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Why study Animal Physiology? and what are Physiology’s 2 central questions?

• Human health and disease
• Evolution
• Understand Behaviour
• Conservation (in terms of climate change we can see how animals respond to changing environments)
• Physiology integrates most of the sciences!
(math-rate functions, chemistry-ATP production, Physics-Locomotion, Psychology-Behaviour)

Physiology’s 2 central questions: how and why (or aka Mechanism and origin)


describe the 4 Important Physiological Concepts

•Homeostasis-physiological processes which maintain
most of the constant states of the organism

• Time- Physiology can change in an animal throughout time (can have programmed changes or changes in response to env)

• Plasticity- The ability of an animal (single genotype) to express two or more genetically controlled phenotypes (the 3 A's)

• Body Size- Most physiological characteristics are a function of body size (Brain size, Heart rate, Age at sexual maturity, Metabolic rate)


define Regulator, Conformer animals

Relationship between the internal and external environment
• Conformer: internal = external
• Regulator: internal ≠ external, costly

• Animals can use both strategies for different characteristics


define Acclimation, Acclimatization, Adaptation

1. Acclimation
• A chronic response to a change in an environment
• Laboratory response

2. Acclimatization
• A chronic response to a change in a natural environment

3. Adaptation: happens over multiple generations, evolution
->When an animal actually evolves to a new environment. Now has a different set of genes.


role of Plasma and intracellular membranes

• Compartmentalize regions of the cells
• Cell signalling
• Transport


describe the membrane bilayer and the flexibility of the structure

Bilayer formed by phospholipids
• Amphipathic (have both hydrophobic and hydrophilic parts)
• Variety of chemical structures

->Phospholipids are flexible and are not set in their structure (Not covalently bound to each other). As the tails become more unsaturated the bonds tend to put a kink in the tail and the membrane becomes more fluid and the cell is more flexible. Butter vs olive oil. Flexibility depends on structure of hydrocarbon tails.


why is membrane fluidity important?

1. it allows membrane proteins rapidly in the plane of bilayer.
2. It permits membrane lipids and proteins to diffuse from sites where
they are inserted into bilayer after their synthesis.
3. It enables membranes to fuse with one another and mix their molecules.
4. It ensures that membrane molecules are
distributed evenly between daughter cell when a cell divides
5. it varies with environment
6. allosteric modulation of membrane enzymes


Membranes respond to a variety of stimuli? (4)

• Fasting
• Dietary changes
• Hibernation
-temperature (High temperatures cause the fluidization of membranes)
• Etc.


describe the 2 Membrane Proteins

-usually permanent and transmembrane

• Bound non-covalently to one side of the membrane
• Can be added or removed easily


what are the Five functional types of membrane proteins?

Channels- allow things to pass through passively. Simple pore
Transporters/carriers- move things actively (it is facilitated diffusion if metabolic energy is not employed)
Enzymes- catalyze reactions with substrates on membrane (covalent bonds are formed or broken)
Receptors- mediate response of cell to chemical messages arriving outside membrane. (bind to specific molecules and initiate change in membrane permeability or cell metabolism)
Structural proteins- connect one cell to another, creates junctions between cells


what is epithelia?

-Sheet of cells that cover a surface or line a cavity (make up bulk of a lot of animals)
-Cell-cell interactions


why are cellular junctions important and what are the 3 types

Important for:
• Cell-cell interactions
• Cell-cell communication
• Transport across epithelia

1. Tight junctions- two cell membranes meet or fuse at ridges
2. Desmosomes- block of passage in-between cells and the contact between cells is strengthened
3. Gap junctions- block passage between cells but also create tiny pores to allow communication via the two cell's cytoplasm


two types of Transport across epithelia

1. transcellular paths- materials must cross both apical and basolateral epithelia cell membranes

2. paracellular path- only small molecules can do this as they have to be able to move past tight junctions between epithelia cells


describe Enzyme Kinetics (what is vmax and km?)

Reaction rate is dependent on substrate concentration (no substrate = no reaction) and enzyme affinity
->At some point the enzymes will become saturated and cannot process the substrate any faster (this value is Vmax). Increasing the number of enzymes can increase the Vmax
->Can use the graphs of different enzymes to determine its Km (not all work at the same speed or have the same affinity for their substrate). Km found at half maximum velocity (Km is the conc of substrate that you need to reach 50% of enzymes Vmax) Km= 1/2(vmax)
*Lower affinity enzymes need more substrate present to get going (high Km) even if they have the same Vmax as a high affinity enzymes


how is The function of an enzyme regulated by allosteric modulation

Allosteric modulation:
 Anything that’s not covalently bound to enzyme
 Inhibited or up-regulated
 Other non-substrate ligands
 Membrane fluidity (for transmembrane enzymes)


how is The function of an enzyme regulated by covalent modulation

regulated by covalent modulation:
 Phosphorylation and dephosphorylation (Protein kinases )
 Allows enzyme to function or not function


what are enzyme isoforms and what is their significance

similar functioning enzymes that are slightly structurally different and may function a bit differently but catalyze the same reaction
-Isoforms allow animals to live in new environments or have new functions
-Inter- and intraspecific isoforms (different isoforms within a species and between different species)
-Enzymes can evolve quite easily. Each animal is related in terms of the LDH allele they express.


describe how Enzymes are instruments of change at all time frames

• Acute: allosteric or covalent modulation
• Chronic: expression of genes for different enzymes or isoforms
• Evolution: mutations to genes over time, acted on by natural selection selection (results in mutations and altered genes)

• Development: programmed enzyme expression
• Circadian rhythms: internally programmed enzyme function


• In all cases, cells require what to communicate to each other?

cells require a receptor for the signal and a transducer to
act on the signal (a way to turn signal into an actual message)


how do receptors work? what are the 4 types

Receptors bind extracellular ligand and usually rely on second messengers to transmit signals (ligands are first messengers)
-ligand gated channel
-G protein coupled receptor and associated G protein system (after binding to ligand, receptor binds second messengers- g protein and enzyme)
-enzyme/enzyme linked receptor
-intracellular receptor (ligand diffuses across membrane before binding with receptor)


what is Signal Transduction

the transmission of molecular signals from a cell's exterior to its interior. Signals received by cells must be transmitted effectively into the cell to ensure an appropriate response
• Receptors activate second messengers: often amplify message to cell
• Cyclic AMP
• Cyclic GMP


what can the cone snail do to fish receptors?

it poisons the fish and paralyzes it by binding its alpha-conotoxin to the fishes receptors and preventing acetylcholine to bind (channels stay closed and muscle cannot contract)


what are Genomics, proteomics and metabolomics ?

- study of the genome
Epigenetics: modifications of gene expression that are transmitted

- The study of proteins synthesized by the cell
-2D-Gel Electrophoresis for protein screening and Western-blotting for protein expression

- The study of organic compounds in the cell, the biochemical phenotype


what are the two main goals of genomics

2 main goals:
o Evolution of genes
o Function of genes


describe what is looked at for the evolution of genes in genomics

Mechanism of gene modification
• Base substitutions
• Duplication
• Partial or full deletions, mutations that block transcription
Timeline of evolution
• When did modifications, loss, duplications, etc. take place? And why did it happen at that particular point in evolution time


why doesnt the Antarctic ice fish produce hemoglobin

Evolved in harsh/cold environments. Only vertebrates that don’t have hemoglobin in their blood which is important for the transport of oxygen. How do these fish survive and why did they end up that way? Is the gene for hemoglobin lost or is it there and just not expressed? In ice fish, they completely lost the beta part of the gene and there is no way for them to produce hemoglobin.

Graph: The loss of hemoglobin gene happened only once, bc everyone after that point doesn’t have hemoglobin either.


Was the loss of hemoglobin in the icefish a disadvantage or an advantage acted on by natural selection?

Less oxygen into the body is usually a disadvantage -> especially if the fish is active. Therefore they probably didn’t lose it on purpose. The ventricles became very big in the fish to pump around more oxygen. Natural selection for the fish without hemoglobin selected for bigger and bigger hearts but now are restricted to living in cold waters because oxygen concentration is higher/more saturated in cold water.


describe what is looked at for the function of genes in genomics

• Newly sequenced genes can be related to previously sequenced similar genes of known function
• This is only a hypothesis and must be tested
• The function might not be the same in a different animal
• The gene might not be expressed at the same time and in the same tissues
• Patterns of transcription
• Patterns of translation
Transcription ≠ Translation


how can we can look at physiology from the top down and bottom up?

Top down:
Here is an animal living in this context, how is it doing that? What are the tissues doing? What are the genes?

Bottom up:
Sequenced the genes of a cool animal, don’t know what the genes do? what proteins do the genes code for?


what are Microarrays

example of gene screening where you take a snapshot of changes of gene expression in two different conditions. Under certain conditions, expresses certain genes.
-Allow mRNA to bind to DNA and gives an idea of expression. Less mRNA will result in a change in color.
-You can tell from this if transcription went up, went down or stayed the same


what is Western-blotting for protein expression

Separate protein in sample based on size by getting transferred from cell onto membrane.
-You can get an image of how much protein was there and whether there was more under one condition or another.


2D-Gel Electrophoresis for protein screening

Take snapshot of all proteins in the cell. separate based on size and isoelectric point. Can run this for cells under different conditions. (high altitude people had different protein concentrations compared to low altitude people)


what is looked at in Metabolomics

Understanding what the proteins are doing to the chemicals in the cells
• Snapshot of all of the metabolites or specific ones. Can do it using mnmr spectrums. Which peaks correspond to what compounds?
• Understand what metabolic pathways are active
• Broad approach to understanding metabolism by screening metabolites
• Biomarkers! (How animals may respond to their environment by looking at the change in their biomarkers)



Modifications of gene expression that are transmitted during gene replication

• Within (development) or between generations (inheritance) of individuals
• Mechanism by which the effects of the environment of one generation can be passed onto the next
• Phenotype passed onto offspring
*Important note: there is no change in the gene sequence! (expression pattern of genes is passed on)
• Genes can be marked by methylation or covalent
modification of histone proteins (Mostly done via DNA methylation) *Mainly in vertebrate animals


what are pros and cons to the Application of the -Omics to physiology

• Fast
• Lots of information
• Generate hypotheses
• Evolutionary information

Cons (if used on their own):
• Limited functional information- cant extrapolate information
• No direct application to the animal


Simple Passive Diffusion

• Concentration gradients drive diffusion; Electrical gradients also influence diffusion
• Some solutes, gases, heat
• Aqueous or gaseous solution
• Uniform distribution without the input of energy
• Molecules move from areas of high concentration to low
concentration across membrane passively


Fick Equation

distance and concentration are the main factors to how fast things move across membrane
J= D((C1-C2)/X)
J= rate of diffusion
D= diffusion coefficient (standardized value for certain membrane at certain temp)
C1= high conc
C2= low conc
X= distance


what is the Boundary layer?

Things will start to slow down because in boundary layer the conc is higher and builds up outside of the cell. Cell in solution where it's not moving, a boundary layer builds up and things move slowly leaving the cell. (important for blood?)


describe Phospholipid Membrane Diffusion

Small, non-charged molecules (O2) or hydrophobic molecules can
diffuse through the membrane relatively easily
• Most other charged, hydrophilic or large molecules require a transporter
The simplest transporters are ion channels:
• Some are open
• Some are gated


what are the 4 different types of transporters/channels

A. Voltage gated channel: pos and neg charge swap sides and the change in membrane potential open gate
B. Stretch-gated channel: more tension = gate stretched open
C. phosphorylation gated channel: Channel often opened by phosphorylation
D. ligand gated channel: Channel may be opened by the binding of a ligand


Facilitated Passive Diffusion

1. Always follows electrochemical/concentration gradient (passive)
2. Require transport proteins (facilitated)
3. Bind reversibly to transport proteins
Example: Glucose (polar)


Active Transport

• Sometimes ions have to be moved against their electrochemical
• Requires energy input
• Rate of transport is saturable
First discovered when studying stomach acids:
• H+ concentration is 2 millions times higher outside the cell than inside!


Primary active transport vs secondary?

-energy is derived directly from the breakdown of ATP
Na+-K+ Pump- active transport 3 Na for 2 K (pumps out Na against concentration gradient). Example of primary active transport (ATP is being used at transporter)
-a transporter protein couples the movement of an ion (typically Na+ or H+) down its electrochemical gradient to the uphill movement of another molecule or ion against a concentration/electrochemical gradient
-ex. = transport of glucose: Na pumped out of cell into extracellular space via ATP and lowers Na conc inside the cell. This creates a conc gradient for the Na which glucose uses to its advantage. Glucose is able to come in by using Na’s conc gradient that was created


what is a hyperosmotic fish

fish has greater concentration of solute ( salt water compared to fresh water) compared to surrounding water
-Fresh water fish always bombarded with an influx of water that diffuses across gills (water tries to counteract the highly concentrated cells inside fish)


Can animals build up an amino acid store?

Animals cannot store unused amino acids or proteins like lipids
• Amino acids are synthesized as needed, or obtained from the diet
• Excess amino acids from the diet are stripped of their nitrogen which is excreted
Even with freely available nitrogen, animals are unable to
synthesize ~10 of the standard amino acids
-Unused aa’s may be deaminated and all that’s left is a carbon skeleton. Pyruvate may be put into the Kreb cycle to make ATP.


Lipid types

• Triglycerides
• Phospholipids
• Cholesterol(precursors for steroid hormones that most animals need)
• Cell membranes
• Storage
• Hormones (steroid)\
o Most animal sp. Cannot make unsaturated fatty acids (add double bond to fats). Therefore most unsaturated and polyunsaturated fatty acids come from eating fish
-Lipids provide a lot of energy (fats).


• 3 roles?

1. Structural support – cellulose, chitin
2. Energy storage – glycogen ->liver and skeletal muscle for a quick need for energy/glucose for high exertion
3. Transport
No essential carbohydrates
• Some animals cannot digest cellulose/chitin on their own


Symbiotic relationships (3)

o 1. Photosynthetic autotrophs
o 2. Chemosynthetic autotrophs- bacteria can use sulfer groups that get fixed and animals can use its products
o 3. Heterotrophic microbes: fermenters – common in mammals with microbes in their gut to digest plant material for them (cows, deer, horses-ones that eat a lot of plant material)


• Digestive enzymes may be located in 3 different places ?

o Intraluminal – in the intestines
o Membrane- associated – connected to cell walls of the lumen
o Intracellular


Carbohydrate Digestion

Larger polysaccharides are broken down in to disaccharides or
• Cellulase: no vertebrates
• Chitinase: some vertebrates
• Amylase: all vertebrates
• Maltase breaks disaccharides into glucose
• Intraluminal and membrane-associated enzymes


Protein Digestion

• More complex than other forms of digestion
• Enzymes are pre-formed as inactive molecules=zymogens
• Activated when they reach the lumen
• Pepsinogen → pepsin (active form in the stomach) *Most common preformed enzyme
• Further breakdown into free amino acids in the midgut
• Trypsin, chymotrypsin, carboxypeptidase, etc.


Lipid Digestion

oDon’t get broken down until the midgut
oSome harder than others to breakdown (phospholipids, cholesterol)
• Pancreatic lipase and bile salts
• Yields glycerol, free fatty acids, monoglycerols
• Phospholipids and cholesterols require other enzymes
• Phospholipase, esterases


how do Ghrelin and leptin work in opposition

Series of hormones (leptin) that travel to the brain to trigger fullness (nutrients needs have been met). Ghrelin signals brain when we need to eat (response to lack of material in digestive system and low glucose levels


Nutritional Changes over Time?

• Number of transporters
• Length/size of digestive tract
• Gene expression of certain enzymes *Gene expression of lactase decreases after young doesn’t need milk anymore

• Affected by dietary changes, development, circadian rhythms (Animals that feed nocturnally will have more transporters expressed at night)
• The gut is highly malleable


Some energy in the food we eat we cannot get access to because we can’t break it down (lost in our feces). What’s left (absorbed chemical energy), goes into 1 of 3 pathways?

1.biosysnthesis 2. Maintenance 3. generation of external work



• Growth
• Energy storage (mostly in the form of adipose tissue or glycogen in liver in small amounts)
• Organic compounds
• Gametes
• Milk
• Mucus
• Hair
• Etc.


2. Maintenance

functions we do to survive
• Circulation
• Respiration
• Nervous system activity
• Gut motility
• Tissue repair


3. generation of external work

Applying mechanical forces outside
the body
• movement


Metabolic Rate

• Rate at which an animal consumes energy
• Produces heat and work
• Calories or Joules
• If you know the metabolic rate, you can calculate the requirement for food (chemical energy)
• Measured using direct calorimetry


measuring metabolic rate

Heat production is the most direct way of
measuring metabolic rate
-Not very functional
-Most now use indirect methods


Indirect Calorimetry

Respirometry= consumption of oxygen per unit time. When you metabolise glucose, it becomes oxidized. Need six moles of O2 to fully oxidize glucose


Respiratory Quotient

Consuming food does not mean it is fully oxidized
Using the RQ we can estimate what compounds are actually being oxidized
RQ =mol CO2 produced/mol O2 consumed per unit time


Basal Metabolic Rate

Least amount of energy an animal needs to maintain itself, to stay alive. Can measure this under a certain set of conditions
• Standardized set of conditions for measuring metabolic rate for easy comparison between animals
1. Same temperature
2. Fasting
3. Resting


Two factors that have a large effect on all animal metabolic rate

• 1. Physical activity- need more energy for your cells to work harder
• 2. Environmental temperature -(depending on whether animals are endo or ectothermic -> we (endotherms) buffer against environmental temperatures and therefore temperature has less of an effect on endotherms compared to ectotherms


There are other less influential factors on metabolic rate

• 1. Digestion- requires energy input to break down meals and absorb all the materials. Protein takes a lot of energy to breakdown
• 2. Body size- bigger animals need more energy because they have more cells to fuel
• 3. Age- typically younger animals have a higher metabolic rate (because they are still growing)
• 4. Gender- males typically have a higher metabolic rate
• 5. Oxygen- metabolic rate varies depending on how much oxygen is in the environment
• 6. Hormone status
• 7. Time of day- diurnal animals have a higher metabolic rate during the day compared to at night
• 8. Salinity


• Specific dynamic action

• Specific dynamic action (immediately after a meal)- creating more energy to break down the meal you just ingested. Period of SDA can change depending on food ingested
-The difference is what nutrients were in the meal. Proteins are more difficult to break down than carbs and therefore requires a higher metabolic rate and increase SDA
-You create heat as a by-product of metabolism as your body works to breakdown the food you eat (common when you eat meat->rich in protein)
more than lipids and carbohydrates


Metabolic Scaling

metabolic rate is not directly proportional to size and it has to scale depending on weight.
-Vole vs. white rhino: on an absolute scale the rhino consumes more oxygen and eats more food.
•f you make it proportional (Weight specific metabolic rate), the vole eats six times its body weight and the rhino eats 3 times its body weight
-Take metabolic rate and divide by weight of the animal. 10g of vole has a higher metabolic rate than 10g of the rhino.


Weight Specific Metabolic Rate

• Smaller animals have a higher weight specific metabolic rate than larger animals because they lose more heat (high metabolism to control for the high heat loss). As you get bigger, the surface area changes and the metabolic rate goes down.


Freshwater Osmoregulatory Strategies

Very similar among all freshwater animals
1. Kidneys produce a very dilute urine, up to 1/3 body weight!
2. Active ion uptake, ions from food


Fresh water gill structure

Fresh water gill structure: two different transporters (co-transporters) to get ions across the gill. Expel bicarbonate to get chloride in. All these transports require ATP (pumping against a strong gradient).


Metabolic costs

•Ion pumping at the gills and kidney (getting sodium chloride back into the animals) is the biggest contribution to the animals resting metabolic rate
~3-7% of the resting metabolic rate


Osmoregulatory strategies for Marine Teleost Fishes

1. Drink water
2. Concentrated urine
3. Excretion of NaCl by the gill
*1/5th of all the energy that it makes goes to counteracting the environmental gradients
8-17% resting metabolic rate


Sharks, skates and rays

• Are hyperosmotic (slightly more concentrated than the sea water)
• They are hypoionic (slightly less of the individual ions than in the sea water).
->They retain osmolites (urea and TAMO) that are not found in the sea water but these animals produce them to prevent a gradient from occurring and losing ions.
• They can adjust how much urea and TAMO they have in the plasma depending on the salinity of the environment
• Rectal gland only in these animals
• Gain both salt and water at the same time (take them in in their food and don’t have to actively drink because the water they take in when they eat is enough). They do take in excess salt however and use rectal gland to get rid of extra


kidney have 3 features in common

1. All are tubular and discharge to environment
2. All eliminate some form of aqueous solution /urine
3. Good at controlling the excretion of water and solutes


Urine Formation
• 2 step process

1. Ultrafiltration (primary urine)
• Glomerular filtration
• Active secretion
2. Refinement (definitive urine)


Thick segment of the ascending loops
of Henle creates the single effect

First, the single effect happens and you have a bunch of other stuff that happen after. Takes place in thick segment of ascending part of loop- it actively pumps out NaCl but not permeable to water (water cant come in or out of tubule).


Countercurrent Multiplication

In the end, the deepest part of the extra
cellular fluid of the medulla are are very
highly concentrated
-Water from the descending loop comes out as it is permeable to water. You have diffusion of NaCl into descending loop. Low concentration in ascending loop and concentrations become almost to equilibrium in descending loop. countercurrent multiparton changes the osmotic pressure vertically. What’s left in the tubule is very dilute and the inertial space is highly concentrated (which is the role of the loop of Henle)