Unit 1 Flashcards
The Chemistry of the Cell (Ch 3,4,5,7)
What’s the matter?
anything that takes up space and has mass
What’s the difference between molecule an compound
molecule: 2 atoms + held together by covalent bonds
compound: molecules of different element
(H2= molecule, CH4= compound)
Which are the most abundant elements in your body?
Hydrogen
Carbon
Nitrogen
Oxygen
Calcium
How do isotopes differ from each other?
same element
same number of protons
same atomic number
different atomic mass
different mass numbers
different number of neutrons
C12 = 6 protons, 6 neutrons
C14= 6 protons, 8 neutrons
Difference between atomic number vs atomic mass vs atomic number?
atomic number = # of protons (constant in isotopes)
atomic mass = # neutrons + # protons (differs in isotopes)
atomic number = # protons + # electrons + # neutrons (differs in isotopes)
What is the relationship between valence electrons and chemical bonds?
the number of valence electrons indicate the number of bonds that an atom can make
i.e: hydrogen has 1 v.e and thus can make 1 bond
Which bonds are formed between atoms in a molecule? Which bonds are formed between
molecules?
between atoms: covalent bonds
between molecules: hydrogen bonding
What two types of strong bonds? How are the two different from each other?
covalent bond : sharing of electrons
ionic bond : transfer of electrons
What is the relationship between covalent bonds, electronegativity, polar and nonpolar
compounds?
covalent bonds can be polar or nonpolar.
the greater the difference in electronegativity = the more polar the bond
Of the most abundant elements in your body, what is the relative electronegative to each other?
O > N > C = H
What are examples of non-polar molecules and polar molecules?
CH4 vs H2O
What type of compound can form ions? Under what circumstances?
What are the purposes of weak bonds?
allow :
- interactions between molecules
- molecules to adhere to each other when they collide
- stability within large molecule (DNA)
What is hydrogen bonding (1st of the 3 types of weak bonds). give an example regarding DNA
Hydrogen Bonding:
-> bond between atom with a partial negative charge and an hydrogen that is covalently bonded with an electronegative element (N, O, F. Often -OH, -NH, -SH groups)
-> individually weak, but collectively very strong
-> important, bc a lot of water molecules in our body
-> interactions between a pair of bases (between cytosine and guanine / adenine and thymine)
What is Van deer Walls interactions (2nd of the 3 types of weak bonds). give an example regarding DNA
Van Der Waals Interactions:
-> nonpolar molecule with temporarily induced dipole moment caused by random movement of electrons
-> weak
-> interactions between the stack bases in DNA (between cytosine and thymine/ thymine and guanine, etc.)
-> helps keeps the DNA structure intact
What is ionic bonds with water (3rd of the 3 types weak bonds)
Weak since each ion gets shielded by its interactions with water molecules
dry, salt crystal has strong bonds,but in water its bonds get much weaker
Why do ionic bonds weaken in water?
Because each ion gets shielded by water molecules that exhibits oppositely charged ions.
Where does oxygen come from in the reaction called photosynthesis?
Oxygen originates from water in photosynthesis NOTTT from CO2
Why do all organisms need water?
dehydration and hydrolysis reactions need water
cells are 70/95% made of water
Describe the unique structure and polarity of water. How many H-bonds can it make
water molecule = 2 positive ends (H) + 1 negative end (O)
water = has poles of partial charges = is a polar molecule
each water molecule can form max 4 Hydrogen bonds with neighboring molecules (2 lone pairs on O + 2x1 electron pair on H). these hold liquid water together, making water very cohesive.
Describe how water acts as a solvent in :
- large molecules
-water= solvent for cells, blood & plant sap
- water dissolves mostly polar/ionic substances
large molecules:
-> they will dissolve in water if they have a polar functional group
Describe how water acts as a solvent in :
- non-ionic polar substances (ie: hydration of glucose)
-> glucose is polar bc of its oxygen atoms
-> water forms H-Bonds with the molecule and removes individual monosaccharides from the solid until it is a homogenous solution
Describe how water acts as a solvent in :
- ionic substances (ie: hydration of NaCl)
-> Cl- will orient itself with H+ of water molecule
-> NA+ will orient itself with O- of water molecule
What is the difference between solvation and hydration?
Solvation: solid is dissolved into a solution
Hydration: solvation where the solvent is water
Describe the property of water (C in CAT)
Cohesion:
- how well molecules of the same substance stay together
- collectively, h-bonds hold a substance together = cohesion
- ex: water = good cohesion bc of H-Bonding
- plants get water from the roots to the leaves, fighting gravity
Evaporation exerts pulling force on water within what tissue?
cell walls??? capillary tissue???
Describe the property of water (A in CAT)
Adhesion:
- clinging of one substance to another (stronger adhesion if they have charged group of atoms on their surface)
- responsible of the meniscus of a graduated cylinder
- water makes thing wet, bc water clings to things
Describe the property of water (T in CAT)
Surface Tension:
- how difficult it is to break/stretch the surface of a liquid, due to cohesion
- strong attraction between water molecules (H-bond) = strong surface tension
- tension of the surface of a liquid= much stronger attractions than those between water molecules or between air molecules
Describe capillary action
tendency of water to move in narrow tubes, against gravity; can be explained by cohesion and adhesion.
- plants: water clings to the cells that forms the veins. it allows it to defy gravity up to the roots.
- water clings to the walls of a capillary tube (adhesion) and can pull more water up the tube (cohesion)
Describe moderation of temperature
- the way water responds to temperature changes depends on the h-bonds
- water heats up -> breaks h-bonds and reduces the degree of cohesion
- water cools down -> opportunity to form h-bonds
What are the 4 advantages of water’s high specific heat?
- it allows water to resist to temperature changes and act like a temperature buffer
1.oceans absorb heat & only increase a few degrees during day and release stored energy to warm the air at night.
-> explains why coastal areas = moderate climate that don’t switch up a lot
- oceans have a constant temperature = stable environment for aquatic life
- most biological reactions only take place within a narrow temperature range. = good for biological reasons
What’s the number of hydrogen bonds in water per molecule in each physical state?
Solid: 4 hydrogen bonds per water molecule
Liquid: 3-1 hydrogen bonds per water molecule
Gas: 1-0 hydrogen bond per water molecule
Types of evaporative cooling? Give 2 examples in biology.
- water cools down = heat evaporates = h-bond can be formed
- water heats up = water molecules break their h-bonds. some bonds break faster than other and escape liquid phase to enter gas phase. the molecules that contains more energy are evaporated thus making the temperature of liquid water less high.
= cool down process (water evaporating takes the heat away)
human= sweat
plants = water transpires from leaf
Describe the relationship between polar/nonpolar covalent bonds in organic molecules and their
solubility in water. (ie. can they dissolve in water? Why/why not?)
polar = soluble
nonpolar = insoluble bc there are no dipoles, which prevents the molecules from making interaction with water molecules.
like dissolves like
Explain the pH of an aqueous solution (ie: what happens when you add acid/base in soln)
the product of the H+ and OH- concentrations in any aqueous solution is constant at 10^-14.
an acid added to a solution will:
1. add hydrogen ions
2. remove OH- ions (since they will combine to the newly added H+)
3. lower the pH
4. digestive liquid in stomach = ph of 2 (only acidic place in our body)
a base added to a solution will:
1. add OH- ions
2. remove H+ ions (since they will combine to the newly added OH-)
3. increase the pH
4. biological fluids, ie. blood/saliva = ph of 6-8
Describe a pH buffer. What is it and what does it do?
addition of acid have much less effect on the pH of blood than the pH of water because blood contains several substances biological buffers. (ie. H2CO3)
pH buffer:
-> substance that minimizes changes in [H+] and [OH-] in a solution by accepting H+ from the solution when they are in excess and donating H+ to the solution when they are in excess.
Why is it important for pH in cells and in other body fluids to be tightly regulated?
change in pH alter the shape of proteins = denaturation = affects function
How does
carbonic acid (H2CO3) play a role in the fluids of the body? Give one nutritional example.
H2CO3 -> HCO3- + H+
this equilibrium rxn acts as a pH regulator
shift right = response to rise in pH (want more H+)
shift left = response to drop in pH (want less H+)
after eating a lot of meat = acidity in stomach = shift to the left to form more carbonic acid and get rid of the acidity in the stomach
What about amino acids/proteins? (see
class notes on proteins)
amino acids also act as biological ph buffers
carboxyl end = acid that donates protons
amino end = base that accepts protons
Explain pH homeostasis regulation by the respiratory system.
pH below normal range:
-> due to respiratory issues
-> to much [CO2] in blood
-> CO2 -> H2CO3 (in water)
-> HCO3 + H+
-> CO3 2-
-> more CO2 = more H+
-> result = acidosis
-> response = faster breathing to exhale more CO2
pH above normal range:
-> due to hyperventilation or diarrhea
-> not enough CO2
-> CO2 -> HCO3 -> H+ -> CO3 2-
-> less CO2 = les H+
-> result = alkalosis
-> response = slower breathing to accumulate more CO2
Explain pH homeostasis regulation by the urinary system
low pH:
- acidosis
- kidney will :
1. excretes excess H+ into the urine
2. absorb HCO3-
high pH:
- alkalosis
- kidney will:
1. excrete HCO3-
2. absorb H+ back into the blood
Why do shells in aquatic animals thin and become fragile as oceans become more and more acidic?
(the H+ + CO3 2- —> HCO3- step is important)
- CO2 dissolves in water -> CO2 with water forms H2CO3 (carbonic acid)
CO2 + H2O -> H2CO3 - more carbonic acid = more H+ (H2CO3-> H+ + CO3 2- ) = lowers ocean’s pH = “ocean’s acidification
- acidic water = extra H+ available that will bind to CO3 2- to form HCO3 -
this will reduce the [CO3 2-] in the water - less CO3 2- = less calcium carbonate (CaCO3) available for animals’ shells
(Too much CO2 in air
CO2 + water = H2CO3 (alot of CO2 creates an excess of H2CO3)
H2CO3 = H+ + HCO3- (excess of H2CO3 leads to more H+ released than what the ocean can buffer
H+ + CO3 2- = HCO3-
excess H+ = more CO3 is needed to complete the reaction = less CO3 2- is available in the ocean for the creation of shells.)
Where do autotrophs obtain organic carbon? Heterotrophs? (Not in class notes but you are
expected to know this from previous bio courses)
How does carbon enter living organisms?
What’s the difference between a biomolecule and an organic molecule ?
Biomolecule
Organic molecule2
Which properties of carbon make it a good building block for organic biomolecules? Which other
elements make up the major atoms used to build these molecules?
it is very versatile (can make single, double,triple bonds)
&
4 single bonds possible -> characteristic called “tetravalence” that makes large complex molecules possible
When carbon is bound to four other atoms, what shape does the molecule generally take?
tetrahedral shape
Review polar and non-polar bonds. Would the following bonds: C-O; C-H; C-N; C-C be considered
polar or non-polar? Why?
C-O polar
C-H non polar
C-N polar
C-C non polar
Describe carboxyl group
R - COOH
C with one double bond to an O and one single bond to an hydroxide.
-> provides polarity
-> BUT, provides certain stability
ie: often COOH -> COO-
-> molecules with carboxyl groups are weakly acidic
-> all amino acids contain a carboxyl group that has the capacity to donate an hydrogen
Give 2 examples of compounds that contain a carboxyl group.
-> formic acid (organic molecule released by formicine ants as a defence mechanism)
-> acetic acid
Describe hydroxyl group
R-OH
provides polarity to molecule that will depend on how many OH groups there are relative to the molecule’s size (C2H5OH + polar than C6H13OH bc smaller chain compared to hydroxyl group)
organic compounds with hydroxyl group = “alcohol”
ie: methanol, ethanol, etc.
glucose = 5 -OH groups & small chain (6 carbons) = highly polar
What do sugars owe their solubility in water to ?
their presence of hydroxyl groups (ie. glucose = 5 hydroxyl groups)
Describe carbonyl group
R- C=O
-> aldehydes = carbonyl carbon bonded to at least 1 hydrogen (extremity of chain)
-> monosaccharides with aldehydes = aldoses
-> ketones = carbonyl carbon bonded to 2 other carbons (middle of chain)
-> monosaccharides with ketones = ketoses
-> provide polarity to the parent molecule since electronegative oxygen attracts covalent electrons
Describe amino group
R-NH2
-> generally weakly basic molecules
-> all amino acids contain an amino group that can accept a hydrogen
-> provide some polarity due to the polar covalent bond between N and H (Hydrogen bond)
ex: nitrogenous bases in DNA/RNA contain amino group
How does amino acid act as a buffer?
each amino acid can :
- donate an H+ into the solution -> acid solution
- accept an H+ -> basic solution
carboxyl group = acidic (this end can donate an H+)
amino group = basic (this end can accept an H+)
= amino acid = pH buffer
Describe sulfhydryl group
R- SH
-> stabilize the internal structure of proteins
-> can form disulphide bridges with another -SH (very strong bond)
-> disulphide bridges form cross-links that stabilize protein structures
Where can sufhydryl groups be found?
in some proteins that contain cysteine amino acids
What is responsible for the stabilization of the straight/curly nature of hair ?
the disulfide bridges between two sulfhydryl groups
Describe phosphate group
R - OPO3 2-
-> constituents of phospholipids (reason for polar heads)
-> provides polarity
-> phosphates can donate H+ into solution and make the molecule weakly acidic
-> this ionization gives a negative charge to the parent molecule
What is the reason for the high energy bonds between the phosphate groups in ATP?
ATP = 3 phosphate groups
-> each phosphate group = negative charge (PO4 3-)
-> negative-negative = they each naturally repel each other and thus create a lot of instability
-> instability + repelling = high energy covalent bonds necessary to hold the phosphate groups together
-> high energy covalent bonds can be used for cell work
In phosphate groups, how many hydrogen ions can each phosphate give up into solution?
2
Describe methyl group.
R -CH3
-> non polar group
-> methyl groups can be added to molecules to act as a identity tag or signal for enzymes
-> ie: methylated DNA affect gene expression
Describe how each of the following contributes to the diversity of organic biomolecules:
o Carbon skeleton
o Functional groups
- carbon skeleton diversity
-> degree of branching
-> ie. butane = straight chain vs isobutane= branched
-> double bonds’ different possible locations - functional groups
-> atom groups that provide a molecule with a particular characteristic/function
-> different # or position of functional groups = different properties
-> most functional groups can form ionic & hydrogen bonds with other molecules and thus give the organic molecule hydrophilic properties.
-> some functional groups are non-polar and give the molecule hydrophobic properties
Define an isomer. Compare a structural isomer and a stereoisomer.
compounds with the same molecular formula but different structures and properties.
yes, because organisms are sensitive to even subtle variations in molecules.
cells will recognize one enantiomer (an isomer that mirror images of each other) but not the other
What are the 3 kinds of isomers?
structural isomer
-> 2 C5H12 molecules but different covalent arrangements (different structures)
stereoisomers (2 kinds) :
1. geometric isomer
2. optical isomer
Describe geometric stereoisomers
-> same covalent arrangement but different spatial arrangement
-> The spatial arrangement differs around the double bond between 2 Carbons
-> cis isomer = both sides of the double bonds mirror each other. ie: 2 hydroxyl groups are on the upper half bond.
-> trans isomer = 2 hydroxyl groups are on opposite sides, across each other (diagonally)
-> ex: rhodopsin (visual pigment in the eye), when hit by light, changes from cis isomer to trans isomer.
Describe optical stereoisomers
-> enantiomers
-> isomers that are mirror images of each other
-> a carbon attached to 4 different functional groups
-> Cells will recognize one enantiomer but not the other
-> 2 drugs enantiomers = different effects
-> We are sensitive to even subtle variations in molecules
List 3 examples of optical stereoisomers and their different biological effects.
R -(+)- Thalomide = sedative
S-(-)- Thalomide = malformation of babies
L-Dopa = helps fighting Parkinson’s disease
D-Dopa = biologically inactive
D- Alanine VS L-Alanine
Would you expect
stereoisomers to have different biological properties than isomers?
Define a monomer and a polymer.
monomers are building blocks of polymers
A, C, H, T = monomers
CHAT = polymer
Describe a hydrolysis and condensation reaction. Which require(s) energy and/or a catalyst?
Hydrolysis
-> breakdown of polymers into monomers by adding a water molecule
-> require catalyst
Condensation (dehydration synthesis)
-> monomers form larger molecules by removing a water molecule and forming a new bond
-> requires energy & catalyst
Describe the major functions of carbohydrates in cells. Give some specific examples for each
- energy storage
-> starch (plants)
-> glycogen (animals) - structural components
-> cellulose in a plant’s cell wall
-> Chitin in fungi’s cell walls and exoskeleton
-> peptidoglycan in bacteria - Energy source
- Protection
-> glycoproteins = mucus = protects respiratory and digestive tracts
What are the 2 types of polysaccharides? Give examples
- Energy storage
-> starch (plants)
-> glycogen (animals) - structural polysaccharides
-> cellulose in a plant’s cell wall
-> chitin in fungi’s cell walls and exoskeleton
-> peptidoglycan in bacteria
What is the general ratio of the three main atoms in a carbohydrate?
carbon, hydrogen and oxygen in a 1:2:1 ratio
Describe the structure of a monosaccharide
monosaccharides = [CH2O]n where n is between 3-7
Describe the structure of a disaccharide.
disaccharides = 2 monosaccharides bonded by glycosidic linkage by dehydration synthesis
Describe the structure of an oligosaccharide
-> Small sugar polymers formed from 2-6 monosaccharides
-> found attached to glycoproteins or glycolipids
Describe the structure of a polysaccharide.
-> 100-1000 monosaccharides linked by dehydration synthesis
-> mostly made of glucose
-> vary in properties due to their different isomers and differently arranged units
What is the bond that links two monosaccharides together called? What type of bond is it?
glycosidic linkage
covalent bond
Why does a monosaccharide have high chemical energy making it a good fuel in cellular respiration?
(The bond between which atoms can be broken?)
its numerous C-H and C-O bonds makes it useful to fuel cellular respiration
when C-H bonds are broken, they release aloottttt of energy that can be used to produce ATP
monosaccharides are stable which allow them to store the energy until needed
What are three monosaccharides that mammals can metabolize? How do they differ from each
other?
glucose
-> carbonyl group at the first carbon
fructose
-> carbonyl group at the second carbon
galactose
-> carbonyl group at the first carbon
all have different arrangement of hydroxyl groups
List the four structural characteristics of a monosaccharide that can vary.
position of carbonyl group
number of carbon atoms
configuration of hydroxyl group
ring or linear form
*confirm with teacher
Define (and identify) an aldose, ketose, triose, pentose, and hexose
2 types of sugar : aldose and ketose
aldose: carbonyl group is located on the first carbon (top end of the chain).
ex: glucose
ketose: carbonyl group is located within the carbon chain, such as on the second carbon
ex: fructose
triose: 3 carbons -> smallest sugar
pentose: 5 C-> in DNA
hexoses; 6 C ->common sugar
Explain why monosaccharides have isomers. Identify whether a monosaccharide pair is a structural
isomer or stereoisomer
glucose, galactose and fructose are all structural isomers of one another.
