BIO Physio Exam

physiology

branch of life sciences concerned with understanding how organisms work

proximate level of causation

physical and chemical mechanisms responsible for a function

• refers to the most-immediate causes of an observation

ultimate level of causation

how physiological systems evolved and how they impact fitness

• refers to a final end-point in terms of causation

hierarchy of physiological systems

molecules cells tissues organs systems whole organism

molecules

consist of atoms joined by covalent bonds

cells

membrane-bound structures that form the fundamental unit of life

tissues

groups of cells that perform a common function

organs

structures that consist of two or more tissues and perform a specific function

nerve cell (brain neuron)

tiny brain neuron -receives electrical information from many other neurons -processes that information -transmits processed information to a large set of other neurons

motor neuron

sends electrical signals from the spine to a specific muscle over a meter way

diffusion

movement of ions or molecules from regions of high concentration to regions of low concentration -occurs passively and spontaneously (without input of energy) -results from random movement of substances in solution

gradients

exist when concentration of an ion or molecule differs from one are to another, or amount of electrical charge differs from one area to another

• steeper the gradient the faster movement will occur via diffusion

• almost all gradients result from differences in concentration or charge on one side of a cell membrane versus the other

what happens when concentration gradient exists

ions and molecules will move from regions of high concetration to regions of low concentration by diffusion

• each type of ion or molecule experiences its own concetration gradient

when theres an electrical potential gradient

result from an overall difference in charge, no matter which types of ions are involved

• ions will move towards areas of opposite charge

• movement driven by forces of electrical repulsion and attraction

• Every ion of the same charge experiences the electrical gradient in the same way

• ions rarely cross membranes on their own—they require assistance from transport proteins

transport proteins

have structures that allow them to embed in cell membranes and interact with the solutions on either side

• categorized as transmembrane proteins or integral membrane proteins

• serve as a path for ions and molecules that are unable to cross a membrane easily

• 3 general types: channels, carriers, pumps

Channel (transport proteins)

opening or pore that allows, under certain conditions, a specific ion or molecule to travel down its concentration or electrical gradient from one side of the membrane to another

• passive movement, no energy used because substances are moving spontaneously down their concentration or electrical gradients

Carriers (transport proteins)

binding site that is specific to a particular molecule. When that molecule hits the binding site and sticks to it, the carrier changes shape in a way that allows the molecule to diffuse down its concentration or electrical gradient, into the solution on the opposite side of the membrane

• passive movement, no energy used because substances are moving spontaneously down their concentration or electrical gradients

Pumps (transport proteins)

involved in active transport

• these proteins use energy in the form of ATP to move ions and molecules against their concentration or electrical potential gradient, from one side of a membrane to the other.

• in many cases, pumps function to create concentration or electrical potential gradients that later drive passive transport through channels or carriers.

lung of surface area importance

The air you breathe in carries oxygen molecules that have to diffuse across the surface area of your lungs to enter your bloodstream. Conversely, carbon dioxide molecules in your bloodstream diffuse across the same surface area to enter the air that you exhale. The amount of gas exchange that can occur is in part a function of the amount of surface area your lungs have.

food example of surface area importance

When nutrients in the food you eat have been broken into small molecules, they have to diffuse or be transported across the surface of your small intestine to enter your bloodstream. The more surface area in your small intestine, the more nutrients can move into your body and be used.

heat surface area importance

You exchange heat with the environment across your skin. On a cold day, the amount of heat that is lost from your body is a function of the surface area of exposed skin.

how size affects volume and surface area

As structures like lungs, small intestines, or whole-bodies get larger, their volumes increase much faster than their surface areas increase

• In the case of structures like lungs and intestines, natural selection has favored alleles that increase surface area

grey matter

thin surface overlying a large volume of white matter

• neurons in grey matter are primarily responsible for processing information

white matter

neurons primarily responsible fore sending information to sections of the brain that have distinct functions

4 types of Tissues

1. epithelial

2. connective

3. muscle

4. nervous

epithelial tissue

structure:

• arranged in sheets of closely packed cells

• maximize cellular surface area

• they also provide for the opportunity for polarization

function:

• protective barriers that line organs and body cavities

• regulating interactions with the external environment

• additional functions to support this through secretion of certain chemicals, detection of sensations like touch, absorption, and protection

cell polarization

where one side of the cell is distinct from the other

• allows apical surface(outer/top) to be optimized for interaction with a body cavity or the external environment while the other surface (called the basal surface) is optimized to convey that signal to the adjacent tissue

Connective tissue

structure:

• made of many different types of cells that form a loose web of fibers that form an extracellular matrix

• can be highly specialized

• adipose tissue is optimized for fat storage, cartilage is optimized for absorbing forces without breaking, and bone is optimized for rigidity

• Some cells stay fixed within this matrix, and others, such as the macrophage (an immune cell), move in and out in response to certain chemical signals

function:

• provide necessary support and connection for other tissues

• can bind and support other tissues, store energy, protect organs, and facilitate the transport of nutrients and waste

• Some types of connective tissue include dense tissues like cartilage and bone and more fluid tissues like blood and lymph

muscle tissue

structure:

• composed of specialized cells that can contract and generate force

• three types: skeletal, cardiac, smooth

function:

• main function is in movement

skeletal muscle

structure

• made up of cells that are long and cylindrical

• shows striations (lines/stripes) due to the arrangement of actin and myosin filaments within the cells

• cells are also multinucleated, with more than one nucleus per cell

function

• attached to bones throughout the skeletal system to allow for voluntary muscle contractions

Cardiac muscle

structure:

• made of short and thick cells that undergo branching

• branch ends meet other cells at specialized junctions called intercalated discs

• the intercalated discs let electric signals pass freely between cells to contract the heart

function:

• found in the heart to facilitate the distribution of blood throughout the body

smooth muscle tissue

structure:

• composed of cells that are short and non-striated (don't have lines/stripes), with a single, centrally located nucleus per cell

function:

• lines the walls of hollow internal organs such as the stomach and intestines for involuntary muscle contractions

nervous tissue

structure:

• consists of neurons and glial cells

• three main parts: soma, dendrites, axon

  • cell body of the neuron (also called the soma), the branches off of the cell body (dendrites), and the long tail (axon)

  • dendrites transfer the nerve impulse to the soma and then to nearby cells through the axon

function:

• facilitates communication, information processing, and regulation of body functions

• interacts with each of the other tissue types, and is essential for voluntary skeletal muscle contraction

• main function of the neurons is to receive and transmit electrical impulses, while the glial cells have more unique supportive roles

neurons

transmit signals through electrical impulses

glial cells

support and protect neurons

• many different types of glial cells as well, each with their own distinct structure to optimize their specific supportive function in the nervous system

homeostasis

self-regulating biological processes that maintain stable conditions in the cell or in the organism in the face of changing external conditions

• if homeostasis is disrupted, illness or death results

• Feedback is one of the most central concepts in homeostasis and is a key element of all homeostatic systems

homeostasis in vertebrates regulates:

• body temperature;

• the concentration of K⁺ (potassium), Na⁺ (sodium), Fe²⁺ and Fe³⁺ (iron), Cu²⁺ (copper), Ca²⁺ (calcium), and other ions in cells and tissues;

• blood pressure and levels of glucose, O₂, CO₂, and H⁺ (pH) in the blood; and

• H₂O, or overall level of hydration.

homeostasis in plants regulates:

• temperature regulation;

• the concentration of Fe²⁺ and Fe³⁺ (iron), Cu²⁺ (copper), Zn²⁺ (zinc), P (phosphorus), Mg²⁺ (magnesium), Ca²⁺ (calcium), and other ions in cells and tissues;

• H₂O, or overall level of turgor; and

• the concentration of photosynthate (molecules produced during photosynthesis).

negative feedback

response by a physiological system that returns the regulated condition back to the normal and preferred level

• corrective, self-limiting step or event

positive feedback

response by a physiological system that increases the amount that a regulated condition differs from the normal level

• opposite of a corrective, self-limiting step

• extremely rare in biological systems

  • ex: Release of the hormone estrogen during the menstrual cycle that culminates in release of an egg, or ovulation// Accumulation of the structures called platelets during blood clotting

homeostatic systems 4 connected elements

1. stimulus

2. sensor

3. comparator

4. effector

Stimulus (homeostatic systems)

Also called the variable or condition, this is the physical entity that is monitored

• common to find homeostatic control over any physical condition that threatens the organism's fitness should its level become too high or too low

Sensor (homeostatic system)

type of cell or protein that changes activity in response to high or low levels of the stimulus

• the monitor or detector—the element in the system that documents the level of the stimulus

Comparator

called the control center, this is the element in the system that compares the level of stimulus detected against a reference or standard

• this reference is often termed the set point

• comparator detects deviations from the set point and changes activity in response

set point

set point of a homeostatic system is the preferred value or range for the stimulus

effector (homeostatic system)

any activity that acts on the stimulus to change its level in a way that returns it to the set point

regulating blood glucose

humans and other vertebrates, it is critically important to regulate the levels of glucose in the blood

• high and low levels of blood sugar can lead to serious illness or death

  • Uptake of glucose by liver and muscle cells in response to insulin signaling acts as a negative feedback when glucose levels are too high

  • release of glucose from liver cells acts as a negative feedback when glucose levels are too low

plant way of life summarized in 3 points

1. do not move under own power. Instead, they stay in one place for their entire lives. That does not mean that they are static, however. They change constantly, altering their growth and activity in response to information they take in about the conditions around them.

2. harvesting diffused resources. This means that the molecules and supplies that plants obtain to stay alive and reproduce exist at low concentration in the environment. These resources include carbon dioxide (CO₂), water (H₂O), selected wavelengths of light, and small molecules that furnish nitrogen, phosphorus, potassium, and other key atoms.

3. using those resources to manufacture all of the macromolecules required to grow and reproduce

molecules at the site of infection (plants

cells at the site of the invasion contain molecules that act as pathogen-alerters, when they bind to molecule from invader it triggers response

• Specialized receptor proteins on the cell surface can detect pathogens in the fluids outside the cells

• Resistance proteins encoded by a plant's R (for resistance) genes detect intruders that enter the cell interior

Hypersensitive response (cells and tissues nearby)

happens when an R-gene product has bound to a molecule from an invader and the infected cell sends a chemical signal

• leads to

  • suicide in cells close of the site of infection

  • wall thickening in cells slightly more distant from the infection site

  • guard cells on nearest leaf or stem surfaces closing to block the pores where gas exchange occurs

• localized responses deprive the invader of food, create a thick "fence" around the site of infection, and prevent additional invaders from entering

Tissues and organs impacted by hypersensitive response

leaves and stems are organs at the site of infection that are impacted by the hypersensitive response

• resistence protein also sends a signal to distant organs

  • salicylic acid carried to leaves and stems throughout the plant via a specialized vascular tissue called phloem

Response from salicylic acid signal

cells in leaves and stems far from the original site of infection begin producing pathogenesis-related (PR) proteins

• PR proteins are specialized for killing fungi, viruses, or bacteria

SAR (Systemic Acquired Resistance)

chain of events triggered by salicylic acid spreading throughout the plant

• resistance proteins are acquired in response to an infection and are produced throughout the shoot system

Leaf’s job

capture light, perform photosynthesis, and export sugars to the rest of the body

Importance of maximizing surface area

Almost every process that depends on an exchange of materials across a surface depends on the amount of surface area available

• To maximize the amount of surface area in a structure, natural selection has favored the evolution of several general categories of shapes

  • Folded elements like the lining of your small intestine, where the digested products of your last meal are being absorbed into your bloodstream

  • Narrow tubes that form branching networks, like the capillary beds that are delivering oxygen and nutrients to your tissues right now.

Stomata

openings in leaves where gas exchange occurs (the singular form of the term is stoma) located in crypt

• gas exchange can only occur through stomata because the leaf surface is covered with a waxy layer called cuticle that is impervious to gases

• openings are regulated, when open:

  • CO2 diffuses from the atmosphere into the leaf interior down its concentration gradient

  • O₂ that is a waste product of photosynthesis diffuses out of the leaf interior and into the atmosphere

  • water vapor (H₂O) also leaves the leaf interior and diffuses into the atmosphere, following a concentration gradient from humid leaf interior to dry atmosphere

stomata are open during the day when photosynthesis is actively occurring and closed at night when photosynthesis is not occurring

stomata location

in crypts that only occur on underside of leaf

• pocket like structure criss-crossed with tiny hairs

• Species that grow in wetter environments do not have crypts, so both sides of the leaf are flat (some have stomata on upper and lower surfaces)

fitness trade off

unavoidable conflict between two features or elements of a trait, meaning that neither can be optimized

Animal way of life (in contrast to plants)

• move around to find and eat ready made macromolecules from other organism

• synthesize few macromolecules

phenotypic plasticity

state of constant change in size, shape, and activity

photosynthesis overview

processes that transform light energy into chemical energy

• source of the sugars that most organisms use to fuel cellular respiration and make ATP

• Like cellular respiration, photosynthesis is a complex, multipart process that involves a large number of small steps

  • inverse of cellular respiration

• product: molecule called glyceraldehyde 3-phosphate (G3P)

  • results in carbon-containing molecules that provide the energy and structural stuff that makes life, growth, and reproduction possible

6CO2+6H2O—> C6H12O6+6O2

what is G3P used for

1. Produce glucose (C6H12O6) that can be

   1. shipped all over the plant body

   2. stored as starch

   3. used by mitochondria to produce the energy in the form of ATP that is required to stay alive and grow

2. Furnish the building block materials required to synthesize the amino acids, nucleic acids, carbohydrates, and lipids needed to maintain the plant body and grow.

Cellular respiration

series of chemical reactions that break down glucose and oxygen to produce carbon dioxide, water, and usable cellular energy in the form of ATP (adenosine triphosphate) and heat

purpose:

• break down the glucose and oxygen produced by photosynthesis to release usable chemical energy in the form of ATP for cellular work

Glucose formula

C6H12O6

plasticity

ability of the same genotype to produce different phenotypes in response to different environmental conditions

What 3 classes of material plants need to survive

1. Mineral nutrients such as nitrogen, potassium, phosphorus, calcium, magnesium and sulfur; 

2. Water

3. Sugars

source

the place the substance comes from or originates

sink

location where a substance is used or stored

substance movement pattern in plants from sources to sinks

• Mineral nutrients move from roots to shoots;

• Water moves from roots to shoots;

• During the growing season, sugars move from shoots to roots for immediate use by root cells or storage;

• After a period of dormancy, meaning when growth stops and metabolism slows due to dry or cold conditions, sugars move from storage areas back to the shoot system.

how do nutrients in soil get into plant body

1. Direct acquisition via active transport (which requires energy) of nitrogen, phosphorus, and other mineral nutrients from soil to the interior of root cells.

2. Acquisition via barter—specifically, an exchange of sugars for mineral nutrients supplied by symbiotic fungi called mycorrhizae.

2 key observation of nutrient absorption by plants

1. Mineral nutrients are at much higher concentration inside the plant body than they are in the surrounding soils;

2. Most mineral nutrients are acquired as ions such as NO₃^- (nitrate), HPO₄^2- (hydrogen phosphate), K⁺ (potassium ion), or Ca²⁺ (calcium ion) that dissolve in water due to their charge.

key points about travel of nutrients between roots and soil(charges and potential energy)

Key points:

• There is a difference in overall charge between the outside and inside of most cell membranes; 

• A separation of charges creates a voltage;

• A voltage is a form of potential energy;

• Potential energy is defined as any form of energy that is based on position. In this case, the position is the location of positive and negative charges on ions located on either side of a phospholipid bilayer.

epidermal cells of plant roots

remember: cell membranes are batteries

• epidermal cells of plant roots, and especially in root hairs, the battery is created by membrane proteins called proton pumps

proton pumps

actively transport H⁺ (hydrogen ions, or protons) out of the interior of the cell to the exterior

• use ATP to create a separation of charge, and thus a voltage

• Specifically, the inside of the cell becomes less positive and thus more negative than the outside

1. once a proton pump has established an electrical gradient, positive ions can enter the cell through specific membrane channels

2. in addition to containing many proton pumps, root hair membranes contain many ion channels for K⁺, Ca²⁺, Mg²⁺, and other key nutrients

co-transport

occurs when a membrane protein transfers one substance across the lipid bilayer down its electrochemical gradient along with another substance that is moving against its electrochemical gradient

• In effect, the electrochemical gradient favoring the entry of protons is so steep that the movement of a proton "pays the way" in terms of the overall energy change required for another ion to move against its electrical gradient

battering with mycorrhizal fungi

species that live in soil and interact with root systems of majority of plants

• barter for nitrogen and phosphorus— highest demand in terms of fueling the plant's growth and reproduction

• Fungal cells penetrate the root system itself and either grow between the cell walls of root cells or actually enter the cytoplasm of root cells

• plant-fungal interface, sugars produced by photosynthesis flow from the plant to the fungus, while nitrogen, phosphorus, or other nutrients harvested from the soil by the fungus flow into the root cells

"Paying" Nitrogen-fixing Bacteria with Sugar

few plant lineages have evolved association with bacteria that that have the ability to fix nitrogen

• Bacterial species that join this partnership have a sophisticated enzyme complex called nitrogenase; plants that join the partnership produce sugars that can be used to generate ATP in mitochondria and supply the energy needed

fixation

type of chemical reaction where the atoms in atmospheric nitrogen gas (N₂) are converted into ammonia (NH₃) or amino groups (-NH₂), which are forms of nitrogen that organisms can use to make important biological molecules

• reactions are extremely complex and energy-intensive

plant vascular system

plants don't expend any energy at all when water moves from roots to shoots. Not a single molecule of ATP is required. Water flows up passively

• branches to form a continuous network that transports material to all parts of the plant

xylem

water-conducting tissue in plants

• two major types of cells: tracheids and vessel elements

vessel elements

short, fat cells that stack end to end, with openings at the top and bottom of each cell that allow water to flow straight up as through a pipe

tracheids

long, thin cells that have numerous gaps in their cell walls where water flows from one to the next

cohesion-tension theory

1. Water reaches the leaf by traveling through the xylem.

2. Water evaporates from the leaf.

3. Evaporation creates a curved water surface, causing surface tension. As water evaporates, the remaining water forms tiny curved surfaces called menisci where water meets the air. This creates an uneven distribution of forces at the surface, producing surface tension.

4. The tension pulls on the water below due to cohesion. The water molecules in the xylem are strongly attracted to one another through hydrogen bonds. This attraction is called cohesion. Because the water molecules are connected to one another, the tension created by evaporation at the leaf can be transmitted down through the continuous column of water. 

5. Water is pulled upward from the roots. 

is water polar

water is polar (one side that holds a slight negative charge (the oxygen-containing side), and it has one side with a slight positive charge (the hydrogen-containing side)

• difference in charge allows it to interact with other molecules through two main types of intermolecular forces (cohesion and adhesion)

cohesion

partially positive hydrogen of one water molecule interacts with the partially negative oxygen of another water molecule through the formation of a hydrogen bond

Adhesion

The water molecules attract to different kinds of molecules (not water) through this difference in charge

sugar transport

not a passive process

• expend large amounts of ATP to transport the products of photosynthesis from leaves to meristematic tissues, where cell division and expansion is rapid, and to storage cells in roots

phloem

sugar-conducting tissue in the vascular system

• found adjacent to xylem in the plant body and comprises two main types of cells: sieve elements and companion cells

• highly branched network that extends throughout the plant body

sieve elements

stacked end-to-end and make direct connections with each other via open pores

• stripped-down cells that often lack a nucleus or other organelles

• get most or all of the proteins, ATP, and other molecules they need from companion cells

• function as pipes that move the sugary solution called sap

companion cells

found alongside sieve elements

bulk flow

pressure-based movement

• sugars move from areas of high pressure to low pressure

sugar movement in vascular system (pressure-flow hypothesis)

1. Sugars are actively loaded into phloem in leaves and stems where photosynthesis is occurring, leading to a high concentration of sugars near sources.
    

2. Near sources, water moves from xylem to phloem via osmosis. The influx of water builds up pressure in the phloem.
    

3. Sugary sap moves passively down its pressure gradient, from sources to sinks.
    

4. Sugars in phloem sap are actively transported from the phloem into root storage cells and other cells that act as sugar sinks. This "offloading" step keeps the concentration of sugars in the phloem near sink cells low, and thus maintains the pressure gradient that moves sap from sources to sinks.

pathogen

Any agent that causes disease—usually a fungus, virus, or bacterium.

dormancy

A period when growth is not occurring, usually because conditions are too dry or too cold to support photosynthesis.

proton pump (vocab)

A membrane transport protein that actively transfers protons against their electrochemical gradient.

co-transport (vocab)

Transport of two substances across a cell membrane by a membrane protein: one down its electrochemical gradient and one against its electrochemical gradient.

Cohesion-tension theory

Tension created by menisci in leaves and the cohesion of water molecules throughout the vascular system draws water passively from roots to replace water lost when stomata open.

Pressure-flow hypothesis

Movement of sugars from areas of high to low pressure, with high- and low-pressure areas in phloem created by the ATP-powered movement of solutes.

Levels of organization in the nervous system

The nervous system can be analyzed at multiple levels, ranging from individual molecules to the whole organism. These levels are nested, meaning smaller levels are incorporated into larger levels, and they interact structurally and functionally to allow the nervous system to process information and coordinate responses.

What are the major levels of organization in the human nervous system?

Molecules → Cells → Tissues → Organs → Systems → Whole organism. Each level builds upon the previous level, with smaller structures working together to create increasingly complex functions.