Topic 1: Chapt 1-5 Flashcards
What is the study of physiology?
-the study of the normal functioning of a living organism and its component parts, including all its chemical and physical processes.
What are emergent properties?
-properties that cannot be predicted to exist based only on knowledge of the system’s individual components
-is not a property of any single component of the system, and it is greater than the simple sum of the system’s individual parts
-result from complex, nonlinear interactions of different components
-e.g., breaking down car parts into its different pieces and materials, cant predict its a car
describe the different levels of organisation
-most basic level is atoms of elements link together to form molecules
-collections of molecules in living organisms form cells (smallest unit of structure capable of carrying out all life processes) –> a lipid and protein membrane separates cells from external environment
-collections of cells that carry out related functions are called tissues.
-tissues form structural and functional units known as organs
-groups of organs integrate their function to create organ systems
What are the organ systems of the human body?
-circulatory
-digestive
-endocrine
-immune
-integumentary
-musculoskeletal
-nervous
-reproductive
-respiratory
-urinary
What are the systems that exchange materials between the internal and external environments?
4 systems:
-respiratory (pulmonary) system exchanges gases
-digestive (gastrointestinal) system takes up nutrients and water and eliminates wastes
-urinary (renal) system removes excess water and waste material
-reproductive system produces eggs and sperm
what are the other systems that extend throughout the body? not the ones that directly exchange materials with the external environment
-circulatory (cardiovascular) system distributes materials by pumping blood through vessels
-nervous and endocrine systems coordinate body functions
-the diffuse immune system, includes but not limited to the anatomical structures known as the lymphatic system (specialised cells of the immune system that are scattered throughout the body). Protect the internal environment from foreign substances by intercepting material that enters through the intestines and lungs or through a break in the skin. Immune tissues are closely associated with the circulatory system
What are the bodies systems that are based on not for exchanging materials from the external environment or in the body?
-integumentary system, skin, forms a protective boundary that separates the body’s internal environment from the external environment
-musculoskeletal system provides support and body movement
Describe the function of a physiological system or event
-its the “why” of the system
-why does a certain response help an animal survive in a particular situation? in other words –>what is the adaptive significance of this event for this animal?
-talks about why, but not how it happens
-this is the teleological approach
describe what the mechanistic approach is?
-the “how” of the system
-e.g., how do red blood cells transport oxygen? –> oxygen binds to haemoglobin molecules in the red blood cells
- talks about how, but not why it happens
- USUALLY this is what they want to answer in questions, to answer how, not why
what is the underlying principle in translational research?
-applying the concept of integrated functions and mechanisms
-uses the insights and results gained from basic medicinal research on mechanisms to develop treatments and strategies for preventing human diseases
what are the major themes of the fundamental concepts of biology:
- Structure and function across all levels of organisation
- energy transfer, storage, and use
- information flow, storage, and use within single organisms and within a species of organism
- Homeostasis and the control systems that maintain it
- evolution
what are the two major ideas when it comes to the integration of structure and functions that extends across all levels of organisation? and describe them
- molecular interactions
-the ability of individual molecules to bind to or react with other molecules is essential for biological function
- molecules function depends on its structure and shape, small change to structure or shape may have significant effects on the function - compartmentation
-division of space into separate compartments
-allows a cell, tissue, or an organ to specialise and isolate functions
each level of organisation is associated with different types of compartments
Growth, reproduction, movement, homeostasis - these and all other processes that take place in an organism require…
the continuous input of energy
describe information flow in the body
-At organismal level, information flow includes translation of DNA’s genetic code into proteins responsible for cell structure and function
-in human body, information flow between cells coordinates function
-cell-to-cell communication uses chemical signals, electrical signals, or combination of both
-information may go from one cell to its neighbours (local communication) or from one part of the body to another (long-distance communication)
-when chemical signals reach their target cells, they must get their information into the cell –> some molecules are able to pass through barrier of membrane, but signal molecules that cannot enter cell must pass their message across the cell membrane
describe homeostasis in an organism
-organisms that survive in challenging habitats cope with external variability by keeping their internal environment relatively stable, an ability known as homeostasis.
describe Cannon’s list of variables that are under homeostatic control
-cannon divided his variables into what he describe as environmental factors that affects cells (osmolarity, temperature, and pH) and “materials for cells needs” (nutrients, water, sodium, calcium, and other inorganic ions, oxygen, as well as “internal secretions having general and continuous effects” –> these are hormones and other chemicals that our cells use to communicate with one another)
What happens if the body fails to maintain homeostasis of the critical variables listed by Cannon?
-normal function is disrupted and a disease state, or pathological condition, may result
What are the two general groups of diseases according to their origin?
-those in which the problem arises from internal failure of some normal physiological process –> may include abnormal growth of cells, may cause cancer or benign tumours; the production of antibodies by the body against it’s own tissues (auto-immune disease); and the premature death of cells or the failure of cell processes. inherited disorders are also considered to have internal causes
-those that originate from some outside source –> external causes of disease include toxic chemicals, physical trauma, and foreign invaders such as virus and bacteria
in both internally and externally causes diseases, when homeostasis is disrupted the body attempts to compensate, if the compensation is successful…
homeostasis is restored
What is pathophysiology?
The study of body functions in a disease state
describe the internal environment of the body
-it is a watery internal environment that surrounds the cells, a “sea within” the body called the extracellular fluid (ECF)
-ECF serves as a transition between an organism’s external environment and the intracellular fluid (ICF) inside the cells
-when ECF composition varies outside normal ranges of values, compensatory mechanisms activate and try to return the fluid to the normal state
what is the law of mass balance
-if the amount of substance in the body remain constant, any gain must be offset by an equal loss
- total amount of substance x in the body = intake + production - excretion -metabolism
the amount of a substance in the body is also called…
the body’s load, as in “sodium load”
what are the body’s two options for output?
-excretion, defined as the elimination of material from the body, usually through urine, faeces, lungs, or skin.
-convert the substance to a different substance through metabolism. nutrients that enter the body become the starting point for metabolic pathways that convert he original nutrient to something different then creates a new mass balance disturbance by adding more of the new substance, or metabolite, to the body. (metabolite is the general term for any product created in a metabolic pathway
what is a xenobiotic?
Any foreign substance in the body
What is mass flow?
-Use mass flow to follow material throughout the body. Mass flow describes the rate of transport of a substance x as is moves through the body fluids or into and out of the body.
-Mass flow (amount x/min) = (concentration of x) X (volume flow)
-where volume flow describes the flow of blood, air, urine, and the like.
what is clearance?
-follow the rate at which the substance disappears from the blood
-usually expressed as a volume of blood “cleared” of a substance x per unit of time
-for this reason, clearance is only an indirect measure of how substance x is handled by the body
what are the two primary organs the clear solutes from the body, and describe them
-kidney and liver
-hepatocytes, or liver cells, metabolise many different types of molecules, especially xenobiotics such as drugs. The resulting metabolites may be secreted into the intestine for excretion in the faeces or released into the blood for removal by the kidneys
when you centrifuge blood, it separates into two parts:
-plasma, the fluid component
-plus the heavier blood cells
describe the dynamic steady state
-in a state of homeostasis, the composition of both body compartments is relatively stable
-this condition is a dynamic steady state
-the modifier dynamic indicates that materials are constantly moving back and forth between two compartments
-in a steady state, there is no “net” movement of materials between the compartments
is steady state the same as equilibrium?
no
what is equilibrium?
-implies that the composition of the body compartments is identical
what is disequilibrium?
has concentration differences, the fluid compartments are not at equilibrium
To maintain homeostasis…
-human body monitors certain key functions, such as BP and blood glucose concentration, that must stay within a particular operating range if the body is to remain healthy
-these important “regulated variables” are kept within their acceptable (normal) range by physiological control mechanisms that kick in if the variable ever strays too far from its “setpoint”, or optimum value.
- there are two basic patterns of control mechanisms: local control and long-distance reflex control
all control systems have three components:
- an input signal
- a control or integrating centre, that regulates incoming information and initiates an appropriate response
- An output signal that creates a response
describe local control
-simplest form of control
-restricted to the tissue or cell involved
-a relatively isolated change occurs in a tissue
-a nearby cell or group of cells senses the change in their immediate vicinity and responds, usually by releasing a chemical
-the response is restricted to the region where the change took place, hence “local control”
describe “reflex control uses long-distance signalling”
-changes that are widespread throughout the body, or “systemic” in nature, require more complex control systems to maintain homeostasis
-e.g., maintaining blood pressure to drive blood flow throughout the body is a systemic issue rather than a local one. Because blood pressure is body-wide, maintaining it require long-distance communication and coordination
-reflex control –> mean any long-distance pathway that uses the nervous system, endocrine system, or both
what can physiological reflex be broken into?
two parts:
-a response loop
-a feedback loop
what are the primary components of a response loop?
3 primary parts:
-an input signal
-an integrating centre
-an output signal
The 3 primary components of the response loop can be expanded into the follow sequence of seven steps to form a pattern that is found with slight variations in all reflex pathways:
Stimulus–> Sensor –> input signal –> integrating centre –> output signal –> target –> response
describe the seven steps that came from the 3 primary components of the response loop
-the input side of the response loop starts with a stimulus –> the change occurs when the regulated variable moves out of its desirable range
-a specialised sensor monitors the variable. If the sensor is activated by the stimulus, it sends an input signal to the integrating centre.
-the integrating centre evaluates the information coming from the sensor and initiates an output signal
-the output signal directs a target to carry out a response. If successful, the response brings the regulated variable back into the desired range
-In mammals, integrating centres are usually part of the nervous system or endocrine system.
-output signals may be chemical, electrical, or a combination.
-The targets activated by output signals can be any cell of the body
what does it mean if a feedback loop is homeostatic?
-designed to keep the system at or near a setpoint so that the regulated variable is relatively stable
-the end result is a regulated variable that oscillates around a setpoint
how well an integrating centre succeeds in maintaining stability depends on…
the sensitivity of the system
What is a negative feedback?
-a pathway in which the response opposes or removes the signal
-negative feedback loops stabilise the regulated variable and thus aid the system in maintaining homeostasis
-negative feedback loops can restore the normal state but cannot prevent the initial disturbance
what type of feedback loop isn’t homeostatic?
positive feedback loop
describe positive feedback loops
-not homeostatic
-the response reinforces the stimulus rather than decreasing or removing it
-the response sends regulated variable even farther from its normal value
-this initiates a vicious cycle of ever-increasing response and sends the system temporarily out of control
-because it escalates the response, this type of feedback requires some intervention or event outside the loop to stop the response
what is feedforward control?
-enables the body to predict change about to occur and start the response loop in anticipation of the change
-e.g., salivation reflex, the sight, smell, and thought of food enough to start out mouths watering in expectation of eating food
what are biorhythms?
-Regulated variables that change predictably and create repeating patterns or cycles of change are called biological rhythms
-the timing of many biorhythms coincides with predictable environmental change, such as daily light-dark cycles or seasons
-biological rhythms reflect changes in the setpoint of the regulated variable
describe circadian rhythms
-humans have circadian rhythms for many body functions, including BP, BT, and metabolic processes
-body temp peaks in the late afternoon and declines dramatically in the early hours of the morning
-many hormones in humans have blood concentrations that fluctuate predictably in a 24-hour cycle. Cortisol, growth hormone and sex hormones (most notes e.g.) –> cortisol concentration in a 9:00am sample might be nearly twice as high as one taken in the early afternoon
-circadian rhythms cued by the light-dark cycle may correspond to rest-activity cycle.
-these rhythms allow our bodies to anticipate behaviour and coordinate body processes accordingly
what is the adaptive significance of functions that vary with a circadian rhythm?
-biological rhythms create an anticipatory response to a predictable environmental variable
describe variability in setpoints associated with changing environmental conditions rather than biological rhythms
-The adaption of physiological processes to a given set of environmental conditions is known as acclimatization when it occurs naturally
-if the process takes place artificially in a laboratory setting, it is called acclimation
What is a hypothesis? And what do they do with it
-a logical guess about how events take place
-they test their hypotheses by designing experiments to collect evidence that supports or disproves their hypotheses, and they publish the results of their experiments in the scientific literature
what are key elements of scientific inquiry?
observation and experimentation
what is a common type of biological experiment?
-either removing or altering some variable that the investigator thinks is an essential part of the observed phenomenon
What is the variable that is altered in an experiment?
the independent variable - the manipulated element - is the cause - its value is independent of other varibles in the study
describe the dependent variable
- The dependent variable is the effect of the independent variable – this is the element that is expected to be affected by changing the independent variable
describe the experimental control
-a control group is usually a duplicate of the experimental group in every respect except that the independent variable is not changed from its initial value
- the purpose of the control is to ensure that any observed changes are due to the manipulated variable and not to changes in some other variable
during an experiment, the investigator collects…
-information, or data, about the effect that the manipulated (independent) variable has on the observed (dependent) variable
-once there is enough information to draw a conclusion, begin analysing data
-
if one experiment supports the hypothesis, then the experiment should be…
-repeated to ensure that the results were not an unusual one-time event –> this step is called replication
When the data supports a hypothesis in multiple experiments…
The hypothesis may become a working model
A model with substantial evidence from multiple investigators supporting it may become a…
scientific theory
describe variability as a variable that could make experiments difficult
-human populations have tremendous genetic and environmental variability
-there are average values for many physiological variables, such as BP, these values simply represent a number that falls somewhere near the middle of a wide range of values
-to show significant differences between experimental and control groups in human experiment, an investigator would have to include a large number of identical subjects
-but getting two groups who are identical in every respect is impossible. instead must attempt to recruit similar in as many aspects as possible.
What is one way to reduce variability within test population?
-do a crossover study
- in a crossover study each individual acts both as experimental subject and a control
-thus, each individual’s response to treatment can be compared with their own control value
(particularly effective when there is a wide variability within population)
describe some psychological factors that makes human experiments difficult
-placebo effect –> give someone a pill and tell the person that it will help alleviate some problem, and there is a strong possibility that the pill will have exactly that effect, even if it contains only sugar or inert substance
-nocebo effect –> if you warn people that a drug they are taking may have specific adverse side effects, those people will report a higher incidence of the side effects than a similar group of people who were not warned
What is a way to circumvent the problems we face with placebo and nocebos effects?
-simplest way is with a blind study, in which the subjects do not know whether they are receiving the treatment or the placebo
-double-blind studies are better, a third party, not involved in the experiment, is the only one who knows which group is receiving the experimental and placebo treatment
-most sophisticated experimental design for minimising psychological effects is the double-blind crossover study –> control group in the first half becomes experimental group in second half, but no one involved knows who is taking the active treatment
What are longitudinal studies?
-designed to be carried out for a long period of time
- a prospective cohort study is a longitudinal study where same participants are followed over a period of time
- a retrospective study is a longitudinal study where some or all cases of disease have already occurred before investigator initiates the study –> match groups of people who all have a particular disease to a similar but healthy control group
what are cross-sectional studies?
-survey a population for the prevalence of a disease or condition.
-Data from cross-sectional studies identify trends to be investigated further
what is a meta-analysis?
-attempt to resolve contradictory results of data
-combines all data from a group of similar studies and uses sophisticated statistical techniques to extract significant trends or findings from the combined data
what elements make up more than 90% of the body’s mass?
oxygen, carbon, and hydrogen
what are organic molecules?
-molecules that contain carbon
what are biomolecules?
-organic molecules associated with living organisms.
what are the major groups of biomolecules?
4 major groups:
-carbohydrates
-lipids
-proteins
-nucleotides
what does the body use for energy?
-carbohydrates, lipids, and proteins –> also used as building blocks of cellular components
describe nucleotides
-biomolecules that play an important role in energy and information transfer
-single nucleotides include energy-transferring compounds ATP (adenosine triphosphate) and ADP (adenosine diphosphate), as well as cyclic AMP, a molecule important in the transfer of signals between cells
-nucleic acids (or nucleotide polymers) such as RNA and DNA store and transmit genetic information
-single nucleotide molecules have two critical functions in the human body: (1) capture and transfer energy in high-energy electrons or phosphate bonds, and (2) aid in cell-to-cell communication
describe lipids
-mostly carbon and hydrogen. Most lipids have a backbone of glycerol and 1-3 fatty acids
-important characteristic of lipids is they are nonpolar and therefore not very soluble in water
-divided into two broad categories:
-fats –>solid at room temperature. most fats are derived from animal sources
-Oils –> liquid at room temperature. Most plant lipids are oils
carbohydrates are primarily…
carbon, hydrogen, and oxygen in the ratio CH2O
proteins and nucleotides contain…
-nitrogen in addition to carbon, hydrogen, and oxygen
- two amino acids also contain sulphur
what are conjugated proteins?
-protein molecules combined with another kind of biomolecule
what are lipoproteins?
-proteins combine with lipids
-lipoproteins are found in cell membranes and in the blood, where they act as carriers for less soluble molecules, such as cholesterol
what are glycosylated molecules?
glycosylated molecules are molecules to which a carbohydrate has been attached to
what are glycoproteins ?
proteins combined with carbohydrates
what are glycolipids ?
lipids bound to carbohydrates
glycoproteins and glycolipids, like lipoproteins, are important components of…
cell membranes
what are polymers?
-large molecules made up of repeating unit
describe fatty acids
-fatty acids are long chains of carbon atoms bound to hydrogens, with carboxyl (-COOH) or “acid” group at one end of the chain
-saturated fatty acids have no double bonds between carbons, so they are “saturated” with hydrogens. The more saturated a fatty acid is, the more likely it is to be solid at room temperature.
-monounsaturated fatty acids have one double bond between two of the carbons in the chain. For each double bond, the molecule has two fewer hydrogen atoms attached to the carbon chain.
-polyunsaturated fatty acids have two or more double bonds between carbons in the chain
describe the formation of lipids
-Glycerol is a simple 3-carbon molecule that makes up the backbone of most lipids
-Monoglyceride –> Glycerol plus one fatty acid
-Diglyceride –> Glycerol plus two fatty acids
-triglyceride –> Glycerol plus three fatty acids (aka triacylglycerol). More than 90% of lipids are in the form of triglycerides
What are 3 types of lipid-related molecules?
-Eicosanoids –> modified 20-carbon fatty acids with a complete or partial carbon ring at one end and two long carbon chain “tails”. Eicosanoids, such as thromboxanes, leukotrienes, and prostaglandins, act as regulators of physiological functions
-steroids –> lipid related molecules whose structure includes four linked carbon rings. Cholesterol is the primary source of steroids in the human body
-phospholipids –> have 2 fatty acids and a phosphate group (H2PO4).
Cholesterol and phospholipids are important components of animal cell membranes
describe carbohydrate
-most abundant biomolecules
-name from their structure, carbon (carbo-) with water (hydro)
-general formula for a carbohydrate is (CH₂O)ₙ or CₙH₂ₙOₙ –> showing that for each carbon there are two hydrogens and one oxygen.
-divided into three categories:
-monosaccharides
-disaccharides
-polysaccharides
describe monosaccharides
-simple sugars
-the most common monosaccharides are the building blocks of complex carbohydrates and have either five carbons, like ribose, or six carbons like glucose
describe disaccharides
-consist of glucose plus another monosaccharide
describe polysaccharides
-glucose polymers. All living cells store glucose for energy in the form of polysaccharide
what are proteins made from
-polymers of smaller building-block molecules called amino acids
describe the structure of peptides and proteins
Primary structure:
-The 20 protein-forming amino acids assemble into polymers called peptides. The sequence of amino acids into a peptide chain is called the primary structure. The 20 amino acids can create almost infinite number of combinations
-peptides range in lengths from two to two million amino acids:
–Oligopeptide: 2-9 aminos acids
–polypeptides: 10-100 amino acids
–proteins: > 100 amino acids
Secondary Structure:
-secondary structure is created primarily by hydrogen bonds between adjacent chains or loops
-covalent bond angles between amino acids determine secondary structure
Tertiary structure:
-is the protein’s three-dimensional shape
-can be a mix of secondary structures. Beta-sheets are shown as flat ribbon arrows and alpha helices are shown as ribbons coils
Quaternary structure:
-Multiple subunits combine with noncovalent bonds. Haemoglobin molecules are made from four globular protein subunits
Describe amino acids
-all amino acids have a carboxyl (-COOH), an amino group (-NH₂), and a hydrogen attached to the same carbon. The fourth bond of the carbon attaches to a variable “R” group
-The nitrogen (N) in the amino group makes proteins our major dietary source of nitrogen
-The R groups differ in their size, shape, and ability to form hydrogen bonds or ions. Because of the different R groups, each amino acid reacts with other molecules in a unique way
-in a peptide bond, the amino group of one amino acid joins the carboxyl group of the other, with the loss of water
-20 amino acids commonly occur in natural proteins. The human body can synthesize most of them, but at different stages of like some amino acids must be obtained from diet and are therefore considered essential amino acids
-a few amino acids do not occur in proteins but have physiological functions
–homocysteine: a sulphur-containing amino acid that in excess is associated with heart disease
–gamma-amino butyric acid (gamma-amino butyric acid) or GABA: a chemical made by nerve cells
–Creatine: a molecule that store energy when it binds to a phosphate group
what are functional groups?
-some combinations of elements that occur repeatedly in biological molecules
-atoms in a functional group tend to move from molecule to molecule as a single unit
what is phosphorylation and dephosphorylation ?
-phosphorylation is the addition of a phosphate group
-dephosphorylation is the removal of a phosphate group
phosphate group - H2PO4
What are the most common functional groups?
amino - NH2
Carboxyl (acid) - COOH
Hydroxyl - OH
phosphate - H2PO4
describe covalent bonds
-the arrangement of electrons in the outer energy level (shell) of an atom determines an element’s ability to bind with other elements. Electrons shared between atoms form strong covalent bonds that bind atoms together to form molecules
-molecules form when atoms share pair of electrons, one electron from each atom, to create covalent bonds
-these strong bonds require the input of energy to break them apart
-if adjacent atoms share two pair of electrons rather than just one pair, a double bond, represented by a double line, results. If two atoms share three pairs of electrons, they form triple bond
describe ions
-if an atom or molecule gains or loses one or more electrons, it acquires an electrical charge and becomes an ion. Ions are the basis for electrical signalling in the body.
-cations are positively charged
-anions are negatively charged
-important ions of the body are:
Sodium - NA+
potassium - K+
calcium - Ca2+
Hydrogen - H+
Magnesium - Mg2+
Chloride - Cl-
Bicarbonate - HCO3-
phosphate - HPO4(2-)
sulphate - SO4(2-)
describe high-energy electrons
-the electrons in certain atoms can capture energy from their environment and transfer it to other atoms. This allows the energy to be used synthesis, movement, and other life processes. The released energy may also be emitted as radiation. e.g., bioluminescence in fireflies is visible light emitted by high-energy electrons returning to their normal low-energy state.
describe free radicals
-are unstable molecules with an unpaired electron.
-they are thought to contribute to aging and to the development of certain diseases, such as some cancers
which common bond types are strong and weak
-covalent and ionic bonds are strong, because they require a lot of energy to make or break
-hydrogen bond and van der Walls forces are weaker bonds that require much less energy to break
describe RNA structure
-ribonucleic acid is a single-strand nucleic avid with ribose as the sugar in the backbone, and four bases - adenine, guanine, cytosine, and uracil
describe DNA structure
-deoxyribonucleic acid is a double helix, a three-dimensional structure that forms when two DNA stands link through hydrogen bonds between complementary base pair. Deoxyribose is the sugar in the backbone, and the four bases are adenine, guanine, cytosine, and thymine
describe the base-pairing
bases on one strand form hydrogen bonds with bases on the adjoining strand. This bond follows very specific rule:
-Because purines are larger than pyrimidine, space limitation always pair a purine with a pyrimidine
-Guanine (G) forms three hydrogen bonds with cytosine (C)
-Adenine (A) forms two hydrogen bonds with thymine (T) or uracil (U)
more energy is require to break the triple hydrogen bonds of G and C then the double bonds of A and T or A and U
what do protons determine
-determine the element (atomic number)
what does the neutrons determine
the isotope
how do you calculate the atomic mass
protons + neutrons in nucleus
What are the responsibilities of electrons
-from covalent bonds
-create ions when gained or lost
-capture and store energy
-create free radicals
describe polar molcules
-some molecules develop regions of partial positive and negative charge when the electron pairs in their covalent bonds are not evenly share between the linked atoms. When electrons are shares unevenly; the atom(s) with the stronger attraction for electrons develop a slight negative charge (indicated by δ+ (delta)) and the atom(s) with the weaker attraction for electrons develops a slight positive charge (δ−). These molecules are called polar molecules, because they can be said to have positive and negative ends, or poles
-polarity makes good solvents
describe nonpolar molecule
-is one whose share electrons are distributed so evenly that there are no regions of partial positive or negative charge
what bonds facilitates reversible interactions
-ionic bonds, hydrogen bonds, and van der Waals forces (all noncovalent bonds)
describe ionic bonds
-aka electrostatic attractions
-results from attraction between ions with opposite charges
describe hydrogen bonds
-a weak attractive force between hydrogen atom and a nearby oxygen, nitrogen, or fluorine atom
- no electrons are gained, lost, or shared in a hydrogen bond
-oppositely charged regions in polar molecules are attracted to each other. hydrogen bonds may occur between atoms in neighbouring molecules or between atoms in different parts of the same molecule
what is surface tension
-hydrogen bonding between molecules is responsible for surface tension of water
-surface tension is the attractive force between water molecules that causes water to form spherical droplets when falling or to bead up when spilled onto a non-absorbent surface. The high cohesiveness of water is due to hydrogen bonding and makes it difficult to stretch or deform
describe Van der Waals forces
-are weak, nonspecific attractions between the nucleus of any atom and the electrons of nearby atoms. Two atoms that are weakly attracted to each other by wan der Waals forces move closer together until they are close that their electrons begin to repel one another, van der Wassl forces allow atoms to pack closely together and occupy a minimum amount of space. A single wan der Waals attraction between atoms is very weak
what is solubility ?
The degree to which a molecule is able to dissolve in a solvent, the more easily a molecule dissolves, the higher its solubility
what substance usually cannot form hydrogen bonds with water molecules
nonpolar molecules, lipids (fats and oils) are the most hydrophobic group of bioloigcal molecules
what are two common protein secondary structures? and describe them
-The A-helix (alpha-helix) spiral
-The zigzag shape of B-sheets (beta-sheets)
-adjacent B-strands in the polypeptide chain associate into sheetlike structure held together by hydrogen bonding, shown as dotted lines (. . .)
-the sheet configuration is very stable and occurs in many proteins destined for structural uses
-proteins with other functions may have a mix B-strands and A-helices
what is the molecular shape created by?
covalent bond angles and weak non-covalent interactions within a molecule
the stable secondary structures of proteins are formed by…
covalent bond angles between amino acids in the polypeptide chain
the tertiary structure of a protein is its 3d shape, created through…
spontaneous folding as the result of covalent bonds and noncovalent interactions
what are proteins categorized into based on their shape?
-into two large groups based on their shape:
-Globular proteins
-fibrous proteins
describe globular proteins
-can be a mix of A-helices, B-sheets, and amino acid chains that fold back on themselves
-the result is a complex tertiary structure that may contain pockets, channels, or protruding knobs
-the tertiary structure of globular proteins arises partly from the angles of covalent bonds between amino acids and partly from the hydrogen bonds, van der Waals forces, and ionic bonds that stabilise the molecule’s shape
-in addition to covalent bonds between adjacent amino acids covalent disulphide (S-S) bonds play an important role in the shape of many globular proteins –> amino acid cysteine contains sulphur as part of a sulfhydryl group (-SH). Two cysteines in different parts of the polypeptides chain can bond to each other with a disulfide bond that pulls the sections of chain together
describe fibrous proteins
-can be B-strands or long chains of A-helices
-are usually insoluble in water and form important structural components of cells and tissues
-examples of fibrous proteins include collagen, found in many types of connective tissues, such as skin, and keratin, found in hair and nails
if free H+ disrupts a molecule’s noncovalent bonds, molecules shape (or conformation)…
can change. A change in shape may alter or destroy the molecule’s ability to function
What is acidity?
the concentration of free H+ in body fluids, measures in terms of pH
where do hydrogen ions in the body fluids come from?
-some come from separation of water molecules (H2O) into H+ and OH- ions
-others come from acids (molecules that release H+) when they dissolve in water
only free H+ contributes to the hydrogen ion concentration, true or false?
true, when the hydrogen is part of the intact acid molecule (e.g., carbonic acid), it does not contribute to acidity.
describe buffer
-body maintains normal pH using buffers
-a buffer is any substance that moderate changes in pH
-many buffers contain anions that have a strong attraction to H+ molecules. When free H+ is added to a buffer solution, the buffer’s anions bond to the H+, thereby minimizing any change in pH
what is a solute?
-any substance that dissolves in a liquid. The degree to which a molecule is able to dissolve in a solvent is the molecule solubility. The more easily a solute dissolve, the higher its solubility
What is a solvent?
-the liquid into which solutes dissolve. In biological solutions, water is the universal solvent
what is a solution?
-a solution is the combination of solutes dissolved in a solvent. The concentration of a solution is the amount of solute per unit volume of solution
-concentration = solute amount/ volume of solution
describe molecular mass
-calculated from the chemical formular of a molecule. This is the mass of one molecule, expressed in atomic mass units (amu) or, more often, in Daltons (Da), where 1 amu = 1 Da
-molecular mass = SUM [(atomic mass of each element) x (the number of atoms of each element)]
describe moles
-Moles (mol) are an expression of the number of solute molecules, without regard for their weight.
-one mole = 6.02 x 10^23 atoms, ions, or molecules of a substance
-one mole of a substance has the same number of particles as one mole of any other substance
describe gram molecular weight
-in the laboratory, we use the molecular mass of a substance to measure out moles
-e.g., one mole of glucose (with 6.02 x 10^23 glucose molecules) has a molecular mass of 180 Da and weighs 180 grams. The molecular mass of a substance expressed in grams is called the gram molecular weight.
describe equivalents (Eq)
-are a unit used for ions, where 1 Eq = molarity of the ion x the number of charges the ions carries
-e.g., sodium ion, with its charged of +1, has one equivalent per mole
-the hydrogen phosphate (HPO4(2-)) has two equivalents per mole
-concentration of ions in the blood are often reported in milliequivalents per litre (mEq/L)
describe percent solutions
-in lab, scientists cannot measure out solutes by the mole. They use the more conventional measurement of weight. The solute concentration may then be expressed as a percentage of the total solution, or percent solution.
-A 10% solution means 10 parts of a solute per 100 part of total solution
-Weight/volume solutions, used for solutes that are solids, are usually expressed as g/100 mL solution or mg/dL
-out of date way of expressing mg/dL is mg% where % means per 100 parts or 100 mL (20mg/dL = 20 mg%
describe molarity
-is the number of moles of solute in a litre of solution, and is abbreviated as either mol/L or M.
-A one molar solution of glucose (1 mol/L, 1 M) contains 6.02 x 10^23 molecules of glucose per litre of solution
-it is made by dissolving one mole (180 grams) of glucose in enough water to make one litre per solution
-typical biological solutions are so dilute that solute concentrations are usually expressed as millimoles per litre (mmol/L or mM)
describe hydrophilic interactions
-molecules that have polar regions or ionic bonds readily interact with the polar regions of water. This enables them to dissolve easily in water. Molecules that dissolve readily in water are said to be hydrophilic (hydro-, water + philos, loving)
describe hydrophobic interactions
-Because they have an even distribution of electrons and no positive or negative poles, nonpolar molecules have no regions of partial charge, and therefore tend to repel water molecules.
-molecules like these do not dissolve readily in water and are said to be hydrophobic (hydro- water, + phobos, fear).
-molecules such as phospholipids have both polar and nonpolar regions that play critical roles in biological systems in the formation of biological membrane
what is an acid?
-a molecule that contributes H+ to a solution
-carboxyl group, -COOH, is an acid because in solution it tends to lose its H+
-acidic solutions have gained H+ from an acid and have a pH less than 7
what is a base?
-a molecule that decreases the H+ concentration of a solution by combining with free H+
-molecules that produce hydroxide ions, OH-, in solution are bases because the hydroxide combines with H+ to form water
-basic or alkaline solutions have a H+ concentration lower than that of pure water and have a pH value greater than 7
Describe pH
-concentration of H+ in body fluids is measured in terms of pH
-the expression of pH stands for “power of hydrogen”
-pH = -log[H+] —-> This equation is read as “pH is equal to the negative log of the hydrogen ion concentration.”
-[] by convention expressed in mEq/L
-Using the rule of logarithms that says -log x = log (1/x), pH equation can be rewritten as: pH= log(1/[H+]) —-> as [H+) goes up, pH goes down
-pH of a solution is measures on a numeric scale between 0 and 14. The pH scale is logarithmic, meaning that a change in pH value of 1 unit indicates a 10-fold change in [H+]. e.g., if a solution changes from pH 8 to pH 6, there has been a 100-fold (10^2) increase in [H+]
-The normal pH of blood in the human body is 7.40. Homeostatic regulation is critical because blood pH less than 7.00 or greater than 7.70 is incompatible with life
what are the most soluble proteins?
Fall into seven broad categories:
-Enzymes – Some proteins act as enzymes, biological catalysts that speed up chemical reactions. Enzymes play an important role in metabolism
-Membrane transporters – proteins in cell membranes help move substances back and forth between the intracellular and extracellular compartments. These proteins may form channels in the membrane, or they may bind to molecules and carry them through the membrane
-Signal molecules – some protein and smaller peptides act ass hormones and other signal molecules
-Receptors – proteins that bind signal molecules and initiate cellular responses are called receptors
-Binding proteins – These proteins, found mostly in the extracellular fluid, bind and transport molecules throughout the body. Examples you have already encountered include the oxygen-transporting protein haemoglobin and the cholesterol-binding proteins, such as LDL (low density lipoprotein
-Immunoglobins – These extracellular immune proteins, also called antibodies, help protect the body from foreign invaders and substance
-Regulatory proteins – turn cell processes on and off or up and down. E.g., the regulatory proteins known as transcription factors bind to DNA and alter gene expression and protein synthesis
What properties do binding sites exhibit?
-specificity
-affinity
-competition
-saturation
What is a ligand?
any molecule or ions that binds to another molecule
what are substrate?
ligands that bind to enzymes and membrane transporters as also called substrates
describe specificity
-The ability of a protein to bind to a certain ligand or a group of related ligands
-Some proteins specific about the ligands they bind to, others bind to whole groups of molecules
-ligand binding require molecular complementarity
-the ligand and the protein binding site must be complementary
-when ligand and protein come close to each other, noncovalent interactions between the ligand and the protein’s binding site allow the two molecules to bind
-protein’s binding site and shape of its ligand do not need to fit one another exactly
-When binding site and ligand come close to each other, the begin to interact through hydrogen and ionic bonds and van der Waals forces
-the protein’s binding site then changes shape (conformation) to fit more closely to the ligand –> this is the induced-fit model
describe affinity
-the degree to which a protein is attracted to a ligand is called the protein’s affinity for the ligand
-high affinity = more likely to bind
-binding is reversible
-reversible binding reactions go to a state of equilibrium, where the rate of binding (P + L –> PL) is exactly equal to the rate of unbinding, or dissociation (P + L <– PL)
-when a reaction is at equilibrium, the ratio of the product concentration, or protein-ligand complex [PL], to the reactant concentrations [P][L] is always the same
- this ratio is called the equilibrium constant Keq, appears to all reversible chemical reactions
Keq = [PL] / [P][L]
-the higher the affinity the larger the Keq
What happens to equilibrium when [P] or [L] changes?
- the equilibrium is disrupted when more protein or ligand is added to the system. Now the ratio of [PL] to [P][L] differs from the Keq
-in response, the rate of the binding reaction increases to convert some of the added P or L into the bound protein-ligand complex
-As the ratio approaches its equilibrium value again, the rate of the forward reaction slows down until finally the system reaches the equilibrium ration once more –> [P], [L], and [PL} have all increased over their initial value, but the equilibrium ratio has been restored ——> this situation describe is example of a reversible reaction obeying the law of mass action
What does the law of mass action say?
-when a reaction is at equilibrium, the ratio of the products to the substrates is always the same
-if the ratio is disrupted by adding or removing one of the participants, the reaction equation will shift direction to retore the equilibrium condition
what is the dissociation constant?
-Kd = [P][L]/[PL]
-reciprocal of the equilibrium constant
-large Kd indicates the low binding affinity of the protein for the ligand, with more P and L remaining in the unbound site. Conversely, small Kd means higher value for [PL] relative to [P] and [L], so a small Kd indicates higher affinity of the protein for the ligand
- if one protein binds to several related ligands, a comparison of the Kd values can tell us which ligand is more likely to bind to the protein.
what are competitors?
- the related ligands that compete for the binding sites are called competitors
-competition between ligands is a universal property of protein binding
what are agonists?
-competing ligands that mimic each other’s actions
-may occur in natures, such as nicotine, which mimics the activity of acetylcholine by binding to the same receptor. Can also be synthesized.
is a proteins affinity for a ligand always constant?
-no, chemical and physical factors can alter, or modulate, binding affinity or even totally eliminate it
describe isoform
-closely related proteins whose function is similar but whose affinity for ligands differs are called isoforms of one another
describe activation
-also known as proteolytic activation
-some proteins are inactive when they are synthesized in the cell
-before such a protein can become active, enzymes must chop off one or more portions of the molecule
-the activation of some proteins requires the presence of a cofactor, which is an ion or small organic functional group –> cofactors must attack to the protein before the binding site will become active and bind a ligand
what is a modulator?
A factor the influences either protein binding or protein activity is called a modulator
What are the mechanisms by which modulation takes place?
the modulator either (1) changes the protein’s ability to bind to the ligand or it (2) changes the protein’s activity or its ability to create a response
What are chemical modulators?
-molecules that bind covalently or noncovalently to proteins and alter their binding ability or their activity
-may activate or enhance ligand binding, decrease binding ability, or completely inactivate the protein so that it is unable to bind any ligand
-inactivation may be either reversible or irreversible
-antagonists, also called inhibitors, are chemical modulators that bind to a protein and decrease its activity.
what are the modulators?
-competitive inhibitor
-irreversible inhibitor
-allosteric modulator
-covalent modulator
-pH and temperature
describe competitive inhibitors
-reversible antagonists that compete with the customary ligand for the binding site
-the degree of inhibit depends on the relative concentrations of the competitive inhibitors and the customary ligand, as well as the protein’s affinities for the two
-The binding of competitive inhibitors is reversible: increasing the concentration of the customary ligand can displace the competitive inhibitor and decrease the inhibition
describe irreversible antagonists
-Bind tightly to the protein and cannot be displaced by competition
-Antagonist drugs have proven useful for treating many conditions
-e.g., tamoxifen, an antagonist to the oestrogen receptor, is used in treatment of hormone-dependent cancers of the breast
describe allosteric modulators
-may be either antagonists or activators
-bind reversibly to a protein at a regulatory site away from the binding site, and by doing so change the shape of the binding site
-allosteric inhibitors are antagonists that decrease the affinity of the binding site for the ligand and inhibit protein activity.
-allosteric activators increase the probability of protein-ligand binding and enhance protein activity
describe covalent modulators
-may be either antagonists or activators
-are atoms or functional groups that bind covalently to proteins and alter proteins’ properties
-like allosteric modulators, covalent modulators may either increase or decrease a protein’s binding ability or its activity
-e.g., phosphorylation
describe the physical factors that effect protein strucutre and function
-temperature and pH (acidity) can have dramatic effects on protein structure and function
-small changes in pH or temp act as modulators to increase or decrease activity
-however, once these factors exceed some critical value, they disrupt the noncovalent bonds holding the protein in its tertiary conformation, loses its shape and activity —> when protein loses its conformation its is said to be denatured
-in few cases activity can be restored if the original temp and pH returns –> usually denaturation produces a permanent loss of activity
what is up-regulation of proteins?
programmed production of new proteins (receptors, enzymes, and membrane transporters
what is down-regulation of proteins?
programmed removal of proteins
is the amount of protein in body consistent over time or does it vary?
varies using up-regulation and down-regulation
the amount of protein present in a cell has…
direct influence on the magnitude of the cell’s response, cells alter amount of protein by influencing both its synthesis and breakdown. Even when the amount of protein is constant, there is still a steady turnover of protein molecules
if the concentration of a protein in a cell is constant, then the concentration of the ligand…
determine the magnitude of the response. Fewer ligands activate fewer proteins, and the response is low. As the ligand concentration increase, so does the magnitude of the response, up to a maximum where all protein binding sites are occupied – called saturation point
what are cells?
The basic functional unit of living organisms, and an individual cell can carry out all the processes of life
what are the body cavities divided into?
Three major cavities:
-Cranial cavity (Skull) - contains the brain
-Thoracic cavity (thorax) - bounded by the spine and ribs on top and sides, with muscular diaphragm forming the floor. Contains the heart, which is enclosed in a membranous pericardial sac, and the two lungs, enclosed in separate pleural sac
-abdominopelvic cavity - abdomen and pelvis form one continuous cavity. A tissue lining called peritoneum lines the abdomen and surrounds the organs within (stomach, intestines, liver, pancreas, gallbladder, and spleen). Kidney lie outside the abdominal cavity, between the peritoneum and the muscles and bones of the back, just above waist level. pelvis contains reproductive organs, urinary bladder and the terminal portion of the large intestine
What are the several discrete fluid-filled anatomical compartments of the body?
-blood-filled vessels and heart of the circulatory system form one compartment
-our eyes are hollow fluid filled spheres subdivided into compartments, the aqueous and vitreous humours
-The brain and spinal cord are surrounded by a special fluid compartment known as cerebrospinal fluid (CSF).
-Membranous sacs that surround the lungs (pleural sacs) and the heart (pericardial sac) also contain small volumes of fluid
what is lumen?
-the interior of any hollow organ is called lumen
-may be wholly or partially filled with air or fluid
if we think of all the cells of the body together as one unit, we can divide the body into…
two main fluid compartments:
(1) the extracellular fluid (ECF) outside the cells
-The ECF subdivides further into:
–Plasma, the fluid portion of the blood, and;
–Interstitial fluid, which surrounds most cells of the body
(2) The intracellular fluid (ICF) within the cells
-dividing wall between ECF and ICF is the cell membrane
what does the word membrane mean?
Has two meanings:
-before invention of microscopes in sixteenth century, membrane always describe a tissue that lined a cavity or separated two compartments.
-after microscope, can also be applied to cell membrane.
What are the general functions of the cell membrane (aka plasma membrane or plasmalemma)
-Physical isolation
-Regulation of exchange with the environment
-Communication between the cell and its environment
-Structural support
what is generally the protein to lipid ratio?
-the more metabolically active a membrane is, the more proteins it contains
describe the fluid mosaic model
-peripheral proteins can be removed without disrupting the integrity of the membrane
-phospholipid heads face the aqueous intracellular and extracellular compartments
-lipid tails form the interior layer of the membrane –> cholesterol molecules insert themselves into the lipid layer
-transmembrane proteins cross lipid bilayer
-extracellular surface glycoproteins and glycolipids
-all cell membranes are of relatively uniform thickness, about 8nm
what are the main types of lipids that make up the cell membrane?
Three main types:
-Phospholipids
-Sphingolipids
-Cholesterol
describe the structure of phospholipids
-made up of glycerol backbone with two fatty acid chains extending to one side and a phosphate group extending to the other
-the glycerol-phosphate head of the molecule is polar and thus hydrophilic
-the fatty acid “tail” is nonpolar and thus hydrophobic
What arrangements can phospholipids orient themselves into?
-The micelle
-the liposome
-the phospholipid bilayer
describe micelles
-small droplets with a single layer of phospholipids arranged so that the interior of the micelle is filed with hydrophobic fatty acid tails
-important in the digestion and absorption of fats in the digestive tract
describe liposomes
-larger spheres with bilayer phospholipid walls
-leaves hollow centre with an aqueous core that can be filled with water-soluble molecules
-liposome-like structure thought to be precursor of the first living cell
-being used as a medium to deliver drugs and cosmetics –> researchers can make immunoliposomes that use antibodies to recognise specific types of cancer cells
