox reactions are important with metabolism
Most energy is released from ATP by removing last phosphate group
September 19, 2012
ORI stands for origin of replication, it starts the replication
Marker- allows plasmid to grow if it has the gene
MCS- has about 20 restriction sites
A restriction site allows the enzyme to recognize where it can cut on the plasmid
Final product is what we call recombinant DNA
Putting the recombinant DNA into a bacterial cell is called transformation
Bacteria competence- bacteria able to take up plasmid
Ligation joining pieces of DNA, enzyme called DNA ligase
Plasmid could close on its own
Liquid needs to contain AMP (amphisiilan)
Bacteria responds to the presence of amphisilan
Selection helps determine which bacteria is growing and which contains the insert
September 21, 2012
Organelle- has to have a membrane around them, have a specialized function, only be found in a
eukaryote, they’re suspended within the cell cytosol
Cytosol is the liquid portion of the cell
Cytoplasm is liquid plus organelles
Endomembrane system- vesicle allows things to fuse with organelles
Nucleus is where rRna is transcribed and small and large ribosomes subunits are made
Nuclear Pore- things can enter and leave
Nuclear Lamina- structural support
mRNA needs to get out of the nucleus
Enzymes need to get in and out of the nucleus as well as ATP and ions
Nucleotides, hormones, rRna, ribosomes are things that need to get in/out of the nucleus
Importance of the nuclear membrane- we keep it separated because we don’t want to damage the DNA
Archaea associate with histone like proteins 4 of them
Image of histones- there are 8 histones, the 4 are doubled, the black is the DNA and once its wrapped
around its called nucleosomes, octomer consists of H2A, H2B, H3, H4
Heterochromatin- tightly packed, you don’t want being new stuff being transcribed while it is being
replicated, mostly 30nm
Euchromatin- loosely packed, 10nm is more spread out
September 24, 2012
Chapter 1-3, 21 and biotechnology for bio test and check moodle- NEXT WEEK
Rough Endoplasmic Reticulum is covered in ribosomes (little dots)
Smooth endoplasmic reticulum- plays a role in lipid synthesis, regulates calcium, carbohydrates, breaks
down some drugs
Vesicle- brings stuff from one organelle to another organelle
Golgi apparatus- after leaving the ER, it moves to the Golgi, in the Golgi a sugar group is added to the
protein which is called glycosylation (the sugar is added after the protein is translated)
Lysosomes- have a very acidic environment; their pH level is around 4.8
Macrophage contains lysosomes
Organelles come from pre-existing organelles
Endomembrane system doesn’t include mitochondria and chloroplasts
September 26, 2012
Dyneins - we find them in animal cells, some in plant cells it is used to transport vesicles and organelles
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Known for flaggeral movement in Eukaryotes
There has to be a motor protein for movement
Dynein moves along microtubules, which allows bacteria’s flagellum to move in a whip like
motion
Cilia moves stuff, they are hair like structures and they can be found in the trachea (helps you sneeze)
Flagella of prokaryotes and eukaryotes ARE NOT EVOLUTIONARILY RELATED
Myosin moves along the actin to generate enough power which produces a muscle contraction
Myosin also plays a role in cell division
Mutation in kinesin (motor protein) will allow organism to not function properly
Extracellular matrix is located outside the cell membrane, it is used to specialize the cell (ex. Bone,
cartilage, skin, cardiac muscle, intestinal villi, skeletal muscle)
ECM- helps to provide structural support and helps to provide its function (don’t confuse with
mitochondrial matrix)
Eukaryotic cells are bigger than prokaryotic cells because they have a bigger endomembrane, volume
will increase but by having the endomembrane system the surface area will support the volume (works
like a balloon blowing up)
Prokaryotic cells can’t support a large surface area because there’s no room
Multicellular eukaryotes evolve:
First theory: The cells combined and formed a multicellular organism.
Second theory: While a cell divided something went wrong and the cell ended up with different
characteristics.
September 28, 2012
Membrane functions- different environments MUST be maintained
Lysosome has a different environment because it has a lower pH
5 million lipids for every nm
Phospholipids- contain polar unit, phosphate group, glycerol, fatty acid chain x2, (polar phosphate
group)
Asymmetry of membranes- brown- sphingle myelin (transport signals), green- phosphapidylsirin, redphosphapidylcholine
Plasma membrane is constantly moving, this fluidity is necessary to maintain the integrity of the plasma
membrane
Higher the temperature=more movement so it will be more fluid
October 1, 2012
Saturated will become a solid first since its tightly packed together
Desaturase is an enzyme to break down the fat
Don’t want too many fatty acids to make membrane fluid
Cholesterol inserted between phospholipids
Phytosterol is a membrane fluid found in plant cell membranes
Gases could pass through a selective permeability membrane, others need a concentration gradient
(curved arrow on diagram needs help going through membrane)
Proteins-Different membranes have different proteins and thus different functions
Transport need to bring stuff in and out of cell for cellular process to happen
Membrane protein could release substances into the cell and they play a role in enzyme activity
Receptor proteins receive signals
Attachment or cell recognition through membrane proteins
October 10, 2012
Integral membrane proteins integrate through the membrane
Polytopic membranes are better for proteins passing through the membrane
Antarctic fish- cold-blooded- unsaturated fatty acids counteract the effects of cold; cold makes
membranes less fluid, UFAs make membranes more fluid
Gated Channel Proteins- switch between open or closed starts
October 12, 2012
Water intoxication leads to hyponatraemia *research it*
Symport- Both move in same direction
Antiport- moves in opposite direction against concentration gradient
Water is able to diffuse through the hydrophobic part of a cell because the lipids repel against each
other making room for it to pass through
October 15, 2012
Exergonic is negative because you are releasing energy, less energy in products than reactants
Endergonic – you have to put energy into that system to be used
Not all energy released by catabolic reactions is used for anabolic reactions
2nd law of thermodynamics- during every transfer some energy becomes unusable (not available to do
work)
1st law of thermodynamics energy cannot be created of destroyed but only converted from one form to
another. Conservation of energy
Thermal energy important for homeotherms who use the heat to maintain their internal environment
Activation energy- initial input of energy to start a reaction, even if it is spontaneous
Enzymes increase the rate of a chemical reaction, they lower the activation energy of a reaction
October 17, 2012
The more inhibitors the more chances of it trying to connect
Allosteric activator- some things will activate once it has too much it will inactivate, without allosteric
activator the activator will bind to the site and increase the infinite site
Optimum ph depends on the enzyme
Enzymes in a lysosome have an acidic ph to break down the cell
Enzymes begin to denature once temperatures go above 40 degrees Celsius  substrate level decreases
Cofactors help regulate an enzymes biological activity, they can be inorganic or organic
Basal metabolic rate is the same as resting rate
Active metabolic rate is how much energy you need to do your daily activities
Feedback inhibition- takes up till it needs it once there’s too much the body will stop it from producing it
October 19, 2012
Glycolysis process is broken down to two pyruvate molecules, 2 ATP, 2NADH
Pyruvate oxidation- produces acetyl COA
Kreb’s Cycle- some ATP, NADH AND FADH2
Electron transport chain- Chemiosmosis associated with it, ATP is not produced by the electron
transport system, the purpose of the system is to set up a proton gradient so ATP is made up after
chemiosmosis
*know the mitochondrion anatomy
Mitochondrial matrix is not the same as the extracellular matrix
Glycolysis- breaks glucose down into pyruvate
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Old process as it doesn’t require oxygen, it’s the only process that doesn’t use oxygen
Energy investment phase- 2 ATPs are placed
Phosphorylation occurs to destabilize the glucose into 2 pyruvate
NADH later takes part in the Electron Transport Chain
Substrate level phosphorylate occurs in glucose- process produces ATP by removing a phosphate group
to ADP in order to form ATP (kinase enzyme is key as it catalyzes the transfer of phosphate from one
molecule to another)
Compare molecules in this reaction:
1) Phosphate group was taken away which results in the production of ATP
If the shape is changed it is called isomerization
G3P2H+one H+ produces NADH
G3P 2H+  one H+ produces NADH
October 22, 2012
Pyruvate is oxidized into Acetyl-CoA by pyruvate hydrogenase
November 5, 2012
Receptors bind to signaling molecule which causes a change and initiates signal transduction cascade
Not a 1:1 relationship between molecules in the pathway
Each step amplifies so the signal is stronger
If phosphatase removes the kinase it becomes prohibited
Cross talk- interaction between pathways
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Where one thing gets activated in one pathway which results activating something else in
another pathway
G protein binds with first messenger causes conformational change which activates G protein, GDP is
remove and GTP is added so now the G protein is active and now it moves to adenylyl cyclase which
moves it to the cAMP the second messenger and then produces Protein kinase A which results in cellular
responses
As long as cAMP is present protein kinase will be activated
Creb travels through nucleus once regulated by Protein Kinase A to initiate transcription
If adenylyl cyclase is not activated, protein kinase A won’t be activated which would lead to no cellular
responses
If phosphodiesterase is not activated- it won’t be able to break cAMP to AMP which won’t terminate the
response
IP3 activates DAG and helps activate protein kinases
November 16, 2012
M checkpoint- checks if spindle fibers are ready
G2- checks if the DNA is replicated
Cyclin dependent kinases phosphorylate other proteins but on their own theyre inactive, to be activated
they bind to cyclins
Phosphorylation can be used to activate or inactivate stuff
Cells have metastasised when cells spread to other organs
November 21, 2012
Proximal region helps in regulation
Enhancer helps transcription works at maximal speed
Activators when bind help turn the transcription process on, transcription factors are recruited
Repressor hinder transcription factors from binding
Polyadenylation- addition of poly A tail
Poly A tail at the end of transcription helps signals that it is done, it assists in exporting out of the
nucleus, and helps prevent the degradation
Exons will be translated into protein, introns won’t so we have to get rid of them
Introns are removed by splicing
Alternative splicing exons can be joined in different combinations, sometimes you include all of them
sometimes pieces of them