Midterm Flashcards
Subdisciplines of biology
o Zoology – animals (no plants, bacteria, fungi)
o Microbiology – bacteria and viruses, fungi and parasites (Viruses – not technically living; not under biology definition)
o Botany – plants
o Mycology – fungi (infectious, naturally occurring, etc)
o Ecology – how organisms interact with their environments
Evolution
- natural selection
- critical mutation
- charles Darwin - 2 main points
Evolution – change that allows organisms to adapt to their environment
Natural selection – species more suited to enviro (physical or chemical conditions) will more likely survive and reproduce
- Reproduction effects – antibiotic resistance develops rapidly because bacteria evolve so quickly
- Changes occur over many generations – typically gradual
- It is possible to have a critical mutation after only one generation (ex. bacterial resistance)
Natural selection – Charles Darwin published ‘On the Origin of Species’ in 1859
Two main points noted in his publication
1. Present day species arose from ancestors
2. The mechanism that produces new species is Natural Selection allows for speciation to occur to increase diversity
- Allows for increased or decreased success depending on what environment selects
- Population with traits better suited to survive will be more likely to survive = more likely to reproduce = larger gene pool and more of said species
- Tends not to apply with humans – too wealthy of a species and society
Common features of all life (6)
- Complex organization – a highly ordered structure
a. Even an individual cell is organized and strategically placed in order to function properly - A highly regulated internal environment – constant internal environment despite changing external environments
a. Ex. going for a run will generate sweat to release heat from muscle contractions
i. Experiencing higher temp is detected by thermoreceptors and creates sweat
ii. Muscle also creates lactic acids – decreases pH; must be able to get rid of acid - The ability to grow and develop – inherited genes control growth and development
a. Growth – tissues must be able to expand
b. Development – allows us to process information and increase balance and coordination
i. Bacteria won’t develop same as human but they still develop - The ability to take in and utilize energy – energy is used to perform all of the necessary life functions
a. Humans – intake of food; enzymes break down nutrients; absorbed to blood; sent to cells and broken down further; must also be able to expel waste - The ability to respond to environmental changes and stimuli
a. Nociceptors and thermoreceptors – prevent excessive irreversible damage
i. Feeling you’re cold; feeling you’re in danger; feeling stove element
b. Chemoreceptors – detect increase in co2 and therefore acid when holding breath; body overrides voluntary control and forces breathing - The ability to reproduce one’s own kind – not everyone can, but most people generally can
Emergent traits
Reductionism
System biology
Each new level is characterized by emergent traits – new traits that occur due to increasing complexity requiring increased arrangement and interaction
o Characteristic gained when becoming part of a larger system
Reductionism – reduction of complex system into simpler components; allows for better understanding
o Must still examine the interactions of the individual components with one another
Systems biology – looks at system as a whole; how changing one variable will affect the function of a system
Levels of organization
- cells - what do they make up, what 2 kinds of cells, common features of all cells
- hepatocytes
- Biosphere – all living things on earth exist within
a. All environments that support life – most area of land, water bodies (bacteria and marine organisms), lower atmosphere (able to sustain life with o2), soil (bacteria)
b. Broken down into ecosystems - Ecosystems – all living and non-living things existing within a particular environment
a. Including all components of the environment with which the living organisms interact – air, soil, sunlight and water; used in transfer of heat and distribution of gases - Communities – all living organisms within a particular ecosystem
a. Sets of populations that inhabit a specific area - Populations – all the individuals of a particular species living within a particular area
a. Example: all of the lady bugs living within the park
b. Specific species – only one type of member - Organisms – the individual unit/one member of the population
a. Example: A lady bug from the lady bug population, a deer from the deer population - Organ Systems – groups of several organs which work together to perform specific functions; all play roles in sustaining life
a. Example: The nervous system, the respiratory system, the circulatory system, etc. - Organs – structures comprised of different tissues; individual units of organ system
a. 2 or more tissues work together as a group to perform specific functions
i. Example: the heart is composed of muscle tissue, connective tissue etc. - Tissues – made of similar cell types; each tissue has a specific function
a. Each organ is made of several different tissue types
b. Ex. muscle tissues cells are able to contract - Cells – membrane bound structures that form the individual units of living matter
a. Make up tissues – ex. liver tissue is composed of hepatocytes (liver cells)
b. May be single celled or multi-cellular organisms
- Multicellular – constantly being replaced; we don’t notice when they die
- Single celled – kills entire organism
c. The most basic unit of life – lowest structural level capable of performing all necessary activities
All have common features regardless of specific differences - All are membrane bound – creates ICF and ECF
- All have DNA as their genetic material
- Structure can differ – linear vs circular
- RNA also holds genetic info – living things don’t have rna store genetic info
- Viruses can – DNA vs RNA viruses
d. Structure and function are correlated to one another – emergent property
e. Types of cells
- Prokaryotes – archaea and bacteria
- Eukaryotic – most complex; protists (no longer one group), fungi, plants, animals - Organelles – the various functional components present on the inside of the cell
a. Not alive – cell is the smallest living thing; only part of the living unit - Molecules – made up of a cluster of atoms
a. Example: DNA, protein, sugar molecules
b. Make up organelles within the cell
Interactions within the environment
- producers
- consumers
- decomposers
- energy
Interaction with environment – organisms within an ecosystem interact with both the living and the non-living components of their environment
Producers – provide food for the other organisms present
- Plants, algae, bacterium – anything that is photosynthetic
- Converts co2 to sugar via photosynthesis
Consumers – eat plants and other animals; everything that is not a producer
- Takes energy from cells stored within other organisms
Decomposers – breakdown wastes and dead organisms; recycle nutrients so that they can be used for biosynthesis
- Fungi, bacteria, small animals present in the soil
Energy – enters the ecosystem as sunlight
a. Transformation of energy from one form into another is inefficient and energy is lost as heat
- Example: muscle contraction
- You will never have 100% efficiency – damage can be caused by too much heat
b. Each subsequent transfer of energy results in less energy available to next organism
Chemical vs energy flow
- bioremediation
- Recycling of Chemical nutrients
a. Biogeochemical cycles – basic chemicals needed for life (carbon, nitrogen, oxygen, etc) flow from air and soil to plants, animals and decomposers (release back into ecosystems) and then back to the air and soil
i. Ex. using bacteria in water recycling to remove feces (bioremediation) - Energy Flow – is constantly gained and lost from an ecosystem (one way)
a. Energy enters an ecosystem when light from the sun is absorbed by plants and other photosynthetic organisms (enters as visible light)
b. Energy exits an ecosystem as heat (exits as infrared heat)
Genetic material of organisms
- genome
Genetic material is present in cells as DNA (deoxyribonucleic acid) – characteristic of all living things
o All cells will have the same genome within despite cell differences (same set of recipe books; cook from different recipes)
o Heritable – DNA is inherited from one generation to the next
Genome – the entire DNA content of the organism
a. DNA is arranged into chromosomes (46)
- Chromosomes are organized into functional units of genes – vary in length/how many genes are present
b. Contained within the cell – needs to be accessible to the cell to use
- Ex. recipe collection – genome; individual recipe book – chromosomes
Taxonomy
- how many are named
- how many are estimated to be known
Taxonomy – branch of biology that names and classifies species into groups based on similarity
o Over 1.8 million species that are known and named – estimates of the true number of species range from 10 million to 400 million
Grouped based on
a. Previously – according to structural and functional characteristics
- However – just because 2 things fly doesn’t imply genetic relatedness
b. Today – DNA sequence homology is used to group different species
3 domains of organisms
- Domain Bacteria (Prokaryotes)
a. Common ancestor of all life – closest to bacteria
- Branched into euks and archaea – more genetically similar than bacteria and archaea (even though they’re both proks) - Domain Archaea (Prokaryotes) – not similar enough to bacteria to be in the same group
a. Suggested to be the first life form – can handle extreme temp and conditions - Domain Eukarya – enough similarity to all exist together
a. There are three kingdoms within Eukarya domain – multi-cellular organisms grouped according to nutritional diversity
- Kingdom Plantae – photosynthetic plants
- Kingdom Fungi – molds, yeasts, and mushrooms
- Kingdom Animalia – animals; vertebrates and invertebrates
- **Protists: single celled protozoans and algae (single and multi-cellular)
Formerly a fourth Kingdom
b. Eukaryotes are often multicellular – there are single celled euks
i. Single celled orgs – anything that happens within that cell compromises ability to live; very vulnerable
ii. First cell type was unicellular proks – evolved to unicellular euks – then multicellular euks
Science
Knowledge obtained through study
• Either by accidental observation or as a result of experimentation
• Science also refers to the body of knowledge gained as a result of these studies
• Dependent on direct observation – seeing is believing
o The more likely you are able to reproduce something – the more validity it holds
2 primary scientific approaches
Discovery Science – the result of verifiable observations and measurements
a. Conclusions from inductive reasoning (bottom up)
i. Inductive – make conclusions based on observations; conclusions which are drawn because of a large number of observations
ii. Example: A conclusion that all living things are made of cells was drawn because observation of all biological specimens over thousands of years all contained cells
Hypothesis-Based Science – observation (from discovery science) -> hypothesis -> testing
a. Hypothesis – a suggested explanation for a given set of observations (cause and effect)
i. Not necessarily true – must be tested by further observations and by specially designed experiments
- Testing supports by not finding evidence that it is false – not by showing it’s correct
- Can never be proven without a doubt – surviving attempts to disprove makes it more likely to be a valid explanation of observation
ii. Must be
- Testable – whether or not it is correct
- Falsifiable – experimentation must be able to show its not true
b. Deductive reasoning – moves from a general statement down to a specific conclusion (top down); if/then statements
i. Example: taking 2 independent statements to deduce if/then
- Premise #1: all living things are composed of cells
- Premise #2: human beings are living
- Deductive reasoning leads to the conclusion human beings must then be composed of cells
a. Can then tests hypothesis
c. Theories – broad; many different observations (more blanket statements); supported by large, growing bodies of evidence
i. Give way to new hypotheses – more specific than theories
Snakes - hypothesis based testing
Uses actual scientific research
Steps
o Begins with an observation – most poisonous animals are brightly colored in order to alert predators to the potential danger, saving the poisonous animal from predation
- There also exist mimics who avoid predation in the same way as the poisonous animals however they do not harbor any poison
Hypothesis – the mimicry functions to reduce the likelihood that the harmless animal will be eaten
Experiments are then designed to test
• Both snake types (brightly colored and poisonous) and (brightly colored and non-poisonous) are found in North and South Carolina
o The non-poisonous variety is also found in areas where the poisonous variety is not – this should hypothetically not provide protection because other animals are not accustomed to bright colours meaning poisonous
New hypothesis – if the hypothesis is true and predators avoid brightly colored snakes because of the association with poison, then predators will attack the non-poisonous snakes more frequently in areas where the poisonous variety is not found (attracted to them) due to lack of conditioning that colourful = poison
Experiment
- Hypothesis was tested by creating two different versions of a fake snake constructed out of plasticine:
- Experimental group: brightly colored fake snakes
- Control group: plain brown fake snakes
- Equal numbers of both snake types were place in areas where both poisonous and non-poisonous snakes are found as well as in areas where only the non-poisonous variety is found
- After an elapsed time of one month the snakes were removed and tested for signs of attack
If the hypothesis is true one would expect the brightly colored snakes to be attacked in the areas where poisonous snakes are absent
Results:
- Poisonous snakes not present – coloured snakes are attacked more
- Poisonous snakes present – brown snakes attacked more
- Control group – brown snakes; allowed analysis of colour alone in predation
Bond types in biochem
- Polar covalent bonds – form when two atoms involved in a covalent bond do not have equal electronegativity
a. N and O are highly electronegative (electron greedy) – any other atom in a biological molecule is ‘non-greedy’
F – the most electron greedy; not present in biological molecules
b. Polar – unequal sharing of electrons
- Partial positive charge on the less electroneg atom (d+) and a partial negative charge (d-)on the electron loving atom
Polar vs nonpolar examples
- Non polar: carbon and hydrogen – have relatively equal electronegativities; electrons are shared equally
- Polar: oxygen and hydrogen – oxygen is more electroneg than hyd; oxygen will have a partial neg charge due to electrons being held more closely
- Hydrogen bonds
o Intermolecular – oppositely charged atoms in different water molecules form hydrogen bonds with one another (attraction between partial pos of hyd and neg of a highly electroneg atom)
Ex. water -> O has partial neg and H has partial pos – attracted to each other
o Intramolecular – polar covalent bonds
o Intermolecular – hyd bonds from partial pos and partial neg (not a full ionic bond)
o Weaker than both covalent and ionic bonds
Bond strength in biomolecules: covalent > ionic > hydrogen > van der Waals
• Specific to biological molecules – ionic bonds are often stronger than covalent otherwise
Hydrogen bonds create molecular networks – can occur between identical molecules or different molecules
Properties of water
- adhesion and cohesion
- temperature moderation
- heat vs temperature
- kinetic energy
- calorie
- specific heat
- heating curve of water
- water specific heat capacity
- hydrogen bonds and temperature
- hydrogen bonds and density
Cohesion and adhesion of water
a. Cohesion – hyd bonds keep molecules in close proximity; creates complex structure
- Allows water to move against gravity from root to shoot in plants – attractive forces allow water to move together
b. Adhesion – molecules hydrogen bond to the walls of the vessels in the plant preventing them from falling back down
Temperature Moderation – water absorbs heat from air that is warmer and releases heat to air that is cooler
a. Kinetic energy – the energy associated with motion; the faster the atoms and molecules move = greater the kinetic energy
- ex. flowing blood carries in in the form of kinetic energy
b. Heat – a measure of the total kinetic energy of a body
- Volume dependent
- Always passes from a hotter object to a cooler object when brought into contact with one another – molecules in the cooler object then speed up because of the gain in kinetic energy
c. Temperature – the average kinetic energy of molecules
- Volume independent
- Objective
d. A calorie – the amount of heat needed to raise the temperature of 1 gram of water by 1c
- 1cal= 4.184 Joules
- Related to specific heat capacity
ex. Water: 4.184 J/g C
g C = (1)(1)
e. Specific heat – the amount of heat that must be absorbed/lost in order to change the temperature of 1 gram of a substance by 1c; differs between substances
Water has a very high specific heat compared to other substances due to hydrogen bonding – buffers the temp; in order to change the temp the hyd bonds must be disturbed
a. Change in the temperature of water will be much less when a certain amount of heat is gained or lost
b. Phase changes must be complete to increase temp/kinetic energy
o Added heat must first be used to break hydrogen bonds of solid
o After the hydrogen bonds are broken the heat can then be used to increase the temperature of the water
o When all hyd bonds have been broken and water reaches 100C – evaporation occurs
Hydrogen bonds and temperature
a. Cooling of water = release of heat as hyd bonds reform
• This results in a decreased speed of the molecules and a decrease in temperature & decrease in kinetic energy
b. Temp is a critical component in the body
• Evaporation of a substance moderates temperature
o The molecules with the greatest energy (the hottest) leave the substance
o The remaining liquid is cooler as a result of this loss
• Ex. boiling water
• Ex. sweating – hyd bonds breaks with heat and evaporates; temp of body decreases
• Ex. enzymes (proteins) – as body temp increases, the hyd bonds within will break and protein will become denatured
Hydrogen bonds and density:
Water exists in 3 states – state is determined by number of hyd bonds; water can form up to 4 hyd bonds
1. Solid – will have 4 hyd bonds
• 4 bonds holds water molecules in crystal lattice – more spread out/less dense than liquid
o Extremely stable
2. Liquid – will have 3.4 hyd bonds (on average)
• Constantly breaking and reforming – allows molecules to be closer together; not held at a rigid length due to crystal lattice
o Less stable than ice
• Results in density of liquid water being higher than solid (this is why ice floats in water)
3. Gas /water vapour– no hyd bonds; all broken
o Solids are always more dense than gas – density is the number of particles (molecules) per unit area
Water as a universal solvent
- solvent
- aqueous solution
- solute
- blood
- why is water a good solvent
- hydrophillic vs hydrophobic substances
Universal solvent
- A solution – a liquid consisting of a uniform (homogenous) mixture of two or more substances; consists of
- Solvent – dissolving agent; usually water (doesn’t have to be water)
- Aqueous solution – when water is the solvent
- Solute – dissolved substance; ex. sugar and salt
- Blood – mostly water; thick due to high concentration of solutes
Water is a good solvent due to polarity
a. Can dissolve ionic compounds
• Adding heat to ionic bond (ex. NaCl) will break into 2 ions -> Na+ and Cl-; ions remain dissolved in the water and form a solution
• Solution forms as Na+ engage with partial neg oxygen and Cl- engage with partial pos h+
• Water molecules creates cages around ions & charges keep them separated
o This holds the ions in solution
b. Non-ionic materials may also dissolve in water due to partial charges – participate in hyd bonding
• Ex. Proteins
• Ex. sugar – have OH groups
o O is partially neg; H is partial pos
o Creates hyd bonds with water
Hydrophilic substances – have an affinity for water
a. Small enough – they will dissolve in water
b. Too large – there’s not enough water to solvate them
• They will form a colloid – stable suspension of fine particles in a liquid
Hydrophobic substances – have zero affinity for water
a. Non-ionic and non-polar – lipid molecules
• Comprised of non-polar covalent bonds – no partial neg/partial pos to form hyd bonds
b. Example: oil and water will not mix
H2o will form only hyd bonds with solutes in the body (for our purposes)
- Some dipole dipole bonds as well – don’t need to know for this course
- Water is able to do this with many molecules (ex. amino acids, sugar) due to polarity
Solute concentrations
- daltons
- molar mass
- molarity
Glucose:
a. C6H12O6 (1 mol)
- Carbon weighs 12 Daltons -> 6x12=72 Daltons
- Hydrogen weighs 1 Dalton -> 12x1=12 Daltons
- Oxygen weighs 16 Daltons -> 6x16=96 Daltons
b. Glucose weighs 180 Daltons
- 1 mole= 6.02x10^23 (Avogadro’s number)
- 6.02x10^23 Daltons/gram -> grams per mole is the same as a Dalton
- Molar mass of glucose (g/mol) = 180g/mol
Molar Mass = grams/mol
Molarity = moles of solute/liter of solution (M)
pH
- neutral
- acids
- bases
- pH
- how much change in concentration results form 1 pH change
In pure water H+ = OH- (pH = 7/neutral)
a. Neutral substance has equal amounts – neutralize each other
- [H+] = [OH-] -> neutral
- Addition of acid or base will disrupt this balance
b. H2O H+ + OH-
- The hydrogen ion has left its electron behind – free in solution as an H+ ion
- OH- that results is the hydroxide ion
c. 2 H2O H3O+ + OH-
- The lost proton attaches to the second water molecule
Acids:
a. Dissociate when placed in water
- Release H+ ions
- Addition of H+ will cause the OH- to decrease -> create water
b. Lower pH = greater acidity
- increase in [H+] = decrease in pH
- Example: HCl -> H+ + Cl –
c. Releases H+ into solution -> makes it acidic
- The more HCl that is added to water, the more H + will be present following dissociation
Bases:
a. Dissociate in water
- Release OH– ions
- Addition of OH- will cause the H+ to decrease -> creates water
b. Higher pH = more basic
- Increase in [OH-] = greater the pH of the solution
- Example: NaOH -> Na + + OH–
- The OH- that is generated from the dissociation of NaOH binds to H+ in and make water
pH scale concentrations a. acidic -> [H+] > [OH-] • pH < 7 o pH = 1 -> most acidic o pH = 6 -> least; near neutral b. neutral -> [H+] = [OH-] • pH = 7 • bind and create water c. basic -> [H+] < [OH-] • pH > 7 o pH= 8 -> least basic o pH= 14 -> most basic
Measured on a scale of 0-14
- [H+][OH-]= 10-14
• Concentrations multiplied together will always = 10^-14
- pH= -log[H+]
o A difference of 1 pH unit represents a 1000x difference in H+ concentration
Buffers
- chemoreceptors and forced breathing
Buffers – substances that allow a solution to offset large and potentially dangerous changes in pH from occurring
• Buffer – a substrate that dissociates to H+ (can bind to OH-) and an anion (can bind to H+)
• Living systems are threatened by very small changes in pH
• Example: carbonic acid (H2CO3) is a buffer found in the blood
Blood pH needs to be 7.35 – changing by .02 is dead
Carbonic anhydrase catalyzes:
Co2 + h2o H2CO3 H+ + HCO3-
- If blood pH drops HCO3- will bind to the excess H+
- If blood pH increases H+ binds to the excess OH-
- As a result, the blood pH will not change dramatically
Holding your breath will cause co2 to fill up
- Increase in co2 causes increase in H+ (carbonic anhydrase reaction)
- chemoreceptors sense increased h+/acidity and force breathing
- Co2 will decrease -> reaction will reverse -> decrease h+
Have limits – buffers can assist but only with what is available to use
Ex. 6hco3- + 6h+
- Adding 7h+ -> will only be able to bind to 6hco3-
- Still acidic because it increases [H+]
Early earth & Miller’s experiments
Early earth – materials needed to be synthesized from abiotic components; supports evolution
Miller showed that complex organic molecules were able to arise under the conditions of early Earth – no life present
- Abiotic synthesis of these molecules near volcanoes was possible – volcanoes serve as a source of energy
Organic chemistry
• Organic chemistry redefined the study of carbon compounds regardless of their origin (biotic or abiotic)
Most organic compounds are synthesized by living organisms – rare that organic carbon containing compounds are synthesized abiotically because energy no longer exists like it used to in the environment
- Enzymes within the body use energy to synthesize organic molecules
Stanley miller’s experiment
- A flask of warm water represented the early sea
- The water was heated so that some evaporated and moved into a second flask to simulate the early atmosphere
- Evaporated – zero hyd bonds
- Liquid – 3.4 hyd bonds - This atmosphere consisted of hydrogen, water vapor, methane and ammonia – all gases thought to have made up the ancient atmosphere in the 50s
- These molecules + water vapour – all molecules essential for life - Electrodes discharged shocks into the flasks to simulate lightning – energy allows covalent bonds to be made
- A condenser cooled the atmosphere, raining water and any dissolved particles back into the initial flask the miniature sea
- Condensation – causes hyd bonds to reform
- Raining – collected organic materials - After one week Miller found a variety of organic compounds in the solution including some amino acids
- organic compounds
- reactivity of carbon
- photosynthesis
- types of carbon chains
- main constituent in what molecules
Organic compounds – contain carbon
a. Exceptions
• Carbon dioxide (co2) – present in body
• Carbon monoxide (co)
• Carbonic acid (h2co3) – present in body
b. Carbon is a good molecular component because of ability to form large and diverse molecules
Reactivity – able to form 4 covalent bonds due to 4ve-
a. C has 6e- total (2 in inner shell)
• Outer shell – will react until 8 e- are present
• At capacity – chemically satisfied/stable
b. Can form single, double, triple bonds
Photosynthetic organisms -> CO2 into sugars (glucose)
6h2o + 6co2 -> c6h12o6
Requires addition of light
Carbon chains – skeleton of organic molecules; large amounts of molecular diversity
a. Can be:
• Straight
• Branched
• Ring
• Contain double bonds – unsaturated; varied in number and location
b. Other atoms may also be attached to the carbon framework – O, N, S, P
Main constituent in macromolecules required for life:
- Carbohydrates
- Lipids
- Proteins
- Nucleic acids
- required for complex macromolecules
- size of molecules
- relative proportions in different species
Also required to form complex macromolecules:
o Hydrogen
o Oxygen
o Nitrogen
o Phosphorous
o Sulfur
o All have carbon as key component
a. **None of the above come close to the quantity of carbon that is used in organic molecules
• Carbs – hyd, oxygen, nitrogen
• Proteins – hyd, oxygen, nitrogen, sulfur
Relative proportions of C, N, O, S, H, P are constant in different organisms
- Differences in the types of molecules found in living organisms allow differentiation
Range of size o Methane (ch4) – organic; very simple o Glucose (c6h12o6) – still fairly simple o Protein – very complex; folding alters function
Valance shell anatomy
Valance shell anatomy – basis for the rules of covalent bond formation
a. Ex. CO2 (O=C=O)
- Carbon is bound to two oxygen atoms each with a double covalent bond
- Each Oxygen shares 2 e- with carbon per bond (4 e- total required to fill shell)
- Ex. Hydrogen only makes one single bond to reach chemical satisfaction
Hydrocarbons
organic molecules consisting of only carbon and hydrogen
Components of fossil fuels – all hydrocarbons
o Example: petroleum
o The name originates from partially decomposed organic matter found in the fuel
Living cells don’t have full hydrocarbon structures – have a ‘dressed’ up structure to get a different behaviors; exist as components of more complex molecules
o Ex. Phospholipids
o Ex. Cholesterol – storage fat within bilayer
Hydrophobic – non-polar covalent bonds between carbon and hydrogen make hydrocarbons insoluble
o Non-polar – equally shared
May participate in reactions that release large amounts of energy – contain lots of energy
o Fossil fuel combustion
o Energy storage in animals
o 1g of fat stores 2x the energy as 1g of carb/sugar – we store energy primarily as fat
Isomers
- how do they change properties
Isomers – compounds with the same molecular formula but different structures
Different structures create differences in properties
o Properties – melting points, boiling points, binding properties
3 types of isomers:
- Structural isomers
a. Differ in the covalent arrangement of atoms – same number of carbons
b. Straight vs branched
- May differ in double bond presence/position – create isomers, even if they are both linear
- differing amounts of hyd for double vs single bond
c. Number of possible isomers increases with the number of carbon atoms
- C5H12 vs C8H18 - Cis/trans isomers
a. Formerly referred to as geometric isomers
b. X substitute must be identical on each side to be considered a cis/trans isomer
c. Carbon-carbon double bonds are rigid structures
i. Double bonds
o Shorter
o Rotation is not possible
ii. Single bonds
o capable of rotation
o longer
d. Spatial arrangements affect stability and bonding abilities – molecules interact very specifically; need structural details in order to function
• Connectivity of atoms does not change between cis and trans isomers – spatial arrangement/placement of atoms differ
e. 2 spatial arrangements possible when carbons involved in a double bond with one another have two different atoms attached
i. Cis isomer:
- Both X substituents are on the same side of the double bond
- X are heavier than carbon
- Having both larger atoms on the same side may cause interference with each other
- Not necessarily less stable
ii. Trans isomer:
- The X substituents are on opposite sides of the double bond
- **Small differences in spatial orientation may significantly affect the activity of the molecule
- Example: human vision – reaction occurs to covert cis to trans to cis - Enantiomers (we won’t discuss these in this course)
- Not superimposable - can’t have them on top of each other and have the functional groups line up
- They are mirror images
Functional groups
- properties
- types
Functional groups – determine behaviour
a. Hydrocarbons – provide framework for more complex carbon containing organic molecules
o Non-polar – can’t participate in hydrogen bonding
b. Functional groups – replace hydrogen on hydrocarbons; allow molecule to form hyd bonds
o Contribute to chemical reactivity directly or indirectly due to shape
o Number of groups and arrangement are important (ex. effects of estrogen vs testosterone)
o Some impart polarity
6 types functional groups
Hydroxyl group Carbonyl group Carboxyl group Amino group Sulfhydryl group Phosphate group Methyl group
Hydroxyl group
a. Name – alcohols
i. names usually end in “ol” (ex. ethanol)
b. Functional:
i. Polar due to electroneg oxygen
ii. Can form hyd bonds with water – helps dissolve
organic compounds with -OH (ex. sugar)
Carbonyl group
Carbon double bonded to oxygen
2 types – depends on other 2 bonds on C
- Ketones – 2 carbons (within a carbon skeleton)
a. Ends in “one” (ex. acetone)
b. Methyl group within carbonyl (ex. acetone) – still a carbonyl, not methyl group - Aldehydes – 1 carbon and 1 hyd (the end of a carbon skeleton)
a. Ends in “al” (ex. propanal)
b. Cannot extend further on hyd side
May be structural isomers (same molecular formula with different placement) – different properties
Form 2 major sugar groups
i. Ketoses
ii. Aldoses
Carboxyl group
Carbon is double bonded to O, bond to C, bond to OH (not hydroxyl; part of carboxyl)
a. Names – carboxylic acid or organic acid (ex. acetic acid)
b. Acid – can donate H+ because bond between O and C is very polar
c. Carboxylate ion – ionized form (-1 charge); found in cells this way
i. Deprotonated carboxyl group
Amino group
a. Name – amines
b. Base – can bond to H+/proton
i. Found in cells in ionized form (+1 charge)
ii. NH2 or NH3+
c. Ex. glycine
Sulfhydryl group
S bonded to hyd
a. Name – thiols
b. Functions
i. 2 sulfhydryl groups can react – form cov bond; crosslinking helps stabilize protein structure
- Ex. crosslinking cytosine in hair protein maintains curls/straightness of hair (perming is reforming crosslinking bonds)
ii. Important in creating complex proteins
Phosphate group
Double bond to one O, single bond to 3 more (exception to octet rule)
a. Name – organic phosphates (PO4)
b. Functions
i. Contibutes neg charge to molecule (ex. dna and rna have net neg charge)
- -2 when at the end of a molecules
- -1 when located internally within chain of phosphates
ii. Molecues can react with water – release energy
Methyl group
C with 3 hyd bonds
a. Name – methlated compounds
b. Function
i. Nonpolar & nonreactive
- Will affect molecular weight and weak interactions
- Changes size and therefore chemical characteristics
ii. Addition to dna or molecules bound to dna – affects expression of genes
iii. Arrangement in male and female sex hormones affect shape and function
Adenosine triphosphate
ATP – energy currency of the cell (can be immediately spent)
• Organic molecule is adenosine – composed of adenine and ribose sugar
Attached to three phosphate groups via high energy covalent bonds
• Inorganic phosphate (Pi) – P group that has been cleaved off ATP by enzymes to release energy
o Inorganic – no longer attached to carbon containing molecule
o Adenosine diphosphate (ADP) is left – has one more high energy bond
Monomers vs polymers
- differences between relatives
• Monomers – individual units of the molecule; similar or identical building blocks covalently linked to one another
• Macromolecules – polymers built from monomers
o Poly=many and meros=parts
o Very diverse molecules (ex. proteins)
Less difference exists between polymers from individuals that are related to one another – ie. there is more similarity in macromolecular structure between parents and children
Polymer synthesis and degradation
Enzymes – protein polymers that increase the rate of reactions; would otherwise occur to slowly to sustain life
o Catalyze synthesis and breakdown
Synthesis – dehydration reaction (water is formed; one monomer contributes hydrogen and the other monomer contributes a hydroxyl group)
a. Not always strictly the case
- Ex. amino acid example – one AA donates O-, one donated 2 H+
b. This reaction is repeated until the entire polymer is synthesized
All polymers are assembled with the same sequence of events (ex. chain of amino acids) Degradation – hydrolysis (adding water) a. Broken off – monomer - The rest is still a polymer b. This is how we digest food
4 Groups organic molecules
Carbs
Lipids
Proteins
Nucleic acids
Monosaccharides
- most common
- consists
- name
- structure
- alpha vs beta group
Carbohydrates – include sugars and sugar polymers; CnH2On
Monosaccharides – monomer
- Mono=one sacchar=sugar
- Most common monosaccharide is glucose (C6H12O6) – has unique connectivity
Monosaccharides consist of a carbonyl group and many hydroxyl groups – location of carbonyl group determines whether it’s a:
- Aldose (aldehyde) – end of carbon chain
a. Ex. galactose and glucose - Ketose (ketone) – middle of carbon chain
a. Ex. fructose
Sugar names generally end in ‘ose’ – size of the carbon skeleton may be used
- Hexose: 6 carbon framework
- Triose: 3 carbon framework
- Pentose: 5 carbon framework
Linear vs cyclical
- Glucose – often depicted as a linear molecule; carbon 1 is not engaged
- Larger sugars – long enough to form cyclical structure (ex. pentose and hexose sugars)
a. Cyclical structures – most stable and most commonly found in solutions
Alpha vs beta sugars
- Alpha – OH group points down
- Beta – OH group points up
Carbs
- uses
- polysaccharides
- storage
- structural functions
- what does epinephrine cause
Sugars are used:
- As a fuel source in the cell
- Canadian money – sugar
- Can be quickly broken down and produce ATP
- most energy is stored as lipids - take longer to break down - To assemble other complex molecules
a. Can be converted to other molecules (ex. amino acids) – requires many different enzymes - If not immediately used (in 1 or 2) – will be stored as disaccharides or polysaccharides
- Formed by dehydration reaction
- Only store sugar as polysaccharide in muscle and liver – the rest/most of energy is stored as lipids
Polysaccharides – macromolecules
a. Covalently linked via glycosidic bonds – covalent bonds; called glycosidic when covalently bonding 2 sugar monomers together
- Can have a few (oligosaccharide) to 100,000 monomers covalently linked
b. Uses
- Storage molecules
- Structural molecules
Storage molecules – can be broken down when the cell needs energy; storage types differ depending on cell storing them
- Starch – plant storage form of glucose; stored as granules in plastids within cell
- All glucose monomers are alpha – linked 1-4
- Hydrolysis – releases glucose from the starch when energy is needed
a. Animal cells also have the enzymes needed to hydrolyze starch – we can break alpha 1-4 bonds to digest them
b. Types of starch - Amylose – unbranched starch
- Amylopectin – branched starch
- Includes 1-6 linkages (linking more fingers makes stronger)
- When its branched – it can continue to create alpha 1-4 bonds
Glycogen – animal storage for glucose
- More branched than amylopectin – with higher frequency (linking whole hand)
- Stored in human liver and muscle cells
a. Doesn’t persist for very long in the cell unless it is replenished - Hydrolyzed at an increased rate when the cell needs energy
a. Epinephrine released by adrenal gland – causes increased rate of hydrolyzation of glycogen in liver for cells
Structural
- Cell wall material – a protective framework exterior to Fungal and Plant cells and bacteria; have a sugar layer (cell wall)
- Allows it to with stand osmotic pressure
- Humans/animals – do not have a cell wall
- Bond position determines architecture and polysaccharide function – whether or not it is digestible (ex. cellulose – not digestible) - Cellulose – component of plant cell wall; all glucose monomers are beta
a. Animals do not have the enzyme to cut beta linkages
- Passes through as insoluble fiber
- Cleans out the intestinal tract – speeds up ‘conveyer belt’ to remove from body; self cleaning
- Cows have prokaryotes living within them that digest cellulose
- Cows themselves cannot digest cellulose - Chitin: polysaccharide component of fungal cell wall
- Similar to cellulose
- Includes a nitrogen containing side group
Lipids
- properties (differences from other molecules)
- fats - what makes them up
- FA composition and types
- WHAT KIND OF LINKAGES
- what are naturally occuring unsaturated FA
- functions
Properties
- The only group not formed from repeating monomers
a. Form a diverse group – fats (triglyceride), phospholipids and steroids - Do not mix with water
i. The only nonpolar group
- Non-polar hydrocarbons
- Exception – some consist of a few polar covalent bonds involving oxygen
Fats – molecules assembled via dehydration reactions
1. Glycerol sugar – forms the neck of the structure
- Has hydroxyl groups – serve as location for dehydration reactions with fatty acids (also have OH group)
- Fatty acids tails – attached to glycerol via ester linkages
Number of FA:
a. Monoglyceride – 1 FA
b. Diglyceride – 2 FA
c. Triglyceride/triacylglycerol – 3 FA
i. Primary fat/energy storage
- May be the same fatty acids or different fatty acids
- Varying lengths
FA Composed of (see above diagram)
- Carboxylic acid
- Non-polar tail – hydrocarbon chain
Types
- May be saturated or unsaturated
1. Saturated fats – no double bonds - Solid at room temp – allows for tight packing
- Makes them straight – increased van der Waals interactions between them
- Saturated with hydrogen
2. Unsaturated fats – contain one or more double bonds - Liquid at room temperature
- Naturally occurring varieties are in the cis conformation – creates a kink in the chain
Functions
- Primary energy storage form
- 1g fat stores twice as much energy as 1g of sugar
- We would weigh way more if we had to store everything as sugar
- Fats allow lowest weight with highest energy - Protects organs and provides insulation
- Thermal insulation – we are endotherms
Types of lipids
Omega-3 fatty acids – cannot be synthesized in the body and must be supplied by diet
- Counting 3 carbons from noncarboxyl end -> that’s where the double bond will be/start
- Omega 6 -> double bond will start 6 up from bottom (non carboxyl end)
Phospholipids:
a. Major component of cell membranes
- Spontaneously assemble into the membrane structure – bilayer formed by nonpolar tails are nonpolar inward and polar head groups face ECF and ICF
b. Polar head group and 2 FA
- Can be both saturated or both unsaturated
- one straight, 1 bent – most common in animal cells
c. It will circularize to close off nonpolar section completely
- Structure – 2 fatty acids are attached to a glycerol molecule (sugar; used in fat molecules to provide a bridge)
d. Phosphate group (PO4-) – attached to third hydroxyl of glycerol
- Neg charge
e. Head group – attached to phosphate
- Determines unique identity of phospholipid
- Polar – hydrophilic
Ex. choline
- Fatty acids – hydrophobic & nonpolar
Steroids:
- Four fused carbon rings – forms a carbon skeleton; hydrocarbons (nonpolar)
- Examples: Vertebrate sex hormones and cholesterol – estrogen and testosterone
Proteins
- how much of the cells weight
- functions
- how many
Proteins are the work horse of the cell
Functions – enzymes, transporters, structural (fibrous & cytoskeleton proteins)
- More than 50% of the cell’s dry weight
Proteins function as:
- Defense molecules
- Ex. antibodies (ex. created by covid vaccines) - Enzymes – catalyze reactions
- Storage – keep molecules within the cell
- Transport – channels and carriers
- Cell communication – cell to cell communication
- Produce proteins that can be excreted (hormones)
- Local and long distance - Structure
- Internally – cytoskeleton proteins
- Outside – ex. collagen (fibrous protein) - Movement – within the cell using cytoskeleton
- Within muscle fibers – allow lengthening the shortening to contract
Thousands of proteins
- Varied 3D structure – fold in very specific way; structure is characteristic of their function
- How an enzyme will engage with its substrate
- Can then design inhibitors and antagonists – manipulate in order to enhance human life (drug development)
- DNA provides info to make proteins
- Unique function
Building blocks of proteins and polymers
- denaturation of proteins
Amino acids – monomers; repeated units of proteins
1. Consist of
a. Centrally located carbon atom: the alpha carbon
b. Ionized carboxylic acid terminus (COO-)
c. Amino terminus (NH3+)
d. R group – 4 groups of AA based on R groups
- Non-polar – hydrophobic (“boring”)
Ex. alanine – R group is CH3 (methyl group)
- Polar – hydrophilic
Ex. serine – R = CH2OH
- Acidic – donate protons in solution becoming anionic; hydrophilic (because they carry a charge)
Carboxyl group is also an acid
Ex. Aspartic acid – R = CH2COOH
- Basic – accept protons in solution becoming cationic; hydrophilic (because they carry a charge)
Ex. lysine – R = (CH2)NH3+
Polypeptides – long string of amino acids bonded together via peptide bonds (cov bonds between AA formed by dehydration reactions )
- Some proteins
a. Are just one polypeptide
b. Most are more than one polypeptide – fold into specific final shapes & assembled to fit specific function
a.
- Has polar components (between N and H) – makes hydrophilic - Polypeptides are constructed from a unique combination of amino acids
- There are 20 different amino acids
- The DNA sequence of the gene dictates the amino acid sequence of the protein - All polypeptides will consist of an amino terminus and a carboxy terminus (carboxyl group)
a. The number of side chains (R groups) out number the two termini – add elements of ionization and polarity
- Chemical nature of the R groups determine the ‘personality’ of the protein as a whole – functions of R groups contribute to overall behaviour of protein
Denaturation – protein structure may be affected by salt concentration, temperature and pH; results in loss of function
- Ex. frying an egg – denaturation of albumin (?) protein
- Ex. milk expiration
Levels of protein structure
- Primary Structure – amino acid sequence of the protein
- Secondary Structure – folding sequence of peptide chain of primary structure; due to local interactions
a. Hydrogen bonds – between different locations of the polypeptide sequence; create secondary structure
- Backbone hydrogen bonding – not between R groups
b. Two types: alpha helices and beta-pleated sheets
- Alpha – loops
- Beta – folded sheets
- Can have multiple alpha and beta sheets within the same secondary structure – will not always; depends on the specific AA - Tertiary Structure – chemical interactions between R groups of individual amino acids that form polypeptide; 3D folding pattern due to
a. Chemical interactions – covalent bonds, ionic bonds, disulfide bond, hydrogen bond
- Becomes more complex as r group bonds form between beta and alpha sheets – not all proteins have multiple beta/alpha complexes
b. Ex. Disulfide bonds form between S of cysteine amino acids in the polypeptide chain - Quaternary Structure- two or more polypeptides (in their tertiary structure) come together to form a functional molecule
a. Uses hyd bonds, covalent bonds, ionic bonds
b. Form either
- Globular – 7 main functions
- Fibrous – primarily structural
structure of nucleic acids
- monomers - where is OH in ribose
- polymers
- size and difference between people
Structure of Nucleic acids
Nucleotide – monomers;
Each nucleotide has three components:
a. Pentose sugar (five carbon sugar) – “prime” when numbering carbons on sugar (5’ and 3’ end)
- Deoxyribose (DNA) – no oxygen
- Ribose (RNA) – alpha hydroxyl group on carbon prime 2
b. Phosphate group – gives negative charge
c. Nitrogenous base – contain nitrogen as part of chemical structure
i. Purine – double ringed structures (Ag makes good rings; is pure)
- Adenine
- Guanine
ii. Pyrimidine – single ringed structures
- Cytosine
- Thymine (DNA only)
- Uracil (RNA only)
Nucleic acid – polymers; nucleotides joined by covalent bonds via dehydration reactions
- Sugar phosphate backbone – phosphate group off of 5’ carbon of one nucleotide bonds to the 3’ carbon on sugar of the next nucleotide
- Covalent bonds WITHIN chains (hyd bonds between chains of DNA)
- Nitrogenous base face interior – allow dna to form double stranded molecules with hyd bonds between bases
Nucleic acids range in size – very specific; depend on function of DNA
a. 100s to 1000s nucleotides
- 1000s – lots of combinations of functional units; makes the number of potential nucleotide combinations infinite
- 4 types of nucleotides in many different combinations (ex. words in language)
b. The various combinations account for much of the genetic variation seen in the world
- Between family – more genetic cohesiveness
- Lots of variation
Genes & types of nucleic acid
- when was dna disovered and by who
- what is DNA able to do
Genes – encode the primary amino acid sequence of a protein (information manual within the cell)
- Made of deoxyribonucleic acid (DNA)
- DNA was discovered in 1953 by Watson and Crick
Types of nucleic acid:
DNA – always double stranded and is found as a double helix
1. Two polynucleotides are wrapped around one another
a. Nitrogenous bases always protrude from the sugar phosphate backbone into the center of the double helix
- Cytosine & guanine, thymine & adenine
- Base pairing – hold adjacent bonds together via hydrogen bonds
A :: T (2 hyd bonds)
C ::: G (3 hyd bonds)
- Complementary strands – amount of one = amount of other
- Most DNA molecules have thousands or even millions of base pairs
2. Adjacent strands are held together by hydrogen bonds
a. 2 hydrogen bonds between T and A
b. 3 between G and C
3. Carries the information needed to make proteins
a. DNA -> transcription -> mRNA -> translation -> protein
- Ex. DNA -> transcription -> Insulin mRNA is created -> translation -> makes insulin protein (functional unit)
4. Is able to self replicate – allows new cells to form; important in development
RNA is always single stranded
- Has ribose sugar
- Uracil instead to thymine
Microscopes
- when were they invented & names to view first cells
- uses
- artifacts
Microscopes were invented in 1590 – know scientist and contribution & general timeline
a. 1665: Robert Hooke was the first to see and describe living cells (they were dead tho)
- Dead cells taken from Oak tree bark – eukaryotic cells
b. 1674: Antony van Leeuwenhoek was the first to observe living cells
- Bacteria that he named animalcules – prokaryotic cells
- Smaller – used a better microscopes
Microscopes – critical for cytology (the study of cells) & histology (the study of tissues)
o The study of cell structures
Artifacts – seen in the microscope image but are not present in the actual sample; problem with all types of microscopy
o Due to errors – bubble or vacuole structure
o Be mindful of when looking at samples
