Biology Lecture - Final Exam - Study Guide

What to think of when drawing dot diagrams

think of only valence shell and trying to fill valence shell

covalent bonds

strongest bond. bond where the elements are sharing valence electrons

electronegativity

propensity of an atom to pull on electrons. electrons are in a cloud around the nucleus and protons pull on this cloud

factors that affect electronegativity

1. how many protons there are

2. how close the electrons are

elements with the highest electronegativity

oxygen and fluorine

carbon and hydrogen are:

have similar enough electronegativities that where there is not much of a difference between them

relative electronegativities tell us:

if a covalent bond is polar or nonpolar

oxygen in water

oxygen has a higher electronegativity and is better at pulling electrons towards its nucleus. causes it to have slightly more negative charge (partial negative)

hydrogen in water

hydrogen has a lower electronegativity and is worse at pulling electrons towards its nucleus. causes it to have slightly more positive charge (partial positive)

noticeable difference in electronegativity

polar bond

unnoticeable difference in electronegativity

nonpolar bond

hydrogen bond

an attraction between a partial negative on one molecule and a partial positive on another molecule or in different regions of the same molecule

H+

1 proton with 0 electrons

acid

a substance that increases the hydrogen ion concentration of a solution. when an acid is in a solution it can give off an H+

Strong acids

HCl, H2SO4, HNO3

HCl

H+ + Cl-

H2SO4

H+ + HSO4-

HNO3

H+ + NO3-

factors that affect the strength of an acid

1. Strength of the HA bond

Strength of the HA bond

the more polar the H-A bond, the more likely it is for H+ to come off. if the electron is spending more time with another element, then the hydrogen is more likely to come off of the molecule

COOH

high electronegativity of O double-bonded to C causes more electrons to move towards O. (double bonds means it is dealing with twice the amount of electrons) O attached to H is going to pull especially hard on electrons of H because the other O is pulling so hard on C's electrons already.. This makes it a weak acid (H sometimes comes off)

COOH

carboxylic acid (commonly found in organic acids)

anything that has carboxyl will:

function as a weak acid

bases

A substance that reduces the concentration of hydrogen ions in a solution

common bases

NaOH, NaHCO3, NH3

NaOH

Na+ + OH-

NaHCO3

NaHCO3 + H+ --> Na+ + H2O + CO2

NH3

NH3 + H+ -> <- NH4+

Weak acid in water

CH3COOH + H2O <- -> CH3COO- + H+

Weak base in water

NH3 + H2O -> <- NH4+ + OH-

pH scale

-log[H+]

Why does the concentration of H+ matter

it affects the structure and form that an amino acid is in. an amino acid could be charged differently in solutions with a high or low pH

functional groups

groups of atoms commonly found together in molecules of living things. when present they have an effect on the molecule

carbon is important because

carbon can make 4 bonds and makes a great foundation for molecules

carbon line and ring drawing

end or bend is a carbon. carbon forms 4 bonds, so any bond not shown is a hydrogen

how to determine how a functional group will impact molecule function

Is it polar?

is it an acid or negatively charged?

is it a base or positively charged?

hydroxyl group

present in alcohols. the oxygen will have a partial negative and the hydrogen will have a partial positive

hydroxyl group questions

Is it polar? - yes

is it an acid or negatively charged? - no (pull is not strong enough because of what the OH is attached to)

is it a base or positively charged? - no

carbonyl group

double bond between carbon and oxygen, so its a very polar bond

carbonyl group questions

Is it polar? - yes

is it an acid or negatively charged? - no

is it a base or positively charged? - no

forms of carbonyl

ketone and aldehyde

what is this?

carbonyl ketone

what is this?

carbonyl aldehyde

carboxyl (carbonyl + hydroxyl but is an independent molecule)

Is it polar? - yes

is it an acid or negatively charged? - yes

is it a base or positively charged? - no

what is this

amino group

amino group questions

Is it polar? - yes

is it an acid or negatively charged? - no

is it a base or positively charged? - yes

what is this

methyl group

methyl group

Is it polar? - no

is it an acid or negatively charged? - no

is it a base or positively charged? - no

phosphate group questions

Is it polar? - yes

is it an acid or negatively charged? - yes

is it a base or positively charged? - no

what is this

phosphate group

alpha carbon

carbon that is bonded to both the amino and carboxyl groups in an amino acid

what reaction creates a bond between two amino acids?

dehydration synthesis

what is the resulting polypeptide of the amino acids bonding called?

amino acid residues (entirety of both molecules is not there anymore)

what is the bond between two amino acids?

peptide bond

what is the first structure of polypeptides?

primary structure

define primary structure

a sequence of polypeptides that form the base of that protein. held together by covalent peptide bonds.

define secondary structure

forms via hydrogen bonds within the polypeptide backbone, forming folded and helical shapes

hydrophobic interactions

nonpolar things interacting with other nonpolar things

types of secondary structures

alpha helix and beta pleated sheet

what is this

alpha helix

what is this

beta-pleated sheets

define a tertiary structure

tertiary structure refers to the three-dimensional folding of a protein due to interactions between R-groups of the same polypeptides

quaternary structure

not all proteins have this. same bonds as tertiary structures. formed via R-group interactions of different polypeptide chains (multiple chains)

hydrogen bonds

weak attraction between a hydrogen atom and another atom (partial charges attracted to one another)

ionic bond

A chemical bond resulting from the attraction between oppositely charged ions.

disulfide bridges

A strong covalent bond formed when the sulfur of one cysteine monomer bonds to the sulfur of another cysteine monomer.

types of bonds/interactions that make a quaternary and tertiary structure

disulfide bridges, hydrogen bonds, ionic bonds, hydrophobic interactions

protein denaturation

process in which a protein loses its 3D structure

things that denature proteins

heat above 50 C, alcohols, salts of heavy metals, alkaloid reagents

heat above 50 C

heat increases means increased kinetic energy, disturbing hydrogen bonds and hydrophobic interactions

alcohols

these form their own hydrogen bond due to OH. this disrupts the intramolecular bonds

salts of heavy metals

forms strong bonds with acidic R-groups

alkaloid reagents

combine with positively charged R-groups. also disrupts ionic bonds

why does water travel thru aquaporins so well reason 1:

Residual carboxyl groups from the backbone form H-bonds with incoming water make a conduction pathway

why does water travel thru aquaporins so well reason 2:

Two asparagine R-groups cause water to turn in the middle of the channel

why does water travel thru aquaporins so well reason 3:

R-groups with rings create a selectivity filter blocking molecules larger than water

How does the structure of insulin facilitate its function? reason 1:

Disulfide bridges between cystines make a stable protein that can travel through the bloodstream

How does the structure of insulin facilitate its function? reason 2:

Shape of insulin facilitates binding to insulin receptor

How does the structure of insulin facilitate its function? reason 3:

Histidines bind to zinc allowing insulin to be stored as a hexamer

c-peptide in insulin

a chain that is cut out and sometimes used to determine metabolic disorders

what is the relationship between a protein and its receptor?

they are complementary in structure and charge, allowing for a perfect fit

insulin

a hormone that regulates glucose levels within bloodstream by converting it into glycogen and storing it in the liver

insulin triggers...

movement of glucose into cell via a cascade and glucose transporter

___ allows insulin to bind to ____

histidine; zinc

aquaporin

a channel protein that is embedded into a membrane and allows water to move into cell (passive transport)

what does water do as it moves through aquaporins?

turns 180 degrees for efficiency and it allows for water to move in a single line

if you have nitrogen, the R-group always a base unless:

it has a C double-bonded to an O

glucose can either be drawn as..

linear or ring

normally simple carbs follow this formula:

(CH2O)*n

ribose

A five-carbon sugar present in RNA

functions of carbs in living things

short-term energy storage, used in plant structure, involved in information molecules, cell to cell recognition

what is an example of a carb used for short-term energy storage

glucose

what is an example of a carb used for structure

cellulose

what is an example of a carb used for information molecules

ribose or deoxyribose in DNA or RNA

what is an example of a carb used for cell to cell recognition

carbs on surface of membrane, key in recognition

things to keep in mind when drawing dehydration synthesis reaction between amino acids

1. it must be a bond between the amino terminal and carboxyl terminal

2. 1 H from NH2 and the OH from COOH is taken out to form H2O

3. The NH2 and COOH that are involved must be attached to the alpha carbons of its respective amino acid

hydrophobic R-groups are composed of which atoms

carbon and hydrogen

acidic R-groups contain ____

carboxyls

what bonds are acidic amino acids likely to form in tertiary structure?

ionic and hydrogen bonds

Basic R-groups contain ______ atoms

nitrogen and hydrogen