Life sci term 2 - Jonah

Reproductive cloning

Putting the somatic cell into a pseudopregnant (induced by hormones) animal to carry the baby.

Molecular cloning

Using living cells to make many copies of a DNA fragment of interest. Inserting the fragment into the vector to make recombinant DNA.

Restriction sites

Endonuclease goes snip-snip. Dont cut the sequence of interest!!!

Antibiotic resistance gene

Important to select which bacteria will survive (the ones with the plasmid with your gene and the antibiotic resistance gene).

Selectable marker

Important to know which mammalian cells will have the gene you want being expressed (not super relevant most of the time)

Genes needed for cloning

1. Gene of interest

2. Promoter sequece

3. Restriction sites

4. Antibiotic resistance gene/selectable marker

Mature mRNA

mature mRNA has been processed, has poly-A tail (can be reverse transcribed)

Reverse transcription

Mature mRNA -> DNA

Steps for molecular cloning

1. Make cDNA

2. Bind oligo dT-primer to poly-A tail

3. Reverse-transcriptase binds to oligo dT-primer

4. Amplify cDNA (using PCR)

5. Insert amplicons into the vector using endonucleases

6. Ligate!

Plasmid

Extra circle of DNA in bacteria

Recombinant DNA

An engineered DNA molecule that comprises a target DNA sequence that has been molecularly cloned into a bacterial plasmid.

Goal of molecular cloning

Many copies of recombinant DNA using host

Recombinant DNA

Engineered DNA for some purpose or another

Gene editing

Changing genome by leveraging the cell's repair mecahnisms

Uses for gene editing

-Fix mutations

-Insert sequences

-Remove sequences

How to repair single-stranded breaks (SSB)

-Base excision repair : Just the one base

-Nucleotide excision repair : The base and it's pair or area around it

How to fix double-stranded breaks (DSB)

-Homologous recombinaition : Repair using template (if available) (must be when there are two copies present like in mitosis)

-Non-homologous end joining : Simply attach the two ends together

Zinc Finger Nucleases (ZFNs)

Nuclease that is used to guide FOK-1 (3 nucleotides at a time x 3-4 ZF in a ZFN)

FOK-1

Protein that when made a dimer, will make a double stranded cut in the DNA at a point it is guided to by TALENs or ZFNs (2 nucleases per FOK-1 snip, 4 nucleases to remove a stretch of DNA)

TALEs

Bind to one nucleotide at a time to guide FOK-1 (easily customizable: 10-12 in a TALEN)

CRISPR

Clustered Regularly Interspaced Short Palindromic Repeats: Tool used to change DNA using bacterial defense mechanism that recognizes viral DNA and cuts it where CAS1 and CAS2 tell it to. (Draw this one out)

4 Steps of Cellular Respiration

1. Glycolysis (does not need O2)

2. Pyruvate processing (needs O2)

3. Krebs/Citric Acid Cycle (does not need O2)

4. Electron transport chain (needs O2)

Glycolysis

Breaking glucose into 2 pyruvate, +2 ATP, +NADH

Regulated by a negative feedback loop (More ATP, less glycolysis)

Pyruvate processing

Turning pyruvate into Acetyl-CoA, +NADH

Krebs Cycle

Turn Acetyl-CoA into CO2, +NADH, +FADH2, +ATP

Electron transport chain

Pump protons across inner mitochondrial membrane, using electrons. NADH at the start, FADH2 at Q. Proton gradient powers ATP-ase

Electron transport chain order

Complex 1 or Complex 2 -> Q -> Complex 3 -> Cytochrome C-> Complex 4

Fermentation

Anaerobic way to keep glycolysis going for a small ATP yield.

Lactic acid fermentation

More common pathway. Pyruvate -> Lactic acid

Ethanol fermentation

Less common pathway. Pyruvate -> Acetylaldehyde -> Ethanol

Photosynthesis

The process of using sunlight to produce carbohydrates. This process requires sunlight, CO2 and H2O, and produces O2 as a byproduct.

Autotrophs

Organisms that use sunlight to produce carbohydrates.

Heterotrophs

Organisms that must meet their need for nutrients by consuming other organisms.

Two linked sets of reactions

-Light-dependent reactions, first part of photosynthesis, requires light.

-Light-independent reactions, second part of photosynthesis, does not require light (Calvin cycle)

What is transferred between light and dark reactions

Chemical energy (NADPH, ATP)

Where does photosynthesis take place

Chloroplasts.

Chloroplast

Cell organelle with a double membrane, filled with granum which are stacks of pancakes (thylakoids), inner fluid is stroma.

Granum (grana)

Stack of pancakes (thylakoids)

Chlorophyll (a and b)

Pigments that absorb red and blue light, reflect green light

How does Photosystem 1 work

-Pass excited electrons to ferredoxin

-Ferredoxin reduces NADP+ to NADPH

-NADPH goes to Calvin cycle

Photosystem 2

-Feeds an ETC that pumps protons to produce ATP

-Photophosphorylation

Z-Scheme

Model of how photosystems I and II interact

Enhancement effect

Effect where when combiend, PS 1 and PS 2 produce more energy than their independent sums.

Photosystem 2 mechanism

-Feed high energy electron to pheophytin (chlorophyll is oxidized)

-Electrons from pheophytin go to ETC in thylakoid membrane

-Plastoquinone (PQ) shuttles electrons across thylakoid membrane, to ETC

-Standard ETC from there on

-*Proton transport increases proton concentration by 1000x

How does photosystem 2 recharge

Get electrons by splitting water (oxygenic hydrolysis) (only way to split water naturally)

P680

Photosystem 2

P700

Photosystem 1

Plastocyaninin

Protein that carries electrons from PS2 to PS1

Calvin cycle phases

1. Fixation (3 RuBP + 3 CO2 -> 6 PEG)

2. Reduction (6 PEG + 6 ATP + 6 NADPH -> 6 G3P)

3. Regeneration (5 G3P +3 ATP -> 3RuBP)

Fixation

First step in Calvin cycle. Fixing carbon to ribulose bisphosphate to make phosphoglycerate.

Reduction

Second step in Calvin cycle. Using ATP and NADPH to turb phosphoglycerate to glyceraldehyde-3-phosphate

Regeneration

Using ATP to regenerate ribulose-bisphosphate from glyceraldehyde-3-phosphate to run the cycle again

How to make G3P

3 Turns of Calvin cycle

Rubisco

-Most abundant protein, fixes carbon to RuBP

-Sluggish

-Photorespiration

Photorespiration

Rubisco uses O2 as a substrate, causes net loss of C fixed, net loss of ATP

Stomata

-Leaf pores for gas exchange

-Normally open during the day, closed at night

C3

Normal pathway (Calvin cycle)

C4

-Photorespiration fix for hot climates

-CO2 fixed to 4-C organic acids in mesophyll cells

-4-C organic acids transported to bundle sheath cells

-4-C releases CO2 then travels back to mesophyll cells

-CO2 used for the Calvin cycle

-Separated by space

CAM

-Photorespiration fix for incredibly hot climates

-Crassulacean Acid Metabolism

-CO2 fixed to 4-C organic acids at night

-4-C releases CO2 for Calvin cycle during the day

-Separated by space and time

Starch

Glucose storage molecule in plants

Difference between fundamental and realized niche

Fundamental niche is the entire set of conditions under which an animal (population, species) can survive and reproduce itself. Realized niche is the set of conditions actually used by given animal (pop, species), after interactions with other species (predation and especially competition) have been taken into account.

Ecology

Science of interactions

Is ecology scale dependent

Yes, ecology is very scale dependent. It can be observed within a petri dish, in a field or in a province.

Structural questions in ecology

What is it, how does it work

Dynamical questions in ecology

How do things change over space and time

Perspectives in ecology

Physiological

Population

Community

Landscape

Ecosystem

Evolutionary (its a loop)

Community in ecology

How populations interact with each other

Population

Individuals of the same species interacting at the same spatial and temporal scale.

Population dynamics

How do populations change over time, what causes them to change

Exponential growth

dN/dt = rN (r = per capita growth rate)

Logistic growth

dN/dt = rN(K-N)/K (K = carrying capacity)

Meta-population dynamics

Interaction of a population through time and space (including immigration and emigration)

Meta-population

Small isolated populations, some movement between them

Population regulating factors

Any parameter (intra or extra) that prevents a population from growing exponentially

Community

An interaction through periodic occupancy of space (interaction, not presence)

Types of interactions

Competition

Consumption

Mutualism

Commensalism (not real)

Competition

Negative - Negative interaction

Consumption

Negative - Positive interaction

Mutualism

Positive - Positive interaction

Competition defn

Any interaction between two spp. where an increase in density of one spp. causes a decrease in per capita population growth rate of the other.

A struggle for limited resources

Mechanisms of competition

Consumption of a resource

Preemption (space)

Allelopathy (using chemicals to compete)

Territoriality

Consumption competition

One species inhibits another by consuming a shared resource

Preemptive competition

Mainly among sessile organisms, where the mere presence of one species reduces a shared resource for another (competition for space)

Allelopathic competition

One species inhibits another by changing the chemical composition of a resource

Territorial competition

One species inhibits access of another species to a resource via behavioral aggression

Competitive exclusion principle

Two species cannot use the same resource in the same way and coexist

For two species to exist, what must be true

intraspecific competition > interspecific competition

If interspecific competition > intraspecific competition

One species is competitively excluded

Classical definition of consumption

Any interaction between two spp. where

-A density increase in spp. i causes an increase in the per capita population growth rate of spp. j

-A density increase in spp. j causes a decrease in the per capita population growth rate of spp. i

Consumption types

Predation

Parasitism

Herbivory

Seed predation

Competition coefficient (aij)

The sp. i proportional effect that sp. j has on sp. i

Predator functional response

Per capita consumption rate of a predator given prey density.

Often becomes saturated. 3 types, first, half and logistic

Zero growth isoclines

Where the population is not growing or shrinking

Disturbance

Any factor which causes a decrease in the number of individuals in a population.

Intermediate disturbance hypothesis

States that areas with intermediate disturbance will have the greatest biodiversity

Niche

The place a species occupies in a community

The environmental requirements of the species

An n-dimensional hypervolume where 'n' equals the number of physical and biological factors important to the survival and reproduction of a species

N-dimensional hypervolume

Fundamental niche

N-dimensional hypervolume + ineractions

Realized niche