1
Q
Atoms
A
- each type of atom is referred to as an element (sodium, zinc)
- all essential and have the same building blocks just put together in several different ways
- smallest function units of matter (smallest you can break down a substance and it is still the substance
- still with the physical and chemical properties of that element
- exampleL Mg- you can make is smaller and smaller until you get a single Mg, once you break that down it is no longer Mg, now it is protons, neutrons and electrons
- can be split into subatomic particles
- protons, neutrons and electrons
2
Q
Atoms as “plum pudding”
A
- “plum pudding” model, electrons scattered through a field of positive charge
- Rutherfords model: mostly empty space with positive charge in condensed center
- plum pudding is how we thought of atoms, especially where the electrons are, mixture of subatomic particles (electrons are raisins in the plum pudding)
- RF model- middle of empty space is P & N and far from nucleus is the electrons
- he figured this out by throwing out many particles of waves that shot out to a thin gold paper
- he figured out by shooting many tiny little particles like gamma rays, to see if they go through the little gold foil. Most of the time the particles would bounce back
3
Q
modern atomic model
A
- protons and neutrons in the middle
- various levels of electrons circulating on the outside
- electrons are moving around all the time, these are regions of probability- area most likely to find a give electron
4
Q
octet rule
A
- atoms are stable when the outer shell is full
- except for the first shell (fills with 2), each shell fills with 8 electrons
- all atoms want to fill the outer shell
5
Q
Octet example: Nitrogen
A
- has 7 protons and 7 electrons
- 2 electrons fill the 1st shell
- 2 in the 1s orbital
- 5 electrons in the 2nd shell
- 2 fill in the 2s orbital
- 1 in each of the three 2p orbitals
- the outer 2nd shell is not full
- electrons in the outer shell available to combine with other atoms are valence electrons
-nitrogen can form up to 3 bonds with something else
6
Q
valence electrons
A
electrons in the outer shell available to combine with other atoms
7
Q
Protons
A
- number of protons distinguishes one element from another
- atomic number- how many protons an atom has
- what makes nitrogen, nitrogen is how many protons it has
- nitrogen atom can change the number of electrons and neutrons it has but for it to stay the same it has to have AN of 7, 7 protons
- if an element loses a proton then it is a completely different element
8
Q
Atomic Number
A
number of protons a atom has
9
Q
Periodic table
A
-organized by atomic number
-what makes an element is how many protons it has
-groups go from left to right
periods go up and down
10
Q
Atomic Mass
A
- protons and neutrons nearly equal in mass
- Atomic Mass Scale- atoms mass relative to others
- most common form of C: 6p & 6N
- AM is 12 Daltons
- H has AM od 1
- Mg AM of 24
- Why don’t we include electrons: not part of the nucleus but is part of the atom, electrons weigh nothing, so tiny and mass is so small compared to a single proton or neutron
11
Q
Isotopes
A
- they differ in the number of neutrons*
- 12C= 6p and 6n
- 14C= 6p and 7n
- Atomic mass= averages of various isotopes
12
Q
Hydrogen, oxygen, carbon and nitrogen
A
- 95% of atoms in living organisms
- H and O: mostly in water
- N: proteins and nucleic acids
- C: building block of all living matter
- Other elements are still essential
- 60-80% of our body is water
- nitrogen is a smaller percentage but DNA is very nitrogen rich and proteins in the body
- Carbon is the building blocks of all the neutrons and backbone of all the organic molecules
13
Q
Chemical Bonds and Molecules
A
-Molecule: 2+ atoms bonded together (O2)
-Compound: molecule composed of 2 ore more different elements (NaCl)
molecular formula: you know every atom that makes up that molecule (C6H12O6) says how many C, H and O
14
Q
Covalent Bonds
A
-atoms share a pair of electrons
-between atoms when outer electron shells not full (valence not full)
-Strongest of all bonds*
shared electrons behave as if they belong to each atom
-you can have a single, double or triple bond, depending on how many electrons needs to be shared
-electrons move around the nucleus
-if you have 2 nuclei then electron moves around both
sharing electrons means sharing some time around each nucleus
-this happens when the valence is not full between atoms
-if you are an atom and your valence is full, you have an octet, then you are stable, you don’t go around reacting with other atoms
-but if you are missing a few then you are more reactive
-example: F, AN is 9, the first has 2 electrons but the outer valence has 7 electrons, it needs one more to be an octet. H has 1 left over and needs one more, so they both are missing one. So now the pair are sharing electrons
15
Q
Polar Covalent Bonds
A
-when distribution of electrons creates a polarity, or difference in electric charge, across the molecule
-electrons being shared but not equally
-electrons spend more time with one atom than the other
-H and Cl-not shared equally, spends more time with Cl
-this creates a difference in electric charge
if it spends more time with Cl and less time with N, then Cl will have a negative charge, H is losing an electron so it’ll have a more positive charge because of unequal sharing
16
Q
Polar Covalent bonds: electronegativity
A
-one atom is MORE “electronegative” than the other, so electrons are NOT equally shared
- electronegative is essentially just how attracted you are to that electron pair, different atoms vary in this
- few different factors: some atoms are more electronegative than others
- example: oxygen atom and 2 H atoms. Here the O is missing 2 electrons and H is missing one, so they form a covalent bond with O. The pairs spend more time with O and O takes the electron charge. This creates polarity across the water molecule. H2O-since electrons spend more time with O, the O side of molecule is slightly negative and H side is slightly positive
- water is a polar molecule because it is made up of 2 different polar bonds
17
Q
Polar Covalent Bonds: What determines electronegativity?
A
- number of protons
- number of electrons in the outer shell
- if you are a bigger atom and have more protons you are positively charged, the more power you have the more you attract electrons towards you and in general if you are larger molecules and everything else is equal
- Oxygen is one of the most electronegative atoms*
- C and H hydrogen bond is nonpolar, they are sharing
18
Q
Nonpolar Covalent Bonds
A
- between atoms with similar electronegativities (attraction to electrons)
- equal sharing of electrons
- no charge difference across molecule
- C and H aren’t exactly equal electronegativities but they are close enough
- because they are sharing equally there is no separation of charge, slightly negative or slightly positive, no charge for these
19
Q
Hydrogen bonds
A
-hydrogen atom from one polar molecule is attracted to an electronegative atom of another
- looking at a weak attractive force between two molecules
- covalent bonds look at atoms within the same molecule
- hydrogen bonds look at one molecule attracted to another molecule
- H2O and another H2O and H bonds and notated by a black line to show attraction
- H atom of one water weakly attracted to the O
- H weak attraction to something with a slightly negative charge
- water molecule is polar (positive side attracts to a slightly negative side)
- water molecules are attracted to other water molecules
- must have 4 molecules for this to happen, charge separation within the molecule
20
Q
Hydrogen Bonds: important to life: DNA
A
- VERY important to life
- glue to hold DNA together
- strand of DNA and is shaped as a ladder and in between space are the molecules that need to be in the DNA sequence, held together with a bunch of H bonds
- dotted lines are H bonds holding the 2 strands of DNA together
- essentially weak polar covalent bonds
- many H bonds can form strong bonds when together
- single H bonds break easily
21
Q
Ionic bonds
A
- what happens when electronegativity is VERY different?
- forget using electrons. Atoms steal electrons
- both atoms carry an electrical charge
- # protons does NOT equal # of electrons
- electronegativity between two atoms are so different that one atom basically steals an electron from another
- example: Cl- valence is 7 and Na valence is 1. to be stable Na can gain 7 electrons or remain same, Cl needs one. In this case electronegativites are so different and the valence is set up so that Na can get ride of one and be stable and Cl gains one. Now Cl went from 17 electrons to 18electrons and has a negative charge(gains one). Na has 11 protons (never changes) and 10 electrons, so overall positive charge (lost)
22
Q
Ionic bonds: ion
A
atom or molecule that has gained or lost electrons
for ionic bonds, it is giving up or totally gaining an electron, we have an unequal number of protons and electrons so now we have an over charge that does not equal each other. This is an ion- something that is carrying a charge
23
Q
ionic bonds: Cations
A
loss of an electron; net positive charge
24
Q
ionic bonds: Anions
A
gain of an electron; net negative charge
25
Water
- life evolved in the water, 3.5 bya
- life existed only in water for, 2.5 by
- when the land was colonized, these organisms carried water within themselves
- water is what keeps things alive
- we carry water within our bodies, we are 50% water
- aquatic organisms
- our bodies had to have special adaptations that allowed us to exist in a dry environment, we had changes in our skin to make sure we don't lose too much water we are still life water based life
- not only do we need water to survive. It is important to do a lot of basic functions; chemical reactions in our body take place in a watery solution
26
Why does the brain need so much water?
- brain needs a lot of water, food and water we consume go to the brain. In the food we eat, the glucose goes to the brain
- water, if it is properly hydrated, it helps the brain to work faster. If dehydrated the chemicals slow down \water is the medium that helps a lot of the single molecules move
27
Water, "the universal solvent"
water is a substance in which a number of things easily dissolve or break down in
28
solvent
medium in which a solute dissolves in
29
solute
dissolves in a solvent to create a solution
30
solution
solvent + solute
31
aqueous solution
- solution in which water is the solvent
| - most chemical reactions within an organism happen within an aqueous solution
32
Hydrophilic
- easily dissolves
- have ionic and/ or covalent bonds
- "like dissolves like"
- "water loving"
- water is a polar molecule
- example: salt, NaCl and sugar
33
Hydrophobic
- do not dissolve in water
- nonpolar molecules
- "water fearing," do not break down or dissolve in water
- examples: oil
34
Amphipathic
- "both loves"
- have both polar/ionized and nonpolar regions
- may form micelles in water
- one part is hydrophobic and the other is hydrophilic
- part of the molecule is polar other part is nonpolar
example: detergents, soap
35
Micelle (amphipathic)
- made up of a molecule
- head region is hydrophilic-easily dissolved in water. The tail region is hydrophobic- does not easily dissolve in water and non polar tail
- they form a protective structure, the hydrophilic head forms a outer portion that is like sphere and the outer portion is protected by the hydrophilic head. the Hydrophobic ail are all protected inside the sphere
example: detergents with grease get trapped on the inside and all hydrophobic tails and wash it down the drain
36
water has 3 states of matter
- solid, liquid and gas(vapor)
- changes in state involve an input or release of energy
- if you heat water up enough it turns to gas
- to change state from a liquid to a solid or gas a lot of energy is required
- liquid to a solid you are removing heat energy so you can change the state
- if you have ice and you add enough heat energy it can become a liquid
37
3 states: heat of vaporization
amount of energy you have to apply to a liquid to solid. the transfer of energy to get a change in state
38
3 states: heat of fusion
how much heat you are removing to go from a liquid to solid. the transfer of energy to get change in state
39
specific heat
- amount of heat energy to raise temperature 1C
- water is extremely stable as a liquid, due to high heats of vaporization and fusion and high specific heat
- water has a very high specific heat and takes a lot of energy to change its state
40
thermal properties of water
- water (w/ high specific heat)
- can absorb a large amount of heat
- heat buffer for the planet
- oceans absorb and release
Example: ocean, it acts as a heat buffer for the plant, all solar energy coming in and striking the earth. A lot of the heat is absorbed by the ocean
Temperature changes would be much more extreme without the oceans
This is the same as our body
As our body gets warmer some of the heat is absorbed by water in our bodies, as a cooling mechanisms we lose heat through sweating- we lose water and solutes in the water
Because water has a high specific heat because it is stable as a liquid and a heat buffers are bodies can preciously regulate our body temperatures
41
Thermal Properties of water: buffer
- water is also a heat buffer in our bodies
- heat absorbed by water in our bodies
- sweating releases heat
- heat is buffer in body
- cooling mechanism we lose heat throughout sweating, cools body down
42
Colligative properties of water
- amount of dissolved solutes influences temperature at which solution freezes or boils
- addition of solutes to water
- lowers the FP below 0C
- raises the BP about 100C
- Colligative properties- of water, tells us that depending on how many solutes or solute concentration is how much stuff can actually dissolve in water. This can actually change the freezing or boiling point in water
- Example: if you have a solution of water with a lot of solutes in there it can both lower FP and increase BP. Increases the range in which you could have liquid water
- Number of organisms that can live in below freeing or in really hot temperatures and they don’t have to worry about water in their body freezing or vaporizing
- If you have a lot of solute in water this can both lower FP or raise BP
- Water by itself can freeze 0degree C and BP is 100 degree C
- Example- wasp larvea can stand freezing temps because half of their bodies is full of particular solutes, a lot of solutes in their body dissolved in water which changes their FP
- Microogranisms can live in extreme environments explain archeae
43
hydrogen bonding
- cohesion: water molecules stick together
- surface tension
- adhesion: water molecules stick to surfaces
- hydrogen is involved in H bonding
- weak bond
- all of bonds together of H is strong
- water is good at H bonding because it is polar, slightly negative side and slightly positive side. where the hydrogens are is the positive charge side and the oxygen is the negative charge
- water molecules because its polar tends to stick with other water molecules
44
Hydrogen bonding: cohesion
- water molecules stick together
- water is cohesive because of beading- this is water droplets forming spheres int the water instead of just bursting and flattening out, it sticks to itself
45
surface tension
- because of H bonds it has a high surface tension, where you have to apply a good amount for it to break through the water
p we have enough mass to easily do this, light weight things can stay right on top of the water because they don't have enough weight to break down the H bonds and break the surface of water
46
adhesion
- water molecules stick to surfaces
- capillary transport
- picture of finger: here your blood is mostly water, it is moving upward against gravity because your water is sticky and not only sticks to itself but also it sticks to the sides of the tube. Blood moves up against gravity because it is attracted to the sides of the tubes
- like to stick to other stuff, things with similar chemical properties
47
the importance of water
1. chemical reactions
- most major chemical reactions in the body are taking place in the solution of water. In an aqueous environment
2. structural support
- for a plant to stay up right, has to do with water to physically hold up right, plants have a permit wilting point, you can neglect it long enough and it will stay in the position
3. eliminates waste- kidneys play an important role of filtering out waste products. the kidneys and hormones in our body ultimately make the decision of how much water you are going to excrete in your urine or how much you will recycle back into your body
4. Regulates temperature- sweating or heat absorption
5. transports nutrients
- taking in water from roots and transporting up several meters. Humans blood takes things from one part of the body to the next which is made up of water
6. Provides Lubrication
- salvia
7. summer fun
48
Acids and Bases
-pH measure of hydrogen ion concentration
-Greater concentration of hydrogen ions the more acidic
-pH is and pH scale is based on and how organisms are not sensitivity to pH changes
Your body has a very limited oH range, stomach exception, we don’t tolerate change in pH
-pH- hydrogen has atomic number 1 and hydrogen in nature is H+ (lost one electron) H ion and more H ions you have the more acidic your solution is
-pH of pure water is 7 perfectly neutral
-Goes from 0-14
-Below 7 is acidic something above is basic or alkaline
-Deviation too far is bad
-Something that is alkaline, high pH, is really far from neutral is bad
-Really low pH is acidic really high pH is alkaline
49
Acids
- are molecules that release hydrogen ions in an aqueous solution
- HCl -> H+ + Cl-
- strong acid releases more H+ than a weak acid
* a change of 1 pH unit=10x difference in the [H+] concentration *
- acidic things have a higher H+ ion concentration
- acids increase the concentration of H ions if you were to put it in water
- example: HCl in aqueous solution breaks down to H and Cl it is increasing concentration of H+ ion so it is acidic
- strong acids release more H+ ions than weak ions
- more acidic something the more it can increase H ion concentration
50
Bases
-the H+ concentration
=come react with water to produce OH-
-NH3 + H2O NH4+ + OH-
*a change of 1 pH unit=10x difference in the [H+] concentration*
- alkaline things have a lower H on concentration- mostly toxic to humans
- bases decrease in H ions
51
pH of a solution can affect
- the shapes and functions of molecules
- the rates of many chemical reactions
- speed up or slow down
- the ability of two molecules to bind to each other
- with chemical bonds
- the ability of ions or molecules to dissolve in water
- water maxes out at a certain level of solute, you get to a certain point it doesn't dissolve anymore, so i you are adding more ions to your solution then you might not be able to dissolve other things in water
- Protein + acid + unfolded = now dont do their function
- pH scale is 0-14 but change of 1 pH scale you are removing 10x the hydrogen in solution
- the lower your pH the more acidic- H+ you have
- protons from acid can change the shape of molecules and the function
52
Buffers: explained
- organisms usually tolerate only small changes in pH
- buffers help to keep a constant pH
- acid-base buffer systems generate or release H+ to adjust for changes in pH
- 6-7= death
- 7-7.35= acidosis
- 7.35-7.45= normal
- 7.45- 7.8= alkalosis
- 7.8-9= death
- chemicals and substances in a cell that protect against large changes in pH
- buffer works really hard to make sure that even if you eat something acidic, your bloodstream stays at a constant pH
- molecule or collection of molecule that have the ability to bind and release hydrogen ions as necessary
- so if pH is becoming alkaline then you want to bring it down, it releases Hions. If pH is to acidic and you want to bring it back....
- buffers make sure solutions in your body are not changing big in pH
53
Tums
- heartburn = excess stomach HCl
- buffer
- theses tums neutralize the pH takes up some of the H+ ons
- instead of having too many H+ these will stick to the carbonate
BIO 111
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