Chapter 1 Flashcards
An element is
a pure substance that cannot be broken down into simpler substances using ordinary chemical or physical techniques
the smallest particle of an element is an _________. Elements differ from one another in their ________ __________
atom, atomic structure
Atoms bind together in fixed numbers and ratios to form _____________
molecules
A chemical compound is
a stable combination of different elements that are held together by chemical bonds
what are organic compounds?
compounds that contain carbon & hydrogen bonds (akhtar & google!
organic compounds in living organism are primarily composed of
carbon, hydrogen, and oxygen. they often include nitrogen as well
about ___ elements made up living organisms
25
what elements make up 96% of the weight of living organisms?
Carbon, Hydrogen, Oxygen, Nitrogen
Most of the remaining 4% of the weight of living organisms is made up of only 7 other elements:
Calcium, Phosphorus, Potassium, Sulfur, Sodium, Chlorine, & Magnesium
- these elements often occur as ions or in inorganic compounds in organisms
(Polly Poppy Came Surfing. Super Cool & Majestic)
Trace Elements
the remaining of the 25 elements are found in such small amounts (<1%), they are called trace elements
- Ex. Iodine & Iron (Fe)
- deficiency in any trace elements=health problems
atoms are
the smallest units that can retain the chemical and physical properties of a particular element
- rmr atoms don’t have a charge, ions do
electrons are not included in the mass number cuz
their mass is negligible compared to the mass of protons and neutrons
Isotopes
are different forms of the same element, with different atomic masses
- since they have the same # of p+ & e-, the behave the same in a chemical reaction
a radioisotope is
a radioactive isotope of an element
-they generally behave the same way in cells as non-radioactive isotopes
Radioactivity
the nuclei of some isotopes or an element are unstable and tend to break down (decay), giving off matter that can be detected as radioactivity
- the radiation from isotopes may damage living cell molecules
GOOGLE: the release of energy from the decay of the nuclei of certain kinds of atoms and isotopes.
Carbon-12 accounts for __% of all carbon in nature
99
Radioactive Decay of Carbon-14
C-14 is an unstable isotope of carbon.
- it decays, giving off particles & energy.
- as it decays, 1 neutron splits into a high-energy electron & a proton. –> it then has 7 neutrons & 7 electrons & protons.
- this is characteristic of the most common form of nitrogen.
- the decay of C-14 transforms carbon atom into nitrogen atom
the rate of decay of a radioactive isotope is _______________ of chemical reactions or environmental conditions
independent
Radioactive decay occurs at a _________ _______, with a constant proportion of radioactive breakdown during a given interval of time
steady rate
Radioactive tracers
are radioisotopes that are used to follow a specific chemical through a chemical reaction
- used because radioactive isotopes give off a radioactive signal as they decay that is easily detectable in cells.
- using the particles emitted as a signal, specialists can trace the the path of the radioisotope as it moves to different parts of the body
- this way, radioactive isotopes have found many applications in biological, chemical, & medical research
Scientist Melvin Calvin
- pioneer in photosynthesis study
- used carbon-14 labelled molecules to determine sequence of reactions in photosynthesis
Uses of Radioactive isotopes
- study biochemical reactions
- perform basic techniques like DNA sequencing
- since most biological molecules contain C & H, carbon-14 & hydrogen-3 (aka tritium) as used as tracers in research
- used in new field of nuclear medicine to help diagnosis & treatment of diseases–> ex, thyroid gland produces hormones that affect growth & metabolism–> it’s the only gland that absorbs iodine. –> if pt’s symptoms indicate an abnormal level of thyroid hormone output, the doc may inject a small amount of radioactive iodine-131 into pt & use a photographic device to scan the gland–> the radioactivity will produce an image like an x-ray, which helps identify the cause
the arrangement of electrons determines the __________ _________ of an atom
chemical properties
- cuz only electrons are usually involved in a chemical reaction
An orbital is
a region of space that 1 or 2 electrons can occupy
- most stable & balanced condition occurs when the orbital contains 2 electrons
electrons orbitals are grouped into ____________
energy levels aka energy shells
How many electrons can be found in each energy level
1st=2
2nd=8
3rd=18
The 1st electron shell orbitals
is the 1s orbital shell
- contains a single spherical orbital
- both hydrogen & helium only have 1s electron orbital
(see page 11 in textbook)
The 2nd electron shell orbitals
contains on 2s orbital and three 2p orbitals
- the 2s orbital is spherical in shape
- each 2p orbital shape looks like 2 balloons knotted together –> the three 2p orbitals bisect in the centre at right angles to each other, giving orbitals their overall shape
the farther the electron from the nucleus….
the greater its energy.
the ______ that is occupied by an electron is what determines its energy level
orbital
the balloon-like 2p orbitals contain electrons that are further away from the nucleus that electrons in the 2s orbital, & therefore hold the electrons with a higher energy level
- in large atoms, some higher energy electrons occupy d & f orbitals, which are more complex
all the elements in living organisms have _________ valence shells
unfilled
- thus, they participate in chemical reactions
Hybridized electron orbitals are
orbitals that result from the sharing of electrons between atoms
- in these orbitals, there is a direct overlap of the valence electron orbitals of the 2 atoms, so the orbital is combo of 2 different orbitals
___________ _____________is the most common way for atoms to bond & form biological molecules
sharing electrons
a chemical bond is
a stable attraction between atoms
there are 4 types of chemical bonds important in biological molecules
- ionic bonds
- covalent bonds
- 2 types of intermolecular bonds
ions are very strongly attracted to ____________________
water molecules
- therefore ionic compounds tend to dissociate & dissolve in water, forming hydrated ions
The strength of a covalent bond depends on the ________________ of the atom’s attraction for additional electrons
electronegativity
Electronegativity is
the measure of an atom’s attraction for additional electrons.
- the more electronegative an atom, the more strongly it attracts e-
- electronegativity is strongly influenced by the atomic # & the distance between the valence e- and the nucleus of an atom
- electronegativity increases as distance between nucleus & valence e- decreases –> Ex O has high electronegativity as the valence e- are close to the nucleus, but hydrogen is less electronegative cuz it has a small atomic number. The greater the number the protons, the higher the positive charge of the nucleus and the greater ability the atom has to attract shared electrons. –> so even though the e- get close in a H atom, the nucleus is small and has weaker attraction
what indicates shared electrons between atoms?
a dash or a pair of dots
Ex, H-H or H:H
structure of CH4
- the bonds between the carbon & hydrogen atoms in the compound methane are arranged in 4 symmetrical orbitals, so the hydrogen atoms are 109.5 degrees from each other –> the e- repel each other, creating this formation
- the overall arrangement of this molecule is tetrahedral
–> the # & tetrahedral arrangement of the bonds around around a carbon atom allow carbon atoms to link together in more complicated biological compounds.
Valence Shell Electron Pair Repulsion theory
aka VSEPR theory
- created by Canadian chemist Ronald J. Gillespie
- it states that becuz e- are negatively charged, valence electron pairs repel one another & move as far apart from one another as possible.
- Ex, in a H2O molecule, there r 2 e- spaces in available on the O2 molecure that the H e- fill up, forming H20
- the theory also takes into account non-bonding electrons in its valence shell–> O has 2 pairs of non-bonding e- in its valence shell. Their negative charge repels the pairs that make up the O-H bonds, so the O-H bonds arrange themselves @ an angle of 104 from each other
due to their high electronegativity, both _________ & __________ form polar bonds with atoms of most other elements
oxygen, nitrogen
difference of <____ can be considered non-polar
0.4
polarity
partial positive or negative charge at the ends of a molecule
molecules as a whole can have a charge
rmr the arrow thingy from chem grade 11 (page 40 - chapter 3)
Polar molecule properties
- they attract and align themselves to other polar molecules & tend to be soluble in water (which is also polar)
- they tend to exclude non-polar molecules, such as oils and fats –> non-polar molecules have very low solubility in polar liquids
Intermolecular forces are
aka van der Waals forces
forces of attraction between molecules
- extremely important becuz they influence the physical properties, such as solubility, melting points, & brittleness, of a substance.
- they act between similar molecules as well as between different types of molecules
- the strength of these forces is dependent on the size, shape, and polarity of molecules
van der Waals forces are
are very weak attractions between two molecules or parts of two molecules when they are close together
Hydrogen Bond
the attractive force between a partially positively charged hydrogen atom and partially negatively charged atom in another molecule
- hydrogen bonds may form between same or different molecules
- strongest & most biologically significant form of van der Waals forces
- Individual hydrogen bonds are weaker compared with ionic & covalent bonds, but they can be very significant & strong when they occur in large #, and they lend stability to the three-dimensional structure of large molecules, such as proteins
- most strongest bonds in living organisms are covalent, weaker hydrogen bonds are crucial to the function of cells & cellular processes
The hydrogen bonds that exist between water molecules are responsible for many of the properties that make water a uniquely important molecule for all living organisms. some of these properties include….
- very high heat capacity
- high melting & boiling points
- cohesion -> trees depends on cohesion to transport water through xylem tissue up from roots.
- adhesion -> adhesion of water to the xylem cells walls of a plant helps to counteract gravity
-surface tension -> help give water unusually high surface tension
Hydrogen bonds begin to break extensively as temperatures rise above __ degrees celcius. At ___ degrees celcius, hydrogen bonds in water are overcome
45, 100
- rmr they are easier to break than ionic & covalent cuz they weaker
Other van der Waals forces
are even weaker and result from the momentary attraction of the electrons of one molecule to the nuclei of another (london dispersion forces)
- occur between all molecules but are only significant when stronger bonds aren’t present–> like between non-polar molecules or between regions of slightly positive and negative charges within a single molecule
- 1 bond=very weak, many bonds= can stabilize the shape of a large molecule, like a fat
The ________ and _________ of a molecule influences the number & strength of van der Waals forces of attraction. Along side these 2 factors, the strength of these forces is also dependent on ________ of molecules
shape, size,
SHAPE - a larger molecule has larger forces of attraction –> ex, small molecule methane = gas @ room temp cuz the van der Waals forces aren’t able to hold them 2gether, whereas large octane molecules are liquid cuz of the cumulative effect of many van der Waals forces between the larger molecules
SIZE - linear molecules can more align more easily with other molecules & therefore the van der Waals forces are stronger
- these influences of size & shape also apply to interactions that involve hydrogen bonds
POLARITY - the intermolecular attraction between polar molecules is obviously greater than attraction between non-polar molecules. rmr creates Dipole-dipole forces = attractive forces between the positive end of one polar molecule and the negative end of another polar molecule
Polar molecules can also experience van der Waals forces between….
the positive & negative ends of interacting molecules
Polar molecules can also experience van der Waals forces: Which molecules have strong van der Waals forces and which ones have weaker
- the effect is strong in long linear cellulose molecules, which have numerous OH functional groups & r able to form very strong fibres
- globular shaped molecules like starches have fewer accessible atoms for van der Waals forces & therefore form less rigid solids
All chemical reactions involve…
the breaking and formation of chemical bonds, thereby changing the arrangement of atoms & ions
There are 4 major types of chemical reactions that are common in biological processes:
Dehydration, Hydrolysis, Neutralization, & Redox reactions
Dehydration reactions
aka condensation reactions
- consist of the removal of an -OH and an - H from 2 reactant molecules (the O and H is usually removed from one molecule, and an H is removed from another i think)
- the removed -OH and -H from H2O and the 2 reactants are joined together to meet valence needs (synthesis reaction)
- most common method used by cells to join smaller molecules & assemble extremely large macromolecules, like complex carbs & proteins
Hydrolysis Reactions are
the revers of dehydration reactions.
- Water acts as a reactant to split or “lyse” a larger molecule –> a bond in the molecule is broken & you add the O & H to one molecule to make it stable and and H to the other in a way that all valence needs are met –> creates 2 smaller molecules
- in organisms, it is used to break down large molecules into smaller subunits
Neutralization Reaction
occurs between acids & bases to produce salts
- H2O often produced
- rmr chem (double displacement reaction)
Redox reactions
- named for “reduction” & “oxidation”, electrons are lost from one atom & gained by another atom –> (any reaction that creates a new ionic gain –> no DD reaction but yes SD reaction)
- oxidation=loss of electrons –> the oxidation of one molecule is always linked to the reduction of another
- reduction=gain of electrons
- in redox reaction, the oxidizing agent (agent that causes the oxidization) is molecule or atom that is being reduced (the one that is gaining e-)
- the reducing agent (agent that causes the reduction) is the molecule or atom that is oxidized (the one that is losing –> species that is oxidized=reducing agent)
https://www.youtube.com/watch?v=Va-82jDcOKU
NOTE: “oxidation” also refers to the transfer of entire hydrogen atoms (including their electrons) from less electronegative atoms to more electronegative atoms, (ex, combustion reactions)
Why do redox reactions happen?
bcuz the electrons involved are more strongly attracted to the oxidizing agent
–> Ex, in oxidization of methane, the electrons in the C-H bonds are more attracted to the O. as the reaction continues, the weaker forces of the C-H bonds are overcome and the atoms separate and r pulled toward and form strong bonds with O atoms
–> this produces much stronger C–O and O-H bonds, compared to the C-H bonds
- redox reaction essentially involve electrons moving from where they are weakly held to where they are more strongly held
Water % in body parts
Human weight=60%
brain=70%
lungs=90%
bone tissue=22%
cytoplasm & cell= more than 90%
What is the “universal solvent”
water
- more substances dissolve in water more than any other substance due to its polarity
Water molecules are special cuz of their ______, _______, ________________, & _________________________________________________________________________
size, shape, polar structure, ability to associate with each other through hydrogen bonding.
The Water Lattice
- hydrogen bonds form readily in water & ice cuz water is a polar molecule, (has a negative and positive end)
- in liquid water, each water molecule molecule forms an average of 3.4 hydrogen bonds with its neighboring water molecules. –> this bonding forms an arrangement called the water lattice
- it is unique –> most particles h20’s size are gases @ room temp
- as a liquid, the hydrogen bonds constantly form and break, allowing water molecules to slip past on another, reforming the lattice in new positions. –> gives water its fluid properties
Water lattice as Ice
- in ice, water lattice is a rigid structure
- each molecule forms 4 hydrogen bonds with its neighbouring molecules.
- due to the rigid structure, the molecules are stuck further from each other than in liquid lattice, making ice lighter (less molecules in a given area) and 10% less dense than water.
Specific heat is
the amount of thermal energy that is required to increase the temp of a given quantity of water by 1 degree Celsius.
Water’s Unique Properties: Specific Heat capacity
- due to its stabilizing hydrogen bond lattice, water has a high heat capacity
- as thermal energy flows though water, much is absorbed by the process of breaking hydrogen bonds–> thus, the temp of water increases relatively slowly as thermal energy is added
- without the hydrogen bond lattice, water would boil at -81degrees Celsius
WHY H20 IS CALLED A TEMP REGULATOR?
- When temperatures drop, water releases stored heat, which helps moderate cooling. This buffering effect prevents extreme temperature fluctuations in areas near large water bodies
Water’s Unique Properties: Cohesion
refers to the attrractive force between water molecules –> produced by the hydrogen bond lattice
- the reason behind water’s high surface tension–> H20 can form hydrogen bonds on all sides, except the side that faces the air. –> this creates an imbalance in bonding, which puts produces a force that places the surface molecules under more tension and makes them more resistant to separation
- it allow insects to walk on water
Surface tension is
the measure of how difficult it is to stretch or break the surface of a liquid
Water’s Unique Properties: Adhesion
refers to the water’s ability to form hydrogen bonds with other polar molecules
Water’s Unique Properties: Cohesion and Adhesion in plants
in plants growing in soil, water moves up an unbroken column within microscopic tubes of xylem tissue that extend from the roots of the plant to the highest leaves
- cohesion helps H20 molecules stick together as they are transported up the xylem tubes (think of pulling a sting of magnet beads)
- adhesion helps the h20 molecules stick to the cell walls as they are transported
- this helps water move up xylem tubes to replace evaporated water
Water molecules are _________ and __________________ - two qualities that allow them to readily surround polar & charged molecules & ions of other substances
small, strongly polar
Hydration Shells
the surface coat of h20
- it reduces the attraction between the polar molecules or ions of another substance (ionic compounds) & promotes their separation
- what happens is as the molecules & ions separate, h20 molecules surround them, forming a hydration shell which prevent ions from re-associating
- the result is an aq solution
- this is why polar molecules and ionic compounds can dissolve in h20
- similarly, hydration shells surround macromolecules like proteins, sugars, nucleic acids, that have polar or ionic regions on their surface. –> the surrounding h2o reduces the electrostatic interaction between these macromolecules and other molecules.
Electrostatic interaction refers to the attractive/repulsive force between objects with opposite/identical electric charges
Hydrophilic Molecules are
(greek= “water-loving)
are polar molecules or charged ions that are strongly attracted to h20
Hydrophobic molecules are
(greek= “water-fearing”)
non-polar molecules that are not strongly attracted to h20
As the solvent in our cells & blood, h20 dissolves thousands of solutes necessary to life, allowing them to ….
float around and collide with each other, enabling chemical reactions to occur
Autoionization is
the process in which a molecule spontaneously dissociates into ions
Autoionization of Water
pure water=more than h20
- any given sample of h20 @ 25^C = mixture of h20 molecules, OH- ions, H3O+ ions –> @ 25^C about 2 in 550 million h20 molecules react with one another–> 1 molecule transfers an H+ ion to the other, forming an hydronium ion (the H3O+) & a hydroxide ion (the OH-)
- this autoionization always produces = # of hydronium & hydroxide ions–> other dissolved substances can unbalance this
Acidic solutions are characterized by
a sour taste, ability to conduct electricity, & turn blue litmus paper red
What happens when u dissolve acids in h20
it increases the H30+ ion concentration, giving the solution acidic properties–> rmr for an acid to show its properties, it needs to be ionized, therefore it needs to be separated into ions which occurs upon dissolving acids in h20
- in high concentrations, it will cause a chemical burn
- acids contain at least 1 ionizable hydrogen ion in their chemical structure. Ex, reaction of Hydrogen Chloride with water to produce Hydrochloric acid: HCl(g) + H2O(l) → H3O+(aq) + Cl-(aq)
- while strong acids like HCI completely ionize in h20, weaker bases may only partially ionize (like HAc)
Properties of a base
a bitter taste, slippery feel, ability to conduct electricity, changes red litmus paper blue
What happens when u dissolve bases in h20
it increases the OH- ion concentration, giving the solution base properties–> rmr for a base to show its properties, it needs to be ionized, therefore it needs to be separated into ions which occurs upon dissolving bases in h20
- in high concentrations, bases are caustic (corrosive) & will cause a painful chemical burn upon skin contact
- the release of OH- ions will happen in one of 2 ways
1) strong bases (like NaOH) may contain an OH group that will dissociate in water, releasing OH- ions
2) Other bases combine directly with H+ ions. Ex, NH3 (ammonia) which is a weak base will combine directly with h20 molecule. A H+ ion from water binds to ammonia, forming an ammonium ion NH4+ and an OH- ion
The pH scale
scientists measure the acidity of a solution using a numerical scale from 0 to 14= the pH scale
- pH = −log10[ H +] –> google to see proper
—> [ H +] represents the concentration of H+ or H30+ ions in an aq solution
- each whole # on the pH scale represents a 10-fold difference in pH –> a change of 1 is a great difference
- concentration of pure h20 @ 25^C is 1.0 x 10^-7
- solutions <7=acidic (coffee), solutions >7=basic (ex egg whites)
