BSC test 1
What is the charge of a phosphate molecule?
-2 There are two negative charges indicated on the structural formula. You can also tabulate e-s about the two charged oxygens; a neutral oxygen atom possesses 6 electrons in its second shell. If you count the bonded electrons just once (one e- belongs to P), then each oxygen has 7 electrons in its second shell.
What is the CHARGE of a water molecule?
0
protons and neutrons each weigh?
1 Dalton or 1.7 x10^-24 g
What are the 6 different Functional groups?
1) hydroxyl 2) carbonyl 3) carboxyl 4) amino 5) phosphate 6) sulfhydryl
Two primary functions of Carbs?
1. Energy source 2. Building material, Carbon source
If a solution has a pH of 3, what is its concentration of protons (hydrogen ions)?
1/1,000 M same as 0.001 and 10^-3
Milli molar or micro mole means______.
1/1000 of a mole per a liter.
How many PROTONS are in one MOLECULE of water (H2O)? H-O-H
10
How many ELECTRONS TOTAL are in a molecule of water?
10 Oxygen has 8 electrons in its valence shell (shown), 4 of which are shared with hydrogen atoms. Two more electrons are found in the first electron shell of oxygen
Pure water has a concentration of?
10^-7 molar (moles per a Liter)
What has more protons? Ex: [H+] = 10^−7 M → ? Ex: [H+] = 10^−5 M → ? and how many more protons?
10^−5 M 100 more protons (1 order of magnitude equals 10x) [H+]=Protons
How many electrons are shared between atoms in phosphate? 6 bonds equals
12 electrons shared Phosphorus alone has 5 bonds and shares 10 electrons.
First electron shell has how many orbitals and what kind of?
1s orbital
2 molar means ___ moles in 1 liter.
2
How many COVALENT BONDS are found in a water molecule? H-O-H
2
How many electrons does each orbital hold?
2 electrons (maximum)
How many more times protons do you have in pH 5 then pH 7?
2 orders of magnitude which 100x more. (1 order of magnitude equals 10x)
How many elements are essential to life? *important*
25
How many Dehydrations were required to build this polymer of 4 monomers?
3 Dehydrations 4 monomers means 3 bonds its always one less If there were 50 monomers there would be 49 bonds.
How many ELECTRONS are SHARED between atoms in this molecule? H-:O:-H
4
carbon makes how many bonds?
4
A water molecule can form a maximum of ____ hydrogen bonds?
4 hydrogen bonds 2 hydrogen donors 2 hydrogen recievers
The second shell has how many and what kind of orbital?
4 orbitals total 1s and 3p orbitals
If the proton concentration was 10^-4 what would the pH be?
4 which is acidic
How many protons are in one phosphate molecule (HPO4^2-)?
48 Each oxygen has 8, phosphorus has 15, and hydrogen has 1.
How many covalent bonds does Phosphorus form?
5 bonds Very common bio-molecule (exception to the octet rule)
How many electrons total are in a molecule of phosphate?
50 Again all oxygens have 8 electrons in their valence shells (shown), and 2 in their first shells. Phosphorus has 10 electrons in its valence shell, but do not to count these twice! It also has 8 electrons in its second shell, and 2 in its first. So (8 + 2 e-/oxygen) x 4 oxygens + (8 + 2 e-/phosphorus) x 1 phosphorus = 50 e-. Also note this molecule carries 2 negative charges, so it must have 2 more electrons than it does protons.
How many covalent bonds are found in a phosphate molecule? (Count double bonds as TWO covalent bonds!)
6 The hydrogen is attached to the adjacent oxygen by a covalent bond. Sometimes covalent bonds are not shown for simplicity. But it MUST be there, because hydrogen forms one bond and oxygen forms two!
Biological fluids pH range from
6-8
A mole of ethanol weighs only 46 g; how many molecules is in a mole of ethanol? C2H6O
6.022x10^23
How many molecules of sucrose are in a mole of sucrose? C12H22O11
6.022x10^23
How many ATOMS are in a mole of sucrose? C12H22O11
6.022x10^23 x 45= 271x10^23 or 2.71x10^25
A BASE decreases?
A BASE decreases the proton concentration. reduces [H+] DIRECTLY Ex: NH3 + H+ <=> NH4+ reduces [H+] INDIRECTLY Ex: NaOH→ Na+ + OH− OH− + H+→ H2O BSC 1-24 1:05 review again
Amino group Know the name and arrangement of atoms
A Nitrogen bonded to 2 hydrogen. Amino group behaves like a weak base because it has a lone pair of electrons. (positive charged) Amino acid is the building block of proteins
What makes an element not reactive?
A full outer shell (valence shell) Elements interact to complete their valence shells
Cells contain an ___________. A mixture that is homogenous at the molecular level. We have 1000s of different solutes in out cell solution (cytosol) Example: Enzymes in your saliva breaking down food SOLUBILIZE it
AQUEOUS SOLUTION
Is Vitalism correct?
Absolutely not. You dont need a life force to make biomolecules, you just need the right chemistry.
Starch is built from
Alpha Glucose Hydroxyl is down (Armadillos "Alpha" down on the ground) (Birds "Beta" up in the sky)
An ACID increases?
An acid increase the proton concentration Ex: HCl → H+ + Cl−
Building polymers is called
BIOSYNTHESIS (within cells) Chemistry of this is called dehydration.
WHERE does Dehydration and Hydrolysis reactions occur?
BOTH occur WITHIN CELLS. Hydrolysis also occurs outside cells
Chemical Reactions involves
BREAKING bonds and FORMING bonds Biological reactions are REVERSIBLE.
Cellular pH is maintained by
BUFFERS. They keep the pH constant. (maintain)Homestasis when [H+] drops H2CO3 <=> HCO3^- + H+ or when the [H+] rises YET: cells/organisms can alter their pH if needed! They only
Sodium hydroxide NaOH is a strong what?
Base It completely dissociates into Sodium ions and Hydroxide ions
Ammonium is a weak what?
Base NH4^+
What does Vitalism mean?
Biomolecules can only be made by living organisms. Which is false biomolecules can be made by chemistry. biomolecules are made by a 'life force'
Monomers are absorbed across the lining of our small intestine, enter are blood stream, which then proceeds to carry them to every cell of our body. They are then utilized to do what?
Build new polymers! (BIOSYNTHESIS) Chemistry of this is called dehydration.
How much does a molecule of sucrose weigh? C12H22O11
C 12x12= 144 Daltons H 1x22= 22 Daltons O 16x11= 176 Daltons = 342 Daltons
How do we obtain the weight of a mole of sucrose? C12H22O11
C 12x12= 144 Grams H 1x22= 22 Grams O 16x11= 176 Grams = 342 Grams
Polar covalent bonds are bonds between what molecules
C and O H and O C and N H and N Polar covalent bonds result in partial charges; partial charges attract water. It is the presence of O and N that explains why most biomolecules are soluble.
What 4 elements make up 96% of living matter?
C, H, O, N 7 make up 4% 14 make up <0.01% called Trace elements
Monosaccharides are formed by multiples of ________.
CH2O (only focus on left (glucose) diagram) (right is fructose)
When covalent bonds form, valence shell orbitals are going to
COMBINE and REARRANGE.
What are the 3 macromolecules?
Carbohydrates Proteins Nucleic acids Macromolecules: greater or equal to 1000 Daltons Lipids dont quite get to 1000 daltons
Which macromolecules form polymers?
Carbohydrates Proteins Nucleic acids Thats how they get to be macromolecules
What atoms can undergo sp3 hybridization?
Carbon Nitrogen Oxygen
Organic compounds are
Carbon and hydrogen containing compounds
Carbonyl Group Know the name and arrangement of atoms
Carbon double bonded to oxygen (Picture is example of a Ketone)
Number two function of Carbs?
Carbon source Monosacharides are used for building polymer
In monosaccharides for every carbon there is Hydroxyl group except for the top one which is what?
Carbonyl group (only focus on left (glucose) diagram) (right is fructose)
What 3 polysaccharides are for STRUCTURAL?
Cellulose Chitin Peptidoglycan
Sharing a pair of electrons is called
Covalent bond Which now becomes a molecule: atoms held together by covalent bonds
The behavior of the cells weak acids and weak bases will depend on the pH of what?
Cytosol And therefore it will determine their charge.
The presence of O and N will also create partial charges in the molecule, which will increase the solubility of the molecule and create places within the molecule where ___________ reactions can occur to build larger molecules.
DEHYDRATION
An atom of carbon weighs 12 ______.
Daltons
An atom of oxygen weighs 16_______.
Daltons
Weight of bio-molecules are given in?
Daltons
weight of a molecule or atom is
Daltons
Radioactive isotopes
Decay and are hazardous to life Exposure causes cancer
Which reaction PRODUCES water? Dehydration or Hydrolysis
Dehydration It has 2 reactants and 2 products
Polymers are BUILT with
Dehydration • requires an enzyme • releases energy Removing hydroxyl and a hydrogen to join atoms together. Removing water is called DEHYDRATION means BUILDING
Carboxyl group Know the name and arrangement of atoms
Double bonded to Oxygen and has a hydroxyl. Its weakly acidic. Acids give protons, proton donor. The proton [H+] can come off. It behaves as an acid and gives off its proton. The molecule that is left behind then becomes negatively charge. The pH dictates if this happened or not.
Number one functions of Carbs?
Energy (given by the monosaccharides)
Having partial charge is the same as being charged or having a formal charge. T/F
False
Which atoms are covalently bonded determines the bonding capabilities and the type of covalent bonds that will form.
For example, CHON form different numbers of covalent bonds, which will directly influence the shape of the molecule.
Moleculare shape leads to?
Function
_______________ are essential to allow molecules to react in a particular way.
Functional groups Removing hydroxyl and hydrogen to join atoms together. Picture: Hydroxyl (OH)
What has more branching starch or glycogen?
Glycogen because there is more places we can break it down.
A mole of carbon atoms weighs 12 ________.
Grams
A mole of oxygen weighs 16 ________.
Grams
weight of a mole is
Grams
Environmental conditions such as the aqueous environment cause biomolecules to clump together, which is referred to as
HYDROPHOBIC INTERACTIONS
Compounds with carbon and hydrogen only are called
Hydrocarbons
When consuming food we chew it dump saliva on it and solubilize it this is an example of
Hydrolysis
Which reaction CONSUMES water? Dehydration or Hydrolysis
Hydrolysis It has 2 reactants and 2 products
Polymers are BROKEN-DOWN with
Hydrolysis • requires an enzyme • releases energy Using water to remove monomers. Breaking with water. "Lysis" means breaking.
What does it mean to be "water-loving" -water sticks to it?
Hydrophilic You can be hydrophilic but now be soluble but alot of stuff that is hydrophilic is soluble. example: cotton towel
What does it mean to be "water-fearing"-avoids water?
Hydrophobic hydrophobic interactions! Example: oils
In monosaccharides for every carbon there is what chemical functional group
Hydroxyl (only focus on left (glucose) diagram) (right is fructose)
Hydroxyl group Know the name and arrangement of atoms
Hydroxyl group Oxygen single bonded to Carbon chain -O-H = -OH Alcohols (end with "ol") have Hydroxyl groups in them -OH Example: picture is Ethanol
Why do some functional groups ionize?
If the molecule is a weak acid or weak base.
How can you tell whether organic molecules are hydrophilic and soluble?
If they contain O and/or N, then they will be both hydrophilic and soluble.
When the carbon chains are identical in length and the arrangement of atoms is different (common in monosaccharides). Variations of the same atoms is called?
Isomers (Same molecular formula C6H12O6)
Which of the following statements about sp3 hybridization is CORRECT?
It involves the formation of four new sp3 hybrid orbitals .Correct; the four old orbitals are replaced by four new ones—each an sp3 hybrid orbital.
Whenever carbon forms single bonds only
Its orbitals undergo sp3 hybridization. both oxygen and carbon formed all single bonds so they are all undergoing sp3 hybridization.
Water makes up 70% of the weight of tissue most of what is left is
Large molecules Large molecules are made up of (Proteins, Nucleic acids, carbohydrates, and lipids)
Chains of carbon will form the backbone of
Larger organic molecules
What molecule is polar and contains thousands of atoms
Macromolecule Over a thousand Daltons typically hundreds of thousand Daltons Example: Enzyme
What is an example of an a weak ionic bond?
NaCl Cl (Chlorine) steals Na (sodium) electron. Now sodium has a full positive charge and Chlorine a full negative charge to make an ionic bond.
If the pH is low a weak acid ionized will or will not ionize?
No it will not ionize. Low pH means we have a lot of protons and the environment is acidic. High pH means we have a lot of hydroxide ions and the environment is basic.
Is water a charged molecule?
No! Water has partial negative charge near its oxygen and partial positive charge near its hydrogen but it is a polar molecule because the electrons are shared unequally..
Electronegativity Pauling scale
O 3.5 N 3.0 ^ High ------------ C 2.5 v Low H 2.1
van der Waals Interaction
Occur between transient partial charges in nonpolar molecules
Every oxygen forms _____ bonds Every carbon forms _____ bonds
Oxygen forms 2 bonds Carbon forms 4 bonds (only focus on left (glucose) diagram) (right is fructose)
Phosphate group Know the name and arrangement of atoms
Phosphorus single bonded to 3 oxygens and double bonded to 1, (5 bonds total) it violates the octet rule (10 electrons in valence shell) . Phosphorus is an acid. (OPO3^2-) Phosphates store energy - ATP!
The 3D shape of biomolecules is ESSENTIAL for their function—it allows two molecules to
RECOGNIZE and INTERACT with one another.
In our cells (aqueous environment) monosaccharides actually have the form of _______.
RINGS in an aqueous environment
Ionic substances are _______ in water. Charged substances!
SOLUBLE
Biological molecules usually bear partial and full charges, which dictate their
STRUCTURES and FUNCTIONS. Ex: DNA and proteins.
Functional groups are going to increase the __________ of biomolecules.
Solubility. because we are adding oxygen and nitrogen
Plants store alpha glucose as
Starch
What 2 polysaccharides are for STORAGE
Starch Glycogen
In orbital hybridization the number of orbitals
Stays the same
Is hydrocloric acid HCl a strong or weak acid?
Strong It completely dissociates into Protons and Chloride ions
For a hyrdrogen bond to form it must be bonded to a?
Strongly electronegative atom Oxygen or Nitrogen
3 common disacchrides are
Sucrose, maltose, and lactose. All C12H22O11
Sulfhydryl Group Know the name and arrangement of atoms
Sulfer makes 2 bond. Form special covalent bonds in proteins - S - H = -SH
In order for a hydrogen atom to be capable of hydrogen bonding, what is required?
The hydrogen must be covalently bonded to a strongly electronegative atom.
When glucose ring forms there is 2 possibilities
The hydroxyl group is DOWN Alpha glucose. (remember: Armadillos DOWN on the ground) The hydroxyl group is UP its Beta glucose. (remember: Birds UP in the sky) They are isomers (same atoms arranged differently.
How is the cell able to generate such large molecules from a construction or mechanistic stand point?
These large molecules are built through a strategy called POLYMER CHEMISTRY. They are all macromolecules.
Most enzymes are soluble. (T/F)
True
Most isotopes are stable? T/F
True
Enzyme Function Requires?
Weak interactions
Covalent bonds hold a hormone receptor together inside the receptor between hormone and receptor are what kind of interactions
Weak interactions perhaps hydrogen bonds secures the hormone when the receptor receives it
How does a monosaccharide ring form?
When atoms are joined by SINGLE BONDS you can rotate the atom and the chain becomes flexible
Aldehydes are
When the carbonyl group is at the end of the chain (orange C=O)
Ketones are
When the carbonyl group is in the middle of the chain (orange C=O)
In synthesis of disaccharides why is it not C12H24O12?
When you do dehydration you remove a water so now you get C12H22O11
Energy level is a term to describe?
Where the electron is in relative to the nucleus
Is glucose a polar molecule?
Yes. It has polar covalent bonds Polar molecules are SOLUBLE
PURE WATER at equilibrium:
[H+] = [OH−] = 10^−7 M = 1/10^7 = 1/10,000,000 of a mole per L
Concentrations: [H+] x [OH−] = 10−14 M (always!) If the proton concentration is [H+] = 10^−8 M then the Hydroxide concentration must be [OH−] =
[OH−] = 10^-6
Concentrations: [H+] x [OH−] = 10^−14 M (always!) If the proton concentration is [H+] = 10^−5 M then the Hydroxide concentration must be [OH−] =
[OH−] = 10^-9
If Carbonyl group is attached to a Hydroxyl on one side what is it called?
a Carboxyl
Polar Covalent bond
a bond were the electrons are shared unequal for an example H2O is a polar molecule
Sometimes when hydrogen bond to an oxygen the water molecule will loose ________.
a hyrdogen proton and obtain a negative charge. H2O <=> OH− + H+ 2H2O <=> OH− + H3O+
A covalent bond between an oxygen atom and a hydrogen atom is best described as
a polar covalent bond
sp3 hybridization requires
a second shell of electrons and only happens when single covalent bonds form
About how much longer was life a water-based phenomenon, in comparison to the time there has been terrestrial life?
about 6 times as long 3,000,000,000 years / 500,000,000 years = a 6-fold difference Earth Formed: 4.54 billion years ago Life appeared: 3-4 byo Life moves to land: ~ 500 myo So: Life confined to water for 3 billion years, before becoming land-based.
"Octet rule" means
after a reaction the elements have 8 electrons in their valence shell. Except hydrogen since it only has one shell it will have 2 electrons in its outer shell
Many ______ are weak acids and weak bases.
biomolecules
Which of the following weak interactions involves nonpolar molecules or nonpolar parts of molecules?
both van der Walls interactions and hydrophobic interactions
4 major types of biomolecules are
carbohydrates lipids proteins nucleic acids
Number one rule of organic chemistry is
carbon makes 4 bonds to give it the octet it needs.
Hydrophobic interactions
clustering of nonpolar molecules away from H2O Example olive oil in water.
Molarity is a unit of
concentration, equal to the # of moles of solute in 1 L of solution.
Hypothetically speaking, which subatomic particle(s) of an atom could be altered in number without changing the identity of the atom (or which element it is)?
electrons or neutrons
Hydrocarbons are energy _____________.
energy rich. but otherwise not amenable to complex chemistry.
Strength of ionic bonds depends on
environmental conditions in water: < 1/10 covalent bonds cells = 70% water
Nonpolar covalent bond
equal sharing of electrons examples are H2, O2, and CH4 (methane)
Biological weak interactions do not have
functional relevance to cells
3 common monosaccharides are
glucose, fructose, and galactose.
How do we store alpha glucose
glycogen stored primarily in the liver and a little in the muscle we only store a 1 day supply
basic solutions have pH
greater than 7
0.5 molar mean _____.
half of a mole in a Liter.
Phosphorus VIOLATES the 'octet rule' in biological molecules by
having more than eight electrons in its valence shell after covalent bonding
Which of the following types of chemical bonds and interactions are relatively WEAK in cells?
hydogen bonds and ionic bonds
Between molecules is intermolecular interactions inside the molecules is
intramolecular interactions example of this when we mentioned that starch and glycogen polymers formed coils, or helicies
Four Weak Interactions in Biology
ionic bonds hydrogen bonds van der Waals Interactions hydrophobic interactions
Chains of carbon can vary in
length shape # of bonds
acidic solutions have pH
less than 7
Polymers are
molecular 'chains' built from similar OR identical building blocks ("monomers" smaller molecules).
Why are polymers broken down to monomers?
monomers are used for ENERGY Monosaccharides are a tremendous energy source for the cell.
In Carbohydrates the monomer, sugar is called the
monosaccharides The unit by which we build polysacharides
Water is a versatile solvent and most biomolecules will
most biomolecules will dissolve
Every oxygen in glucose has a partial ____ charge.
negative When bonded twice
Intramolecular weak interaction form within large molecules due to their ________________________ , and have a tremendous influence on the final shape of the molecule.
partial and full charges
Which of the following organisms are classified as eukaryotes? (Please consult the evolutionary tree diagram from the slides and Chapter 1!)
plants and protists
Every hydrogen and carbon in glucose will have a partial ___ charge.
positive
Biomolecules are built and constructed by
putting small molecules together to make a larger molecule the process by which this happens is called a CHEMICAL REACTION
There are 1,000s-1,000,000s of ______, _______, and _________ in solution, for ONE biochemical reaction.
reactants, products, and enzymes in solution, for one reaction # molecules → MOLE → # g, mg, mg AMOUNT _______________________ ↓ _________molarity (M, mM, mM) _____________CONCENTRATION
pH of the solution is important, because it will dictate the charge of weak acidic and basic functional groups. The full charges that occur at cellular pH allow for ionic bonding and also affect the
shape of molecules
The requirement for sp3 hybridization is
single bonds only (atoms sharing 2 electrons)
Acids and bases means that
some of the solutes in a solution are charged and it has to do with the pH of the solutions because charges stick together and opposites attract.
The shape of methane (organic compound) is tetrahedral. The Hydrogens are located in the corners due to
sp3 Hybridization
Cohesive means
sticks to itself
Adhesive means
sticks to other things
When you have enough energy you begin to
store surplus monosccharides. You do this by building them into polysccharides. Polysccharides usually serve a storage role. They are also primary building material in plants.
Carbohydrates are?
sugars and 'sugar polymers' •monosaccharides •disaccharides •oligosaccharides •polysaccharides
High specific heat means
takes a lot of energy to raise the temperature (resists change) Hydrogen bonding is the reason for high specific heat
A mole is:
the # of GRAMS of an atom or molecule. A Mole is numerically the same as a Dalton.
Different elements have different behavior, the behavior is dictated by
the number of electrons in the valence shell (outermost shell)
If the pH is 3 what would the proton and hydroxide ion concentration be?
the proton concentration [H+]=10^-3 the hydroxide ion concentration [OH-]=10^-11
When pure water reaches a chemical equilibrium between whole water molecules and dissociated ones
the reaction continues to run in both directions, the concentrations of reactants and products are no longer changing, and the speed of the forward reaction is equal to the speed of the reverse reaction
All polymers are BUILT and BROKEN-DOWN by
the same basic chemistry.
Chemical equilibrium is the point in a chemical reaction when
the speed of the forward reaction is equal to the speed of the reverse reaction Although the concentrations of reactants and products are not equal, at equilibrium their concentrations are no longer changing.
Chemical equilibrium is
the state of a reaction where the rate forward EQUALS the rate of the reverse reaction
What weak interactions involves nonpolar molecules
van der Waals interactions hydrophobic interactions
Cells are SURROUNDED by
water and CONTAIN water. (70% of the weight of the cell)
Water is
water is 'sticky' •cohesive (sticks to itself) •adhesive (sticks to other things) •high specific heat