Midterm 1 Flashcards
Physiology definition
& emergent properties
Comes from Greek word PHUSIOLOGIA – knowledge of nature
Today’s definition – physiology is the study of the normal functioning of a living organism and its component parts
o Structure and function relationships
o Chemical and physical interactions (ex. the way nt bind to nt receptors)
Emergent properties – living organisms possess; cannot be predicated to exist based only on knowledge of the systems individual parts
o Organized in a way that gives rise to complex life – the whole is greater than the sum of it’s parts
o Properties that are a result of non linear interaction between component parts
Ex. mona lisa from component parts
What defines if something is alive (4)
- Made of one or more cells
a. Cell – basic unit of life - Regulate its internal environment
a. Single cell – intercellular enviro
b. Multicellular – Humans; enviro of cells and collection of cells that make up body - Respond to stimuli
a. “sensory systems” to detect stimuli – Important for survival - Capable of reproduction
a. Self-replication – one cell is able to replicate
i. Viruses cannot self replicate – need a host cell in order to replicate; not actually alive (according to physiology)
Levels or organization
- Biomolecules – lipids, carbs, proteins, nucleic acid and nucleotides
- Cells – smallest units of life capable of carrying out all life processes
- Tissues – group of cells with similar function
- Organs – 2 or more tissues; structural and functional
- Organ systems
- Organisms
- Population of one species
- Includes atoms – responsible for electrical excitability in neurons
Organ systems
Integumentary system – skin; protective; separates the internal from external environment
Musculoskeletal – provides support and body mvmt; skeletal muscles and bone
4 systems exchange material between internal and external enviro
- Respiratory/pulmonary – gases; lungs and airways
- Digestive/gastrointestinal – nutrient and water uptake & waste elimination; stomach, intestines, liver, pancreas
- Urinary/renal – removes excess water and waste material; kidneys and bladder
- Reproductive – produces eggs/sperm; ovaries and uterus and testes
Circulatory/cardiovascular – distributes materials by pumping blood through vessels; heart, blood vessels, blood
Nervous (brain and spinal cord) and endocrine – coordinate body functions
- A continuum more than 2 separate and distinct systems
Immune – anatomically the lymphatic system (not limited to this); specialized cells throughout the body
- Protects the internal enviro
Why is physiology important & exciting
Important:
Leads to treatment of diseases in humans and other organisms
o Pathophysiology – treating diseases
Helps us understand how organisms cope with environmental stressors – helps understand the environment
o Ex. climate change
Foundation of understanding of the philosophical question “What is life?”
o What does it mean to be alive – physio helps define critical processes
Organization:
Fundamental understanding of how life works
Post-genomic era
- Personalized medicine, “$1000 genome” – to know your genome
- You can submit a sample of your cells and they’ll send you the entire sequence of your genome
- Can be used for personalized medicine
- Molecular basis of evolution
- Allowed understanding about molecule basis of evolution
- Structure of individual proteins and how they can be modified with new drugs
Pathway and drug discovery
o Intelligent design drugs
New tech
o Computing, robotics, nanotech
Themes in physio (5)
Structure and function are closely related – particular shape (anatomy) of a protein/cell/organism and how its related to what it does o Organs o Cells (ex. neurons have an axon) o Molecular interactions (ex. protein has a particular structure because it will bind a ligand that will allow it to be part of the signaling pathway)
Information flow coordinates body function
o Electrical/neural signaling throughout the body
o Hormonal communication
Need for energy
o Processing of ATP – metabolism that is dependent on it
Evolution
o Nothing in Biology Makes Sense Except in the Light of Evolution
-Theodosius Dobzhansky
o Different processes happening in a similar way in different species – studying other species give us insight to how humans function
Homeostasis and control systems
o Mastering A&P -> study area ->animations ->bioflix-homeostasis
Homeostasis definition
- who named & first mention
- internal parameters that must be maintained
- does not mean
The ability to maintain a relatively constant internal environment even when the external environment is variable.
o 1800’s Claude Bernard called this “la fixite du milieu interieur”. – the constancy of internal enviro
o Word was coined by Walter Canon, 1929
Internal environmental parameters must be maintained within a certain window of acceptable values – respond to fluctuations in external enviro
o Temperature
o pH
o Salinity (concentration of ions and other solutes)
o Oxygen, carbon dioxide
o Nutrients
Homeostasis does not mean “equilibrium” or never changing
Homeodynamics – we observe a dynamic steady state inside vs outside cells
- Ex. Ions are not equal on ECF and ICF but these states must be maintained in order to maintain homeostasis
Requires energy to maintain (ATP)
- not an “equilibrium” - often functions to maintain states of disequilibrium
Control systems
- definition
- pathway
- vary in 3 ways (& what affects intensity)
monitors and adjusts regulated variables at set point; respond to loss of homeostasis
o Requires compensation from external (ex. temp) or internal (ex. ate something) change
Pathway:
- Input signal
- Integrating center
- Output signal
- Response
Long or short distance
1. Local – restricted to one tissue
• Relatively isolated change occurs in a tissue
• Nearby cells sense changes within their vicinity and respond
2. Long distance reflexive control – can be more complex and have input from multiple sources and output that acts on multiple targets
• Endocrine & NS control & neuroendocrine
Vary in speed and specificity
1. Neural – aimed at specific target, fast acting, shorter lived
• Frequency of electrical signals proportional to signal intensity
2. Endocrine – target specificity determined by only receptors, longer to act, tends to last longer
• Will contact almost every cell in body – cells must have a receptor to effect it
• Amount of hormone released proportional to signal intensity
Feedback loops
- sides
- process
2 sides
- Response loop
- Feedback loop – to monitor if compensation was effective; Modulate the response loop
Process
- Stimulus
- Sense or receptor
- Afferent pathway – brings info to brain/integrating center; ex. sensory NS
- Integrating center – ex. brain
- Efferent pathway – acts on target; ex. motor NS
- Target or effector
- Response
Negative feedback
- effects/loop
- properties
- ex. glucose
homeostatic; stabilize variable/cancelling out
Initial stimulus – response – decreased stimulus – response loop shut off
o Error signals act to maintain ‘cruise control’ limits
Properties
- Keeps system near a setpoint
- Response acts to negate the stimulus
- Response can restore homeostasis, but cannot prevent the initial perturbation
Ex. control of glucose – video from mastering A&P Bioflix
o Secretion of insulin – decreases glucose
o Low glucose levels no longer generate signal for insulin to be released – within ideal set of limit
Positive feedback
- effects/loops
- properties
- homeostatic?
- ex. labour
reinforce a stimulus; brings further from set point; some argue not homeostatic
Initial stimulus – response – increases stimulus – feeds into response – feeds into greater response
o An outside factor is required to shut off
Properties
- Brings a system further from a setpoint
- Response acts to reinforce the stimulus – makes error signal stronger
- Requires an outside factor to shut off.
Non-homeostatic? – however, the process of the baby being born is homeostatic and is critical to survival of mother
- Must look at larger context
- Ultimately it is homeostatic
Ex. Labour
o Baby drops in uterus and stretches the cervix – stretching is detected by sensory system
o Hypothalamus secrets oxytocin – contacting uterine muscles cause uterine muscles to contract
o Pushes baby down pushing on cervix more and cycle repeats
o Baby being born stops pos feedback cycle
Feedforward control
allow body to anticipate change; generate response before variable change to prevent severity
o Argued not a loop
o A small stimulus sets off a chain of events aimed at preventing a perturbation.
Requires a complex “program”, or a “reflex”
1. Ex. Mouth watering in anticipation of food is an often-used example
• Psychologists may disagree because of the influence of learning
2. Ex. bag of salt and vinegar chips causes increased salivation when you smell it
o Effects PSNS – salivary glands
3. Ex. Response to exercise
• Respiration, heart rate increase at the beginning of exercise, before changes in O2/CO2
4. Ex. “Fight or flight” activation of sympathetic NS
Ex. Bear in woods – it’s not touching you, but it activates the response nonetheless to prepare your body to survive
- Stimulus was a small visual input – response was a complicated series of events from activation of SNS
Walter Cannon’s Postulates
describe regulated variables and control systems (July 1929) – 4 postulates
1. Nervous system has a key role in regulation of internal environment (often controlling endocrine system – slight bias; most people recognize NS and endocrine as equally important)
o Regulates parameters
2. Some systems of the body are under tonic control
o ‘volume button’ – you can turn it up or down
o Ex. Applies to blood vessel dilation
3. Some systems of the body are under antagonistic control
o 2 opposing factors that balance each other out
o Ex. heart rate – one branch of autonomic NS causes increases and the other causes decease
4. One chemical signal can have different effects in different tissues (communication lecture, ANS lecture)
o ex. epinephrine – blood vessels contract in some areas and contract in other areas (tonic control)
Biomolecules
- organic molecules
- types of biomolecules
Organic molecule that is commonly associated with life
Organic molecule – contains carbon; not technically naturally occurring or healthy
o Exceptions – co2, co, h2co3
Types
- carbohydrates
- nucleic acids/nucleotides/nucleosides
- lipids
- proteins
Carbohydrates
- general chemical formula
- common examples
- properties
- types
CnH2nOn
Common types
o Glucose – C6H12O6 (hexose)
o Ribose – C5H10O5 (pentose)
Properties
1. Hydrophilic (mostly) – water soluble/loving/polar
2. Very abundant
3. Used for:
a) Energy – almost all euk cells can use glucose for energy and can store some form of glucose (monomer or polymer) for energy
• Although most energy is stored as fat
b) Structure
i) Glycosylated proteins – have carbs added to them
o May need to become activated
o May be important for transcription
o May determine localization (ex. moving out of cell membrane)
ii) Glycolipids – carbs attached to lipids
Types – Monosaccharides form disaccharides form polysaccharides
o Monosaccharides – glucose, fructose,
o Disaccharides
ex. Sucrose – glucose + fructose
ex. Maltose – glucose + glucose
o Polysaccharides – most abundant carb; used for structure and energy
ex. Glycogen – storage molecule; polymerized glucose stored in organs (ex. liver)
Nucleotides
- structure
- types
Structure a) 1 or more phosphate group b) 5 carbon sugar c) Nucleobase – carbon-nitrogen ring Structure determines type o Adenine o Cytosine o Guanine o Thymine o Uracil
Types:
a. Adenosine – a neurotransmitter
b. Adenosine triphosphate (ATP) – basic molecule of energy storage in most organisms, including animals; energy is stored in bonds between phosphate
- & Adenosine monophosphate & adenosine diphosphate
c. Cyclic AMP (cAMP) – important signalling molecule within cells
- Adenylyl cyclase (enzyme) – converts ATP to cAMP
d. Guanosine triphosphate (GTP) – energy source in physiological reactions; important in communication pathways (ex. adenylyl cylase pathway)
- & Guanosine monophosphate & guanosine diphosphate
e. Cyclic GMP (cGMP) – important signalling molecule within cells
- Guanylyl cyclase (enzyme) – convert GTP to cGMP
Lipids
- properties (contain)
- structure
- roles
Properties
- Hydrophobic (generally; or have parts that are hydrophobic)
- Contain mostly C and H; a few O, N, P
- Very diverse
Fatty acids
a) Structure
- long, unbranched hydrocarbon chains with 8-28 carbons
- carboxyl (= acidic) functional group
b) Saturated FA – no double bonds; form a straight chain
c) Unsaturated FA – has double bonds; create a ‘kink’
- More double bonds = less likely to be solid at room temp
- Don’t stack as well – pack together more loosely
- More double bonds = greater curl
Roles
a. Structure of cells – define the cell
- Waterproof – separates ECF and ICF
- Pliable
b. Energy source – can be metabolized and converted to ATP
c. Communication – within and between cells
Types of lipids (6)
Glycerides – derivative of FA; glycerol backbone with 1-3 FA
- Types
1. Mono = 1 FA
2. Di = 2 FA
3. Tri = 3 FA - Primary storage product – major component of fat (high = lots of body fat)
Phospholipids – derivative of glyceride - Structure 1. Glycerol backbone 2. 2 FA 3. Phosphate group 4. R group – commonly an amino acid molecule (ex. serine, choline, ethanolamine) The R group: a. Identifies species of phospholipid b. Variable polar group - Amphipathic – has hydrophobic and hydrophilic components 1. FA – nonpolar 2. Phosphate head – polar - Form 3 structures in water 1. Bilayer – cell membrane 2. Liposomes – spherical with aqueous core (bilayer forms sphere) 3. Micelles – difficult to form; not often found in nature; energetically unfavourable
Sphingolipids – analogous to phospholipid in structure
- Contributes to cell membrane formation
- Structure
1. 1 FA
2. Phosphate group
3. R group
4. Sphingosine – instead of glycerol and additional FA
5. Contains nitrogen – usually at bend (be able to recognize by this feature)
Glycolipids – attached carb; contributes to structure, function, localization
see diagrams!
Steroids
- Basic structure – three 6-carbon rings and one 5-carbon ring (17 carbons)
1. Planar/flat molecule – allows protein receptors to recognize and bind
2. Functional R groups – confer different function - Function in: Communication and cell structure
- Examples – same basic structure with ‘décor’
1. Cholesterol – used to make hormones (ex. estrogen, testosterone, cortisol)
Oxylipins – oxygenated metabolites
Eicosanoids – subset of oxylipins
- Structure:
1. Polyunsaturated FA with 20 carbons (fishhook shape)
a. Many are derived from FA arachidonic acid & other unsaturated FA - metabolization of arachidonic is important
- Function
1. Not generally stored – only synthesized as needed
a. Main function is communication between and within cells
i. Inflammation, pain, platelet aggregation
ii. Include prostaglandins and leukotrienes
Protein structure
oligopeptide vs polypeptide
Macromolecules
o Short chain – peptide
o Long chain – protein
Structure of protein:
- Primary structure – sequence of amino acids
a. Linear chain of amino acids – generally
- Oligopeptide – 2-9
- Polypeptide – 10-100 - Secondary – covalent bond angles between amino acids determine secondary structure
a. Secondary structure – created by hyd bonding (cov bonds) between local (adjacent) interactions of amino acids
- A-helix
- B-pleated - Tertiary – 3 dimensional structure of proteins
a. Combine secondary structures
- Formed from chemical interactions between R groups of individual AA (can be cov, ionic, van der waals; depends on AA R group)
b. Pieces can also be removed if not needed on protein
4. Quaternary – interaction of multiple subunits to form active protein; noncovalent interactions Often either fibrous or globular a. Fibrous – not soluble - Ex. collagen – structural protein b. Globular – often soluble - Ex. hemoglobin
Structure of amino acids
- how many
- structure
- properties
- components
Components
a. R group – determines properties (polar/nonpolar/basic/acidic)
b. *20 amino acids encoded by the universal genetic code (debatable – 2 additional may be incorporated)
- 9 of 20 are essential – we need to consume them; our body does not synthesize them
- 11 of 20 are nonessential – we can synthesize them
Varying properties
- Acidic, basic, polar, nonpolar
- Alphabet – analogous to AA and proteins
- Chains can be up to 10,000 AA - Usually a couple hundred or thousand
Structure of amino acid – same basic structure with varying properties Central carbon – 4 bonds are: 1. Carboxyl group (-COOH) 2. Amino group (-NH2) 3. Hydrogen 4. R group – can have varying properties
Functions of proteins
- how many types within mammalian cell
Highly complex
- Determined by the sequence of AA – encoded in genome
- Don’t need to know specific structures of AA – know they have different properties based on structure
Functions of proteins – extremely versatile
o In mammalian cell – between 10,000-15,000 types of protein expressed
o Don’t often do single job (swiss army knife)
Ex. ATPase – uses energy to move; enzyme and transporter
Fibrous vs globular
1. Fibrous – generally insoluble
• Structural (ex. collagen & keratin)
- Globular – generally soluble
Functionally – 7 categories of soluble protein
a. Enzymes – facilitate chemical reactions; without, reactions may not be possible
- Ex. proteases
b. Membrane transporters – sits in membrane and shuttles solute molecule that could otherwise not cross
c. Signal molecules – within and between cells there is communication
- Ex. g-protein – become activated; part of a signalling cascade
d. Receptors – protein that binds something else; does so as part of a communication process
- Ex. hormone receptors – insulin receptors binds insulin and causes reaction
e. Binding proteins – main job is binding something else; sequestering
- Ex. calcium binding protein – binding free calcium inside cells and keep concentration within low
f. Regulatory proteins – many physiological processes occurring; regulatory proteins turns processes on and off
- Ex. DNA binding proteins regulate transcription
g. Immunoglobins – protein binds to antigens
Ligands
- definition
- effects on proteins
- endogenous vs non
- affinity & specificity
- types of effects on proteins (2)
- how types of ligands enact effects (2)
Ligand - molecule that binds to protein site
Protein binding – In order for protein to activate, it must interact/bind to other protein; binding site and activity
- Very specific – shape of binding site is precise
- Ex. insulin receptors bind insulin – insulin is the ligand
Endogenous ligand – occurs naturally in body (ex. hormone, nt)
Nonendogenous – may be a drug/toxin; still a ligand
Affinity
- High = binds strongly
- Low/weak = binds weakly
Types
1. Agonist – ligand that binds to protein site and alters the state of protein resulting in biological response
• Ex. hormone or nt; insulin – all cause response in cell
• Drugs can also be agonist – mimics nt
2. Antagonist – ligand reduces the action of the agonist; binds but causes no biological response; inhibitors/blockers
• Drugs can be antagonist
Agonist and antagonist can both be
1. Competitive – act to block agonist at its normal binding site; binds to it instead
• Acts at the normal binding site
2. Allosteric – block competitive agonist by binding to the protein away from binding site and inactivating the binding site; prevent normal agonist from binding by changing shape of binding site
• Acts at a distant site
Factors that alter protein binding
- isoforms (example)
- activation of proteins (2 methods) & inactive forms
WHAT CAN ATTACH - types of modulators
- physical
- chemical (3)
- saturation
Isoforms – closely related proteins whose function is similar but affinity differs
i. Quaternary structure – subunits acting together; other proteins that are expressed by the body may be similar
ii. Ex. fetal vs adult hemoglobin
Activation
- Cofactors – proteins may need cofactor to function properly; ion or small organic functional group must attach before binding site will activate
- Ex. Mg++ ions binds to slightly alter 3D shape and expose binding site - Protein processing – when proteins are expressed, that may not be the final version
a. Ex. may need to be glycosylated
b. Proteolytic activation – enzymes chop of 1+ portions to activate
- Common in hormones and enzymes
- Inactive forms – ‘pro’ prefix ang/or ‘ogen’ suffix
Types of modulation
i. Changes the ability to bind to a ligand
ii. Changes proteins activity or ability to create response
Physical factors/modulators
- pH, temp – can cause structural changes
- proteins may become denatured – can often not return to normal shape and resume function
Chemical modulation – can be covalent or non; may increase/decrease activity, activate binding site; reversible or irreversible; not necessarily making it ‘functional’
- covalent modulation – can be activating or antagonistic
a. phosphorylation and dephosphorylation – addition or removal of phosphate from protein
- kinases – enzymes, covalently add phosphates
- phosphatases – enzymes, remove phosphate
- phosphorylation may cause activation or inhibition of protein – may allow it to become fully active/activate binding site
Edwin Krebs and Edmond Fisher 1992 Nobel prize – described how important phosphorylation process was in regulating protein activity
a. Described sites proteins are phosphorylated at
- Serine, threonine, and tyrosine AA side chain
- Addition of lipid or carbohydrate
- Presence of agonist or antagonist
a. Antagonist – inhibitors; decrease activity; block binding sites
- Competitive – reversible; degree of inhibition depends on concentrations of ligand vs antagonist and proteins’ affinity for both; Increasing customary ligand can displace competitors
- Irreversible – tightly bound; cannot be displaced
b. Allosteric
Reaction rates can reach a maximum
i. Constant protein concentration – ligand concentration determines response
ii. Saturation – ligands are plentiful but all proteins are active and no binding sites are available
4 functions of cell membrane
- Physical barrier – separates ICF from ECF
- Gateway for exchange – controls mvmts of solutes and regulates concentration in ECF and ICF
a. Semipermeable – allows some to cross, prevents others - Communication – receptors that detect physical and chemical changes and starts cascade response
a. Ex. contracting muscle cells – detect chemical stimuli that cause contraction - Cell structure – some membrane proteins hold cytoskeleton proteins to give cell structure
a. Neurons – have a very specific shape; cell structure is critical to function
b. May also form specialized junctions
- Synapses – specialized
- Tight junctions