Bio - Mid semester test Flashcards
Features common for all lifeforms
- comprised of a common set of elements
- comprised of cells
- contain genetic information
- grow and change
- respond to environment
- use molecules to make new molecules
- extract energy and use it
- exist in populations and can evolve
What evidence does DNA provide to explain evolution?
All organisms share the same genetic code, chemical composition, and cellular structure
2 hypotheses for the forces that created life on Earth
- Life formed spontaneously on early Earth (Miller-Urey experiments)
- Extra terrestrial origin - life formed on another planet or comet (evidence from meteorite)
Miller-Urey Experiment
Recreated early Earth environment, found:
- bases in DNA and RNA
- all 20 amino acids
- a range of 3- and 6- carbon sugar
- fatty acids
- vitamin B6, NAD, organic acids
Extra Terrestrial origin
1969 meteorite contained:
- amino acids
- DNA bases
- sugars
- fatty acids
- proteins
Stromatolites
Layers of limestone that trap water and other debris, locking it away. Fossilised cyanobacteria has been found, demonstrating evidence of early life.
Properties of water that are critical to the chemistry of life
Hydrogen bonding allows for:
- high specific heat
- high boiling point
- high melting point
- high heat of vaporisation (sweating)
- cohesion (hydrogen bonding between water molecules - allows water to go from tree roots to leaves)
- adhesion (water’s attraction to other molecules - allows for surface tension)
What are the major elements of life?
Carbon, hydrogen, nitrogen, oxygen
Why was water’s high specific heat crucial for early life to form?
By having a high heat capacity, water can absorb a lot of energy before it heats up. This allowed for the ocean to be energy dense, allowing organisms to thrive and reactions to occur. There was a greater chance of amino acids to collide and form more complex structures.
Pyrimidines
Single ring - Cytosine, Uracil, Thymine
Purines
Double ring - Adenine, Guanine
Microbodies structure
- single membrane bound
- neutral pH
- contain oxidative enzymes (generated by ribosomes in cytoplasm) that generate hydrogen peroxide and enzyme catalase to break down the excess H2O2
Microbodies function
NOT PART OF ENDOMEMBRANE SYSTEM
Another recycling bin in animal and plant cells
Break down amino acids (peroxisomes) and fatty acids (glyoxysomes)
Type 1 topisomerase
- prokaryotic DNA replication
- DNA ahead of the fork of replication get extremely coiled and highly strained
- to relieve this, Type 1 topisomerase creates a nick in the DNA to allow the other strand to pass through, and ligates the DNA back together
What enzyme relieves highly strained and extremely coiled DNA in prokaryotes by creating a nick in the DNA and allowing a strand to pass through before ligating the DNA back together?
Type 1 topisomerase
ORC (Origin Recognition Complex)
Eukaryotic DNA Replication
Recognises and binds to origin of replication sites, then recuits Helicase to unwind the DNA
What binds to the origin of replication site and then recruits helicase to unwind the DNA in eukaryotic DNA replication?
ORC (Origin recognition complex)
What does PSII do? (4 steps)
- absorbs photons and becomes excited
- e- passes from one pigment to another in the reaction center until reaching reaction center.
- e- transfered to P860(a pair of chlorophyll a molecules)
- e- then passed on to primary e- acceptor via the process of PHOTOACT
- Splits H2O into H and O to replace electrons from P680. H+ enters thylakoid, O becomes O2 and is released into atmosphere.
What does PSI do? (5 steps - remember there is more after NADPH is made)
- Electrons are transported to PSI via electron acceptor molecules
- The reduced P700 complex absorbs light and relays an excited electron to PSI’s unique electron acceptor (ferredoxin)
- Above Ferredoxin, FNR (Ferredoxin-NADP plus reductase) synthesises NADPH
- The transfer of electrons through electron transport chain releases energy that is used to pump protons into the thylakoid space, creating a proton gradient
- ATP synthase utilises this proton gradient to attach a third phosphate group to an ADP and produce ATP via chemiomosis
What are the 3 stages of the calvin cycle?
- Carbon fixation
- Reduction of 3-PGA
- Regeneration of RuBP
What happens in the first stage of the calvin cycle? 1. Carbon Fixation
Rubisco fixes CO2 from the atmosphere to regenerate RuBP(5C compound). It is unstable to it forms 2 3PG molecules.
What happens in the second stage of the calvin cycle? 2. Reduction of 3-PG
12ATP phosphorylate the 3-PG molecule and 12NADPH molecules reduce 3PG to form 12 G3P molecules.
2 G3P molecules move out of the cycle to make hexose while the others (10) continue to regenerate RuBP.
Golgi body structure
Flattened membranes stacks: golgi stacks made from cisternae
Polar structure: one end is the cis face (receives vesicles), the other end is the trans face (excretes vesicles)
Golgi body function
Proteins, glycoproteins, and other molecules formed in the ER are transported to the Golgi body in vesicles to be biologically modified (e.g. sugars added or trimmed). Polysaccharides can also be formed here.
Many molecules such as hormones and digestive enzymes exit the golgi body in secretory vesicles and exit the cell via exocytosis. Other molecules are packaged into vesicles such as lysosomes to remain in the cell
Plant vacuoles
PART OF THE ENDOMEMBRANE SYSTEM
Equivalent of lysosomes
Single membrane bound called the tonoplast
Certain hydrolytic enzymes serve as degradative compartments
Other functions: storage of nutrients, pigments, maintenance of cell pressure
Lysosome structure
- single membrane bound
- pH of 4.5
- plenty of enzymes derived from RER and golgi to break down pathogens and organelles
Lysosome function
PART OF ENDOMEMBRANE SYSTEM
‘Recycling’ in animal cells
Breaks down material ingested by endocytosis or recycles old organelles
Microbodies structure
- single membrane bound
- neutral pH
- contain oxidative enzymes (generated by ribosomes in cytoplasm) that generate hydrogen peroxide and enzyme catalase to break down the excess H2O2
Prokaryotic cell division process
Binary fission:
1. replication of the circular prokaryotic chromosome starts at the ORI and starts in both directions at once
- the cell elongates. FtsZ proteins migrate toward the midpoint of the cell and forming a cleavage furrow that eventually becomes a septum
- replication finishes. The plasma membrane is pinched inward by a tubulin-like protein and a new cell wall is deposited after the septum is complete
- the two daughter cells result
Microbodies function
NOT PART OF ENDOMEMBRANE SYSTEM
Another recycling bin in animal and plant cells
Break down amino acids (peroxisomes) and fatty acids (glyoxysomes)
FtsZ Protein
Forms “Z ring” essential for cell separation in prokaryotes
DnaA
Initiator protein that serves as a key regulator in the cell cycle progression in bacteria, promotes the unwinding of DNA at oriC
What do cyclins and CDKs (Cyclin-dependant kinases) do?
Initiate the cell cycle. When they bind together they form an activated complex which allows CDK to phosphorylate (add a phosphate group) to a protein target. This stimulates the start of the cell cycle.
They regulate the cell cycle at the checkpoints by interacting with other signalling pathways to prevent the progression of the cell cycle if certain conditions are not met.
What is mitosis?
Division of the nucleus including genetic material
What happens in prophase in mitosis?
Nucleic chromatin condenses into sister chromatid pairs attached at centromere junctions. Outside the nucleus, centrosomes migrates to opposite sides and microtubule rods grow from each heading towards the nucleus and towards the cell membrane. This forms a spindle apparatus.
What happens in prometaphase in mitosis?
Nuclear envelope dissolves. Protein structures (Kinetochores) appear on each side of the centromeres and microtubules fasten to them, each sister chromatid tethered to a different cell pole.
What happens in anaphase in mitosis?
Kinetochore fixed microtubules shorten and sister chromatids are pulled apart, now known as chromosomes. Cell is elongated.
What happens in metaphase in mitosis?
Spindle apparatus rearranges the chromosomes in the middle of the cell.
What happens in telophase in mitosis?
Spindle apparatus disbands, genetic material loosens, two nuclear envelopes form around each set of chromosomes
What happens in cytokinesis in telophase?
Cell is cytoplasmically divided, a cell pair results.
What happens in the third stage of the calvin cycle? 3. Regeneration of RuBP?
10 G3P molecules turn into 6RuBP when 6 ATP molecules phosphorylate them
Where does the citric acid cycle occur?
Mitochondrial Matrix
Where does pyruvate oxidation(Link reaction) occur?
Mitochondrial matrix
Where does oxidative phosphorylation occur?
Inner mitochondrial membrane
What happens in the energy investing phase of glycolysis? (steps 1-5)
Phosphroylated Glucose breaks down into 2 3C compounds which are then oxidized by NAD to NADH and ADP picks up the Phosphate group to form ATP and then Pyruvate is formed
What happens in the energy harvesting phase of glycolysis? (steps 6-10)
Two molecules of 3-carbon glyceraldhyde 3-phosphate are converted into 2 molecules of pyruvate alongside NAPH and ATP
These molecules then enter mitochondria for citric acid cycle
What happens in pyruvate oxidation?
Pyruvate is oxidised to acetate and CO2
Acetate binds to Co-enzyme A to form acetyl CoA
What is the electron acceptor in lactic acid fermentation?
Pyruvate
Is pyruvate oxidation exergonic or endergonic?
Exergonic; one NAD+ is reduced to NADH
What is regenerated after every citric acid cycle?
Oxaloacetate
What happens in oxidative phosphorylation?
Electrons are shuttled through the electron transport chain to eventually accept O to synthesise water. H+ is transported into the intermembrane space creating a high concentration of H+. This high concentration allows for the synthesis of ATP, as hydrogens use ATP synthase to travel back into the mitochondrial matrix.
Two stages of oxidative phosphorylation
Electron transport chain and chemiosmosis
3 key points of protein metabolism
- proteins cannot be stored (left over protein will be converted into carbohydrate or fat and the nitrogen eliminated through urea cycle)
- essential amino acids must be consumed daily for proteins to be made
- proteins are always degraded, therefore, a constant supply of quality protein is needed in order to maintain body structure
Transamination definition and type of reaction
The transfer of an amine group from one AA to another and is used to synthesise nonessential amino acids. Both catabolic (breaking the amine group) and anabolic (synthesising a new amino acid)
When the amount of amino acids exceeds the required amount for the synthesis of nitrogen, it is broken down into GLUTAMATE and Alpha-keto acids
Lipogenesis definition and type of reaction
Formation of fats from surplus glucose. Anabolic process
Beta-oxidation definition and type of reaction
A reaction that converts fatty acids to acetyl CoA to enter the Krebs cycle. Catabolic process
Deamination definition and type of reaction
The removal of an amine group as ammonia. Ammonia is used to synthesize urea in the liver. Catabolic process.
Glutamate is converted into NH3+ and alphaketoglutamate, left over carbon can be used in krebs cycle or other metabolic pathways.
Two ways to measure reaction rates of enzymes
- measurement of decreasing concentration of substrate
- measurement of increasing concentration of product
Gluconeogenesis(Almost a reversal of Glycolysis)
Synthesis of new glucose from noncarbohydrate precursors. Anabolic process
An entire cell signalling process is known as a signal ______ pathway
Transduction
Endocrine signalling
A mode of transmission for signalling molecules that act on cells that are far from the cell that secretes them.
Paracrine signalling
When a cell releases a signalling molecule that acts on a neighbouring target cell
Synaptic signalling
Type of signalling that occurs over a very short distance called a synapse such as between 2 neurons.
Contact-dependant signalling
Direct physical contact through signal molecules found in the plasma membrane of the signalling cells and receptor proteins present in the plasma membrane target cell
Autocrine signals
Act on the same cell that secretes them
Juxtacrine signals
Affect only adjacent cells (physical contact)
Paracrine signals
Affect nearby cells
Hormones
Travel to distant cells, usually via the circulatory system
3 steps in cell-to-cell communication
- signal perception
- intracellular signal transduction
- cellular response
What stimulates and inhibits phosphofruckinase? (glycolysis)
Stimulates: AMP (from ADP)
Inhibits: ATP
Describe the steps in the transition to multicellularity from a unicellular organism (4 steps)
- Aggregation of cells into a cluster
- Intercellular communication within the cluster
- Specialisation of some cells within the cluster
- Organisation of specialised cells into groups (tissues)
How do large multicellular organisms overcome their small SA:volume ratio?
Lots of folding and branching to increase surfaces where molecules and bind or diffuse. e.g. lungs and thin surfaces
How do multicellular organisms overcome the large distance from their internal cells to the external environment?
A circulatory system - bulk flow - provides pressure to move fluids through the transport system
Negative feedback (homeostasis)
The product of a reaction reduces the initial stimulus.
Positive feedback (homeostasis)
The product of a process stimulates further increase in its production, leading to an increased response.
Describe the function of the liver in maintaining blood glucose levels
Eat sugary food
High levels of glucose detected by B-islet cells and they release insulin
Liver takes up glucose and stores it as glycogen
Blood glucose levels drop - insulin release ceases
Exercise and fasting cause glucose levels to drop
A-islet cells release glucagon
Liver breaks down glycogen and releases glucose into blood
Glucose levels rise, glucagon release ceases
Morphogenesis
The process by which cells and tissues organise and arrange themselves to create the final form of the body
House-keeping genes
Genes that are expressed in all cells
What happens in gastrulation?
- body plan is established
- formation of three germ layers (ectoderm, mesoderm, endoderm)
Ectoderm
The outer germ layer that develops into skin and nervous tissue
Methods of measuring reaction rates
- The decreasing conc of substrate
- The increasing conc of products
Substances commonly involved in active transport
Na+, K+, Ca2+, Mg2+
Measuring reaction rates is called
Kinetic Measurements
Michaelis-menton Constant relationship with Enzyme-substrate affinity
High Michaelis-menton Constant = Low affinity
Low Michaelis-menton Constant = High affinity
Irreversible Enzyme inhibition
Covalently bonds to the enzymes active site permanently inactivates the enzyme (E.G. Aspirin)
Allosteric enzymes
They can be either activated or inhibited by the non-substrate molecules that attach to them.
ATP and ADP in enzyme regulations
ATP can act as a inhibitor as they can lower Catabolic enzymes affinity towards the substrate
ADP acts as activator
Cell-Cell communication
- Signal detected by target cell, chemical signal binds to receptor protein.
- Signaling molecule binds changing the tertiary structure if receptor protein initiating TRANSDUCTION.
- Transduce signal finally triggers a cellular response
4 Types of Receptors
- Enzyme linked
- G-protein coupled
- Ligand-gated ion channel
- Intracellular receptor
4 Types of CHEMICAl signaling
- Endocrine(Hormones) - distant cells
- Autocrine - self target
- Paracrine - Signal affects nearby cells
4.Juxtacrine - Adjacent cells
Molecular clock
Technique using mutation rates of dna to deduce the time in evolutionary history where 2 or more life forms diverged
Drawback of multicellularity
Individual cells cannot survive or their own(lose independence)
Benefits of multicellularity + example
- Multicellular cells can do more than 1 thing at a time. In Chlamydomos(Unicellular), it has to PHASE switch between swimming phase and non swimming(cell division) phase. Whilst the volvox(multicellular) can do both things at once, Swim+Reproduction
- Larger size prevents them becoming filter feeders’ food
- Cells working in unison, the speed of Volvox is higher than Chlamydomos
As the volume of an object increases, SA:V ratio decreases what is the consequence?
Less of the INTERIOR is exposed to the Exterior
As multicellular organisms grow larger what happens metabolically?
The need for resources and rate of waste production increases significantly faster than the SA over which these metabolic needs are exchanged
What is the solution to insufficient contact with the external environment to meeting exchange needs of multicellular organism?
Evolution of organs that provide massive surface areas for that exchange to occur (e.g. lungs in humans)
Requirements of Circulatory system
Rapid movement of exchange substances
Highly branched internal structure
Bulk flow
Pressure used in moving fluids throughout the circulatory system of animals(Pumps are active) and plants(transpiration is passive)
Process of insulin
Insulin activates the enzymes Glycogen Synthase AND Glucokinase(inhibits Glucose-6-phosphatase)
It also leads to more glucose transporters leading to more glucose being transported into the cell
Glucokinase
Adds phosphate groups to glucose to prevent them from diffusing out of the cell. It also inhibits Glucose phosphatase which adds phosphate groups to glucose.
Glycogen Synthase
coverts glucose into glycogen
Nervous system
Enormous amount of information is received and integrated in this system. Used to control tissue and organ functions.
Gap junctions
Communication channels between adjacent cells: allow ions and molecules to pass through
Resting membrane potential
The imbalance of electrical charge that exists between the interior of electrically excited neurons and their surroundings
Stages of an action potential
- stimulus
- depolarisation
- repolarisation
- hyperpolarisation(refractory period)
What happens in depolarisation in an action potential?
Sodium ion channel opens and sodium ions rush into the cell
What happens in repolarisation in an action potential?
Sodium ion channels close as potassium ion channels open, potassium ions rush out of the cell
Refractory period in an action potential
No matter how much more stimuli, another action potential will not fire. Limits the number of action potentials that a given nerve cell can produce per unit of time
What are the target cells of abscisic acid (ABA)?
Guard cells
How does abscisic acid get to guard cells?
Xylem
What produces abscisic acid?
Root cells
How can one genome produce many different cell types?
Genes can be turned on and off, the particular combination of genes dictates cellular morphology and function
what is the synapse
where 2 axons meet with each other
Electrical Synapse
Direct communication between the cells using Gap Junctions, often involved with rapid activity coordination.
Chemical synapses
Most synapses are chemical synapses. Contain presynaptic cleft + postsynaptic cleft. The area between the the synaptic cleft.
Action potentials cannot travel across the synaptic cleft so electrical signals are converted to chemical signals at the synapse
Process of chemical synapse
1.Voltage gated Ca channels open at presynaptic cell. calcium rushes unto the presynaptic cell
2. Triggers the fusion of vesicles in the membrane
3. Release of Neurotransmitters into the synaptic cleft
4. Neurotransmitters bind to receptors of post synaptic cell
5. This can result in a decrease of increase in postsynaptic membrane potential
Protein structures
Primary protein - Covalent peptide bonds
Secondary protein - H-bond interactions of Alpha helices and Beta pleated sheets
Tertiary Protein - Disulfide bridges form Ionic, hydrophilic and hydrophobic(non-polar) interactions between R groups
Quaternary protein - A unit of 2 or more polypeptides attach to form together to form a larger macromolecule
Primary endosymbiosis
Eukaryote cell ingests photosynthetic cyanobacteria
Formation of organelles Invagination theory
The invagination of the cell’s membrane after folding(most likely to try and increase cell SA) lead to tje organelle ER being formed
Endosymbiosis + advantage
When a hose cell ingests another smaller cell and that cell’s function is retained but loses its autonomy. The ingested cell also transfers its genetic material to the the host cells. Both have a symbiotic relationship as they both benefit from each other.
Seperation of biochemical processes to optimize each process
Secondary endosymbiosis
Eukaryote ingests another eukaryote with a chloroplast stealing it via phagocytosis
3 stages of DNA replication
- Initiation
- Elongation
- Termination
Evidence for endosym
- Very similar morphologically to bacteria
- Has double membrane
- Own set of DNA/RNA
Retain machinery for protein synthesis
Similar metabolism to prokaryotes
Helicase
Prokaryotic and eukaryotic DNA replication
Binds to DNA at the origin of replication and moves along the DNA, unwinding and separating it
SSB (Single stranded DNA binding proteins)
Prokaryotic and eukaryotic DNA replication
Binds to the single stranded DNA to inhibit it from rewinding
DNA polymerase iii
Prokaryotic and eukaryotic DNA replication
An enzyme that catalyses the formation of the DNA molecule. Can only synthesise from the 5’ to 3’ end of DNA
DNA primase
Present close to the opening of the replication fork
Synthesises RNA primers on the lagging strand as the DNA unwinds
DNA polymerase uses these to jump to the right spots and synthesise from 5’ to 3’
Okazaki fragments
Short fragments of DNA on the lagging strand between the RNA primers
RNase H
Removes RNA primers so DNA polymerase can fill the gaps
DNA ligase
Joins the Okazaki fragments back together (fills in the nicks) by joining the 3’ to 5’ ends
Gram bacterias
”-“
- more toxic
- less susceptible to antibiotics
- 2 complex thin layers of cell wall
- higher lipid content
”+”
- less toxic
- more susceptible to antibiotics
- 1 thick simple cell wall
- lower lipid content
Coupling reactions
Reactions that use another reaction’s energy so that it isn’t wasted.
E.g. the hydrolysis of atp and formation of G3P are coupled.
4 signal transduction pathways
- Distribution - Distributes the signal to more than 1 effector protein
- Relay - Related signal throughout the cell
- Amplification - Small amount can have a huge impact
- Detection - integrates the signal before Relaying it
What are Enzymes
Enzymes are biological catalysts that lowers the activation energy of reactions.
Increases rate of chemical reactions
How do enzymes lower Activation energy
- Properly orientate the substrates together
- Physically strain the substrate
- Adds chemical charge to substrate
Consequences of no oxygen in ETC
NADPH and FADH2
3 types of Cytoskeleton
- Microtubules(25nm)
- Intermediate filaments(12nm)
- microfilaments(7nm)
Purpose of Cytoskeleton
To maintain the cells structure by scaffolding and allows movement of organelles in the mitosis
Microtubules
Made of tublin dimer(alpha and beta)
Are responsible for girders that maintain the cell structure and play a role in moving chromosomes in mitosis
Intermediate filaments
Made of Keratin proteins that supercoil into thicker cables
Maintains shape by bearing tension
Anchors the organelles in the cell
Microfilaments
Made of actin protein that intertwine with each other
Maintains shape by bearing tension
Involved in muscle contraction and the cleavage furrow in mitosis
Cytosol
Jelly like fluid where biochemical processes occur.
Is the space between organelles and endomembrane
Free ribosomes can synthesize in the cytoplasm
Intermediates are shuffled around
Silent mutations
Mutation doesn’t change the amino acid sequence.
Photorespiration
Reduces overall CO2 fixation due to rubicso acting as both Carboxylase or Oxygenase.
Wasteful pathway
Evolutionary relic
C3 plants
Most plants are C3 plants, NO SPECIAL FEATURE to combat photorespiration
C4 plants
Minimize photorespiration by using PEP carboxylase instead to rubisco
CAM(Crassulacean acid metabolism)
Dry plants that separate Calvin cycle and CO2 fixation by time.
Stomata opens at NIGHT allowing CO2 to diffuses in.
During the day they photosynthesize but don’t open stomata
Embryogenesis
Formation of a multicellular organism from Zygote(single cell)
Zygote
Product of fertilization, leads to multiple rounds of cell division producing specific cell types along MAJOR SPATIAL AXES Patterns arranged according to the Body plan
NOT RANDOM
Plant Body plan
Anterior region has cells associated with structures of the head
Basal region has structures giving rise to the roots are found in the of Plant embryo
Cell fate establishment (Determination)
Arises during early stages of Embryogenesis
They commit to a particular path of differentiation
They become progressively more RESTRICTED
Instructive cues
Determine the developmental trajectory of cells
Takes the form of CYTOPLASMIC Factors
CYTOPLASMIC Factors
they are unevenly positioned between diving cells
or in positional formation in the form of a cell signalling molecule
Morphogenesis
SHAPES and Generates the body and its constituent parts
Processes:
- Cell division
- Change in shape(via cell expansion,movement detachment)
- Apoptosis(cell death) e.g human fingers used to look like frogs during embryogensis
Differentiation
Different genes expresses different Properties, Shapes, Functions
Housekeeping Genes
Expressed in all cells
- Proteins involved in protein synthesis
- Components of DNA replication
- Proteins involved cellular respiration
Differential Gene expression
Some genes expressed in 1 type but not another
Plant Morphogenesis associated with:
- Growth: Oriented Cell division(MORE PRECISE&Sedate) greatly influences cell’s fate
- Size expansion
- NO CELL MOVEMENT
- Differentiation
- Cell-cell communication: Regulates gene expression influencing differentiation
Animal Morphogenesis associated with:
- Cell divides more randomly(can still be orientated)
- Cell shape changes substantially
- Cell movement(GASTRULATION)
- Cell adhesion and de-adhesion forming tissue
Plant embryogenesis Body plan established
APICAL/BASAL axis established Shoot and Root + Polarity to establish which is the tip and which is the base.
Animal embryogenesis Body plan established
Anterior and posterior body plan
Formation of segments
Animal Post Embryonic growth patterns
No metamorphosis
e.g elephants
Plant Post Embryonic growth patterns
Indeterminate pattern of growth due to adaptation to a sedentary lifestyle
Key stages in animal development
- Fertilization
- Cleavage
- Gastrulation
- Organogenesis
- Metamorphosis
Animal development leads to formation of 3 germ layers
Outer layer - ECTODERM
Middle layer - MESODERM
Inner Layer - ENDODERM
Cleavage(In animal cell development)
- Zygote undergoes rapid division dividing Cytoplasm into smaller cells
- Division has NO GROWTH phases resulting in an embryo with a simple arrangement of undifferentiated cells
Blastula
Embryo with simple arrangement of undifferentiated cells
formed at the end of cleavage
Gastrulation:
- Establishes the BODY PLAN and Germ layers
- Simple embryo undergoes dramatic rearrangment, cell move into embryo folding inwards producing GASTRULA
- Body plan established with:
The main axes of the animal(anterior posterior right left dorsal ventral axes)
Sea Urchin development
- 3 laters of tissue in early embryo called germ layers established
- Cells at Blastula base break free from neighboring cells and migrate into the cavity to form MESODERM
- Short stubby bulge extends through cell rearrrangement and pulling force generated by cells at the tip of the bulge
Invaginated cells become the Endoderm
Invagination eventually forms a large thin tube becoming the gut - Once identities are established(Blastula base flattened)Gastrulation initiates.
- Opening created by invagination at the base of the blastula is the BLASTOPORE becoming the Anus
Stem cells
undifferentiated cells that can divide indefinitely
Stem cell division
Divides into a stem cell and a daughter cell
Gut’s stem cells residing at crypts divide to form intermediate daughter cells that form various types of cells in the lining of the gut
Cell potency
Totipotent: Highest potential, all cell types
Pluripotent - All cell types EXCEPT Extraembryonic tissue like placenta. (Embryonic cells and induced pluripotent stem cells)
Multipotent - Produce many cell types but are restricted(intestinal stem cells)
Unipotent - only 1 cell type(Skin stem cells)
Plant Hormones vs Animal Hormones
Plant
-Peptide, Small organic molecules
- Usually at many location
- Local or Distant
- Often diverse effects
- Regulated biochemical feedback
Animal
- Peptide, proteins, small molecules
- Specialized glands/cells
- Specific effects at 1 location
- Usually distant(transported)
- Regulated by Central Nervous System, ions and feedback
Plant stimuli and response
Light
Day length
Temperature
water availability
gravity
nutrients
–>
Shoot growth
Tropism(bending)
Flowering
Root growth
Factors affecting guard cell sizes
CO2 concentration
Air humidity
Temperature
Present of light(red and blue)
Hormones sent from the root when soils are dry
Plant hormone functions
-Controls growth and development
-seed dormancy
-Defense against herbivores and microorganisms
-Response against environmental stress
How is water regulated by hormones?
ABA(Abscisic acid) hormone reesponds tp environmental stress
Under environmental stress, ABA is translocated to guards cells increasing 20 fold in conc. The Osmotic potentail changes due to activation of Potassium efflux channels and potassiums influx channels deactivating leading to net loss of K+ out of guard cells.
Water potential less - than cell’s water potential
water MOVES OUT of guard cells closing apature as they become flaccid
Conditions for ABA accumulation
Water stress(Hot windy day, reduced water in soil and atmosphere)
ABA and drought response
- ABA bindings to Cellular receptors leads to TOTAL CLOSURE of Stomata
- Specific genes activated promoting longer term response to drought affecting plant growth. Decreasing shoot and Increasing root growth to extract more water from the soil
- ABA activates a group of genes that also encodes for hydrophobic proteins that bind to to membrane proteins to stabilize them preventing them from clumping together as that is what would happen in a drought
Plant Embryogenesis(4 steps)
- Establishes Apical & Basal axes of embryo + polarity.
Cell fates establishes by Cytoplasmic factors that are unevenly distributed in the cytoplasm - Formation of the spherical embryo and Linear suspensor from orientated cell divisions. Nutrients and signals conducted to to developing embryo
- Embryo goes from Radial symmetry to Bilateral symmetry caused by Cotyledons(Organic molecules)
Grasses & Cereals have 1 cotyledon(NOT bilaterally symmetric)
Forms shoot of meristems and radial pattern of tissue - Embryo becomes cylindrical in shape, cotyledon elongates
Differentiation develops shoot and root meristems at the “heart” in torpedo stage. - Extensive cell divisions and expansions and differentiation prepare for dormancy
End product of embryogenesis
A dormant seed
Cylindrical shape is well established
Root and stem generally retain this shape throughout their life.
3 Tissue systems of embryonic plant arranged CONCENTRICALLY, each with their own characteristic features
Apical and Root Meristems become apparent
Meristems
Plant tissues contain undifferentiated cells that can perpetually divide
Primary growth
Lengthens Root and Shoots
Undifferentiated cell at apical meristem divides eventually to become Primary Meristems
Secondary growth
Widens roots and stems
Lateral meristems(Cork and Vascular cambrium) contribute to secondary growth
Act to support the plants lengthening
Primary meristems consist of
Protoderm: Dermal tissue(Epidermis) protective outer layer + promotes gas exchange
Ground Meristem: Ground tissue, most of the body(Pith + cortex)
Procambium: Vascular tissues(Xylem+phloem)
Lateral meristems consist of
Cork cambrium: Produces Periderm cork to the outside and phello derm to the inside forming the
Vascular cambrium produces secondary xylem(wood) and secondary phloem(bark)
3 over lapping zones of cells
- contains root apical meristem
- New cells lengthen and extend root tips
- Cell differentiate into distinct types
Lateral shoots
or Branches grow from AXILLARY buds. Don’t grow near active apical meristems due to hormones inhibiting them. This is APICAL DOMINANCE
Lateral roots
Originates in the PERICYCLE(near the center of the root)
Disrupts outer tissue as they emerge
What does damage to apical meristem do to apical dominance?
Apical dominance disrupted to PRUNING encourages growth
4 types of tissue
Connective tissues
Muscle tissues
Epithelial tissues
Nervous tissues
Definition of tissue
Group of structurally similar cells working together as functional units
Tissues in Small intestine
Network of Nervous tissues
Smooth muscle
Epithelial and connective tissue
Epithelial tissue
Mucosa(connective tissue)
Functions:
1. Network of nervous tissue
2. Smooth muscle
3. Epithelial tissue
4. Epithelial and connective tissue
5. Mucosa(connective tissue)
- Controls and coordinates contractions of smooth muscles + provides sensory function
- Moves food through gut
- Secrete digestive juices, hormones, and some absorb nutrients in lumen
- Covers abdominal organs and line abdominal activity
- Secretory cells present
Organ systems function
Group of organs that work together to carry out certain functions
Circulatory system
Its central to the proper functioning of the body interacting with the:
Respiratory
Digestive
Excretory
Endocrine
to achieve a functioning organism
Respiratory system
Blood flows through the walls of air sacs(Alveoli) ensure the rapid exchange of gases, oxygenating and depleting CO2 in the blood.
Digestive system
Circulatory system transports nutrients ions Fe water from the gut to rest of the body
Endocrine system
Circulatory system ensures that hormones move throughout the body
Excretory system
Removal of nitrogenous waste by circulatory systems supply these organs with blood with waste + force that is required by kidneys to extract waste from blood.
3 types of cell-cell junctions
1.Tight
2. Anchoring
3. Gap
Tight junctions
Hold adjacent plasma membranes together and acts as barrier to flow of molecules through intracellular spaces
Anchoring junctions
Form interconnected cytoskeleton network across cells that helps resist mechanical forces
Gap junctions
Dispersed throughout plasma membrane(particularly to basal end) acting as communication channels between adjacent cells allowing molecules
Extracellular matrix
Interconnected network of fibers and ground substance mostly interstitial fluid filling the space between the cells connective tissue fibers and capillaries
Nervous tissue regions(4 regions)
Dendrites
Soma
Axon
Axon terminals
Gilal cells
Provide mechanical and nutritional support for neurons(e.g SCHWANN Cell)
They DO NOT GENERATE action potentials
Skeletal muscle
Composed of bundles of muscle cells(AKA fibers)
Have multiple nuclei in them and contain MYOFIBRILS whici are made from Sarcomeres composed of thick Myosin and thin Action Filaments.
Myosin using atp
Use energy from from ATP to undergo a movement pulling action filaments resulting in them sliding pass each other
Sarcomeres shortens to
contract muscle
Why do plants need nitrogen?
Protein, DNA synthesis, continual growth
Why do plants need phosphorus?
DNA synthesis, ATP, phospholipids
What happens if plants lack iron
They turn yellow because of irons important role in the biosynthesis of chlorophyll and the maintenance of chlorophyll
Advantages of an open circulatory system
Exchange of material is direct between hemolymph and tissues.
There is no diffusion barrier
Disadvantages of an open circulatory system
Little control over the distribution of hemplymph to body regions.
No mechanisms for reducing flow to a specific part of an organ
Advantages of a closed circulatory system
Fine-scale control over the distribution of blood to different body regions is possible.
Muscular walls of vessels can constrict and dilate to vary the amount of flow through specific vessels.
Blood pressure is fairy high and circulation can be vigorous.
Disadvantages of a closed circulatory system
It more a more complex system which requires a lot more energy for blood distribution
Fish circulatory system
2 chambered heart, blood flows through gills, systemic capillaries, and back to heart. Heart only pumped deoxygenated blood. Very high blood pressure.
Amphibian circulatory system
Partial double circuit
3 chambered heart, 2 atria delivers blood to same ventricle mixing both oxygenated and deoxygeneated blood.
Separation of pulmonary and systemic circuits by structural feature allow only partial mix.
Bird and mammal circulatory system
4 chambered heart, the complete separation of the systemic and pulmonary circuits. The two circuits operate at different pressures.
Do insects have closed circulatory systems?
No
Does the circulatory fluid in a closed circulatory system move faster compared to an open circulatory system?
Yes
Are the circulatory fluid and the interstitial fluid capable of mixing in a closed circulatory system?
No
Are valves that ensure one way flow present in both open and closed circulatory systems?
Yes
Are separate pulmonary and systemic circuits present in birds?
Yes
Superior vena cava
A vein that carries deoxygenated blood from the head, neck, arms, and chest to the heart (right atrium)
Inferior vena cava
A vein that carries deoxygenated blood from the legs, feet, and organs in the abdomen and pelvis to the heart (right atrium)
Pulmonary artery
Carries deoxygenated blood from the heart to the lungs
Pulmonary vein
Carries oxygenated blood from the lungs to the heart
Aorta
Carries blood from the left ventricle into systemic circulation
Apoplast vs Symplast
Apoplast: space outside plasma membrane that allows free movement of material, non-living, slightly faster
Symplast: interconnected pathway through cells via plasmodesmata, living, slightly slower
Casparian strip
Forces water and solutes to cross the plasma membranes of endodermal cells instead of slipping between the cells.
Degeneracy of the genetic code
More than one codon can code for an amino acid(the 3rd codon is responsible for degeneracy)
Advantage of degenerate genetic code
Safe guards in case of mutation
Translation initiation difference in prokaryotes vs eukaryotes
Prokaryotes - ribosome binds to shine-dalgano sequence
Eukaryotes - ribosome binds to AUG codon
Germline mutation
Mutation present prior to fertilisation, entire organism carries mutation, passed onto new generation
Somatic mutation
Mutation present after fertilisation, specific cells carry mutation, not passed onto new organism
What are the three common DNA repair mechanisms?
- Base excision repair - fixing hydrolytic dna damage
- Nucleotide excision repair - UV & some carcinogens
- Mismatch repair - Fixes faulty base incorporation during replication
When does independent assortment occur?
Metaphase 1
When does crossing over occur?
Prophase 1
What does RNA polymerase bind to in transcription?
Promoter
What does the 5’ cap do for mRNA?
Protects the end from degradation
Helps ribosome to bind to mRNA
What does the 3’ tail do for mRNA?
Protects the end of the transcript from degradation
Signals to transport molecules the mRNA is ready to leave the nucleus
What does spliceosome do
Cuts out introns
Attaches exons together
Are there any tRNAs that recognise STOP codons?
No
How can mutations be induced?
Agents from outside the cell cause mutation:
Nitrous acid - causes deamination
Benzopyrene - adds chemical group to guanine
Radiation - X-rays and gamma-rays can break sugar-phosphate backbone of DNA
UV radiation can cause covalent bonds between adjacent thymine bases
Small mutations
Point mutation
Insertion
Deletion
Large mutations
Gene duplication
Inversion
Genome duplication
Insertion mutation
A small number of bases is added
Deletion mutation
A small number of bases is removed
Point mutation
One base is swapped for another
Gene duplication mutation
Entire gene is copied
Inversion mutation
Change in the orientation of a chromosomal region
Genome duplication mutation
Double number of chromosomes in an individual
Synonymous mutation
A change of one nucleotide to another that does not effect the amino acid specified
Non-synonymous mutation
A nucleotide substitution that does change the amino acid sequence encoded by a gene
Missense mutation
Non-synonymous: Amino acid is changed
Non-sense mutation
A stop codon is added instead of amino acid
What are copy number variations (CNVs)?
Segments of DNA that are duplicated or deleted
Can be problematic or not
What are single nucleotide polymorphisms (SNPs)?
Variation at a single base pair
What is the law of segregation?
Every diploid organisms carries two copies of each gene, called alleles.
Formation of gametes in meiosis causes chromosome pairs to seperate so that the offspring receives one allele from each parent
Autosomal recessive
Requires both copies from the parent for the phentoype of be shown
What is epistasis?
The effect of a gene mutation is dependent on the presence of absence of mutations in one or more other genes
Parental alleles in the cis arrangement
The parental chromosome has both wild type alleles on one chromosome and both mutant alleles on the other chromosome
Parental alleles in the trans arrangement
When the wild type allele of one locus and the mutant allele of the other are on the same chromosome and vice versa
3 types of horizontal gene transfer
- transformation
- transduction
- conjugation
Lytic cycle
Bacteria cellular machinery is taken over
Host DNA is destroyed
Forced to produce more viral components
Lysogenic cycle
Phages reproduce without killing host
Phage DNA recombines and integrates with the bacterial genome
How did the griffifths experiment prove dna was genetic material
R and S strains were added together, strands were responsible DNase injection was the one that didn’t kill the mouse, protease and RNase killed mouse.
PCR
denatures dna bond and then uses dna polymerase from hot springs to synthesize new dna strands doubling the dna sequence over and over again
Bacterial transformation technique
Bacteria can either be naturally or induced to be competent
Induced:
The bacteria’s plasmid will be inserted with the target gene and then added to solution of competent bacteria. It undergoes heat shock treatment allow bacteria to take up dna
Then antibiotic resistance is added to allow resistant bacteria to thrive
Fertilization
2 haploid cells fuse to produce a diploid
DNA damage
Heat
Radiation
Oxidation by free radicals from Respiration
Hydrolytic damage causing deamination and depuriniation in bases
Meiosis 1
Prophase: Chromosomes condense, HOMOLOGOUS Chromosomes pair forming TETRADS. CROSSING OVER occurs.
Metaphase: Dissolution of nuclear envelope + Formation of Meiotic spindle. Paired homologous chromosomes randomly positioned, centrosome of each chromosome in the tetrad attaches to opposite poles of spindle. independent/random assortment
Anaphase: centromeres pull homologous chromosomes apart, now 2 haploid sets of genome
Telophase: Chromosomes decondense+nuclear membrane reforms around each haploid
Cytokinesis: 2 Haploid daughter cells
Meiosis 2
Prophase: Thickens and shortens chromosomes. Meiotic spindle forms + nuclear membrane dissolves
Metaphase: Chromosomes line up at equator attaching to spindle fiberes from both poles.
Anaphase: Sister chromatids that make up the chromosome are pulled apart after undergoing independent assortment
Telophase: Nuclear envelope reforms and chromatids decondense( chromosomes remain unreplicated)
Cytokinesis: Divides each parental cell into 2 haploid cells.
3 steps of transcription
- Initiation - Pre-initiation complex assembles around core promoter of gene + RNA Polymerase recognises the promoter and binds. Pre-initiation complex unwinds a short stretch of DNA upstream of transcription start site
- Elongation - Elongating RNA produces and Complimentary RNA nucleotides introduced by RNA Polymerase
- Termination - Release of RNA polymerase from DNA and releases the RNA transcript
RNA splicing
Removal of introns and splicing exons. 5’ cap & 3’ tail removed
Prokaryote vs Eukaryote polymerase
Eukaryote:
- Multiple general transcription factors assist to recruit RNA polymerase to the promoter
- 3 DNA polymerase each transcribe different classes of RNA(Pol1:Ribosomal genes, Pol2: Protein encoding genes, Pol3: tRNA small RNA suRNA)
Prokaryote:
- Transcription factor called sigma associates with core enzymes producing rna polymerase HOLOENZYME to initiate transcription
- 1 DNA polymerase consisting of 5 polypeptide subunits(2 alpha, b, b’ omega)
tRNA
Anticodon complimentary to mRNA codon
No tRNA corresponds to stop codons
Charged tRNA
when tRNA attaches to AA it becomes charged, specfici enzymes(tRNA Synthetase) is required to charge each tRNA
Gene regulation(2 ways )
- Epigenetic(histone) modifications - Modify the structure of DNA molecule WITHOUT changing its sequence via Methylation or Acetylation
- Small regulatory proteins
Can inhibit translations stopping the gene from being expressed in protein
Translation 3 steps
- Initiation - start codon recongnized by either shine dalgadro sequence(pro) or start codon(euk) and then initiator tRNA(with met) is placed at complementary AUG start codon and large subunit associates
- Elongation - Ribosome moves from 5’ to 3’ tRNA enters in P sit with ribosome catalysing formation of peptide bond between AA as the ribosome repositions uncharged tRNA is released from E site
- Termination - Stop codon reached, tRNA does not recognise but release factors do releasing the entire AA sequence
Open reading frame
A region of DNA sequence that corresponds to mRNA transcript tjat can be translated
Transposons(jumping genes)
DNA elements that can move from 1 position to another via TRANSPOSITION
Create or reverse mutations
DNA elements that in both Euk and Pro.
Contain DNA sequence of 100-1000 nucleotide bp
They genetally carry genes that encode enzymes needed for movement
Replicative transposition
Transposons copies itself to new part of the genome. If it lands within a gene, protein coding sequence may be interrupted.
DNA damage factors
Heat
Radiation
Oxidation(from respiration)
Hydrolytic damage(deamination and depurination)
Why do plants needs water
required for:
- Photosynthesis
- transporting solutes between organs
- Cooling plant(Latent heat loss)
- Structural support(Turgor pressure)
Source vs Sink
Source: Tissue that creates carbohydrates more than it requires from photosynthesis
Sink: Tissue(roots or stems) that consumes sugar for its own growth
Latent Heat loss
Occurs from transpiration, it lets plants remain cool. H2O moves from cells to intracellular spaces changing phases from liquid to gas and vapor diffuses out from Stomata to atmosphere
Cation exchange(for minerals)
Plant roots release H+ and CO2. CO2 tform HCO3-(bicarbonate) with water. The H+ binds to soil particles releasing + charged ions(k+) to soil solution making nutrients available for to plants
Roots absorption for minerals and water
Mineral(active):
Minerals actively transported to maintain gradient
H2O(Passive):
H2O passively diffuses into the apoplast
How to water and minerals enter the symplast?
Cell-cell communication
Trachieds vs Vessel elements
Trachieds:
“s” spindle shaped cells with cavities going through secondary cell walls allowing H2O to move with little resistance from 1 trachied to its neighbors
Vessel elements
Larger diameter than trachieds
Meet end to end partially breaking down end walls for an open pipeline for H2O flow
Transpiration
Drives H2O movement in the the Xylem
H2O vapor diffuses out from stomata down the conc gradient allowing for surface of mesophyll cells to create SURFACE TENSION. Increased surface tension pulls the water out of the veins into the APOPLAST of mesophyll cells. Tension in leaf veins pull H2O from the stem
Translocation
Distributing/moving sugars to other plant tissues
Phloem sap is made of(4 things):
Sugars
AA
Hormones
Minerals
Phloem vs Xylem cells
Xylem:
Dead
Carries H2O and minerals
Phloem:
Alive
Carries sugars, proteins AA
Pressure Flow hypothesis
H2O follows sugar into phloem by OSMOSIS increasing PRESSURE with in the phloem driving phloem sap movement
Companion cell
Provides all substances needed to keep SIEVE TUBE ELEMENTS ALIVE by perfomring metabolic functions form them
Connected to plasmosdesmata
Mass flow hypothesis 5 steps
High pressure to Low pressure
1. Loading(atp required)
Sucrose and other solutes actively transported from SOURCE to Companion cells. Flow into sieve tube cells through plasmodesmata
2. More - solute potential in Sieve Tube elements from sucrose accumulation. Sucrose conc is higher than surrounding cells and water enters from adjacent xylem via osmosis
3. Entry of H2O causes increasing in turgor pressure causing more + water potential. Entire fluid content of sieve tube pushed towards Sink with lower pressure.
4. Sucrose unloaded into sink cells both passively and actively from the companion cells
5. H2O leaves phloem via osmosis reinforcing the pressure gradient
Gas exchange in lungs
- O2 goes into lungs mixing with residual air decreasing Alveolar partial pressure of O2 and increasing uptake of O2 in lungs
- O2 diffuses through alveoli into neighboring capillaries(lower Partial pressure)
- Tissues where partial pressure O2 is lower leads to O2 dissociating from Hemogloblin
- CO2 follows partial pressure as well diffusing from tissue to blood and transported back to the lungs
Heart anatomy(3 layers of tissue )
EPICARDIUM - Outermost and surrounds by perocardium
MYOCARDIUM - Cardiac muscle cells making up majority of heart’s wall
ENDOCARDIUM - Lines the myocardium
Cardiac cycle
Rapid coordination of contraction(SYSTOLE) and relaxation(DIASTOLE)
Cardiac cycle steps
- Electrical signal sent for SA node near right Atrial wall causes both atria to contract pushing blood to ventricles
- When pulse reaches AV node, it pauses 1/10 of a second for blood to empty from the Atria. The CHARGE SPREADS through HIS BUNDLES down the intraventricular septum through the bundle branches until in reaches PURKINJE FIBERS inducing Ventricular CONTRACTION pumping blood to AORTA
- While Atria in DIASTOLE is filled with blood when ventricles relax, blood enters it and cycle repeats
Blood flow is regulated by
Neurological signaling and hormones
How is blood regulated during exercise
VASODILATION to muscle cells
VASOCONSTRICTION away from the digestive system
How does high pressure mitigated?
Aorta to smaller ARTERIALS AND CAPILLARIES reduce pressure due to increased combined diameters
Why does blood flow slow down
Allows time for gas and nutrient exchange with small blood vessels
Why do extreme pressure swings dampen as blood enter MAJOR ARTERIES
Extreme pressure swings dampen as blood enter MAJOR ARTERIES as their elastic property allow them to stretch and store energy VENTRICULAR CONTRACTION. When ventricles RELAX the pressure decreases the walls return to being their normal diameter providing force to countinue supplying the pressure to drive blood through the body. Leads to SMOOTHER Blood flow
When does pressure drop
As it move down the capillaries, LOWEST AT RIGHT VENTRICLE.
Measuring blood pressure with cuff(3 steps)
- Inflated cuff cutting off all blood flow
- Air is released until the sound of blood pulsing through main artery can be heard
- Further air released from the cuff until sound of blood in the arm vessel continuous
Cuff below the diastolic pressure in artery
Air pathway
Trachea
Bronchi
Bronchioles
Alveoli
Fine capillaries cover the alveoli, site of gas exchange
Slow Flow
Maximizing time for exchange
Large proteins do what to osmotic pressure
Present in blood plasma and CANNOT leave capillaries due to size to STABILIZE OSMOTIC PRESSURE
Does pressure potential(BP) vary along the length of capillary, difference in pressure
Yes
Filtration process
H2O and solutes diffuses through space of Endothelial cells, special regions in capillary wall called FENESTRATIONS
What does BP do to H2O potential?
BP lowers H2O potential of capillaries and its lower than Interstitial fluids. H2O moves back via osmosis
What happens when:
BP more than Osmotic pressure
BP lower than Osmotic pressure
Fluids leave capillary
Fluids return
