basics of biochem

Question 1

what order do orbitals and shells fill in?

Answer 1

• Orbitals and shells fill with e– in order from _lowest to highest energy

Question 2

define valence shell and valence electrons

Answer 2

• Valence shell: outermost shell, containing electrons
• Valence electrons: outer shell electron associated with an atom that can participate in the formation of a chemical bond

Question 3

how many valence electrons does oxygen have? how many to fill its valence shell?

Answer 3

• How many valence electrons does Oxygen have? 8

* How many electrons are needed to fill its valence shell? 2 more

Question 4

atoms with incomplete valence shells are ____?

Answer 4

• Atoms with incomplete valence shells are _Reactive______________
o Interact with other atoms to complete their valence shells

Question 5

define chemical bonds. what do they allow?

Answer 5

• Chemical Bond Definition: Attraction between atoms that holds them together due to sharing or exchanging of electrons
o Allows atoms to complete valence shell to create a stable atom

Question 6

what bonds are there in biological systems?

Answer 6

• In biological systems there are . . .
o Strong bonds: Covalent and ionic
o Weak bonds: Hydrogen bonds
o Sharing results in a chemical bond

Question 7

define covalent bonding. what does it form?

Answer 7

• Definition: sharing of electrons by two atoms to complete their valence shells
• Forms a molecule
o A group of atoms held together by covalent bonds
o 1 e– pair shared = single bond ie. Water
o 2 e– pairs shared = double bond ie. O2

Question 8

• How are electrons shared? Use electronegativity to determine

Answer 8

o	Higher χ = pull toward nucleus
o	H – 2.1
o	C – 2.5
o	N – 3.0
o	O – 3.5
up to 2.5 is weak

Question 9

define non polar covalent bond

Answer 9

• Non-polar covalent bond: Electrons are shared equally
o Occur between atoms of the same χ
o Difference of less than 0.4

Question 10

define polar covalent bonds

Answer 10

• Polar covalent bonds: Electrons are not shared equally
o Occur between atoms of different χ
o Results in separation of charge- partial negative charge or partial positive charges
o If the difference in electronegativity is greater than 0.4, it is polar

Question 11

describe ionic bonds

Answer 11

• Atom with high electronegativity takes the lone valence electron from atom with low electronegativity → produces ions -completes its valence shell
• Strong attraction forms between anion and cation

Question 12

when are ionic bonds formed?

Answer 12

ionic bonds are formed when one atoms takes a valence electron from another atom
the ionic bond is actually an attraction between opposite charges

Question 13

define hydrogen bonding

Answer 13

• Definition: Attraction between the δ+ H atom of one polar covalent bond and the δ– atom of a second polar covalent bond

Question 14

what are the 5 rules of hydrogen bonding?

Answer 14

1. Each atom in the H-bond is covalently bonded to something else
2. An H-bond always involves a partially positive H atom
3. The second atom in an H-bond is always partially negative (usually O or N)
4. Electrons are not shared in an H-bond. It is an attraction between opposite partial charges.
5. Each H atom can form one H-bond.

• H-bonds are weak in biological settings, but very important!

Question 15

what is water? 3 properties?

Answer 15

• Water is the biological solvent
o Interacts with all cellular components
o Determines cell structure and function
o Highly polar

Question 16

what can water bond with?

Answer 16

• Water can H-bond with polar molecules- other things containing partial charges

Question 17

describe hydrophilic properties (3)

Answer 17

o Have polar covalent bonds
o Form H-bonds with water
o Dissolve in water

Question 18

describe hydrophobic molecules

Answer 18

o Have non-polar covalent bonds- don’t have partial charges, cant interact with water
o Little affinity for water – cant form H bonds
o Interact with other non-polar molecules and excludes water

Question 19

what is carbon? how many bonds can it form? what are ch only chains called?

Answer 19

• Carbon is the basis of all organic molecules
o Forms 4 covalent bonds- bc 4 unpaired valence electrons
o Can form chains
o C + H - only chains called hydrocrabons

Question 20

what variations in carbon chains can be used to produce a variety of different molecules?

Answer 20

length
double bond position
branching
presence of rings

Question 21

what are geometric isomers formed how?

Answer 21

• Carbon chains with double-bonds can form geometric isomers:
o Atoms are in the same order, but with a different spatial arrangement
cis and trans isomers

Question 22

cis vs trans isomers

Answer 22

cis: the two xs (any atom) are on the same side
trans: the two Xs are on opposite sides