BIS2A Midterm 1

Evolution

change over time

Natural Selection

filtering of traits to lead to better fitness, pressure put on a population so that survival of the fittest appears (genetic changes)

Scientific Method

make an educated guess, design experiment to test, analyze data and figure out what it means

Early Earth

very hot (terrestrial and marine volcanoes), oceans very acidic and mineral (Ni, Fe) rich, full of gas but little to no O2 available

When did liquid water form

4 billion years ago

What type of environment did life evolve in?

hostile

98% of living organisms are made up of?

Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur

Life is made up of _____ which are made up of _______

atoms; subatomic particles (protons, neutrons, electrons)

Electronegativity

pull atoms have for electrons, fundamental principle of bonding

Ionic bonding

electrostatic interactions formed between ions of opposite charges, high difference in electronegativity between atoms, transfer of electrons, can form a salt, any individual bond is pretty weak

Covalent bonds

sharing of electrons, electronegativities are decently close to eachother

Polar covalent bonds

unequal sharing of electrons, partial positive and negative charges

Nonpolar covalent

equal sharing of electrons

Hydrogen Bonds

interaction between dipoles, single H bonds are weak but as a group are strong, either Oxygen or Nitrogen

Water

universal solvent, liquid at room temp due to bent geomentry

Hydroxide Ion

OH, overall negative charged base

Hydronium Ion

H3O, overall positively charged acid

Equillibrium

dynamic, but not able to change, net-change of 0

Steady-state

a state. with no net-charge, able to change, dynamic

pH=

-log10[H+]

Biomolecules

molecules involved in biology (proteins, lipids, carbohydrates, nucleic acids)

Condensation

bond formation with loss of water molecules, water is a product of reaction

Hydrolysis

bond breakage with addition of water, water is a reactant

Lipid function

store or gather energy (fats to burn, photosynthetic pigments), structure (membranes), insulation (thermal, electrical), signaling molecules

Plant fats

unsaturated, liquid at room temp

animal fats

saturated, solid at room temp

carbohydrates

sugars, name is based on number of carbons

Nucleic acids

made up of carbohydrates, pentose, attached to pentose, attached to phosphate group

Function of nucleic acids

energy, coding of genetic information, and signaling

proteins

linear array of amino acids, amino acids are the building blocks

Function of proteins

enzymes, membrane structure, signaling molecules

Types of transport

uniporter (one direction), symporter (brings at least 2 items together into or out of the cell), antiporter (brings something in and out)

Active transport

requires energy by cell to do it, costs something usually ATP

nonpolar covalent EN value

0-0.4

polar covalent EN value

0.5-1.9

ionic bond EN value

2.0+

EN of Sulfur

2.4

EN of Phosphorus

2.1

EN of Oxygen

3.5

EN of Nitrogen

3.1

EN of Carbon

2.5

EN of Hydrogen

2.1

carboxylic acid

organic acids found in some lipids and are a feature of proteins, can form ionic bonds when deprotonated

protonated carboxylic acid

O

||

R—C—OH

deprotonated carboxylic acid

O

||

R—C—O^-

Amine

weak bases, feature of proteins, form ionic bonds when protonated

deprotonated amine

H

|

R—N—H

protonated amine

H2

|

R—N^+—H

phosphate

negatively charged found in nucleic acids

phosphate functional group

O

||

R—O—P—O^-

|

O—H

Amide

defining features of proteins

Amide functional group

O. H

||. |

R—C—N—R

Hydroxyl

commonly found in carbohydrates and amino acid R groups

Hydroxyl function group

R—OH

Methyl

very stable and occur in many organic compounds

methyl functional group

H

|

R—C—H

|

H

Thiol

R—SH

Thioester

O

||

R—C—S—R

Repeating unit of carbohydrates

H-C-OH

Repeating unit of lipids

C-C bonds with OH

Repeating unit of nucleic acids

5 carbon or phosphate group

Repeating unit of proteins

amide groups

Polar compounds can interact with water by forming ?

Hydrogen bonds

_____ is the measure of how strongly an atom will pull on an electron

Electronegativity

CH3 is an example of a nonpolar ______ found on lipids

functional group

Basic structure of amino acids

backbone (amine group and carboxylic acid group attached by a central carbon- alpha carbon) and a variable group

N-terminus

end of protein with free amino group

C-terminus

protein end that has the free carboxylic acid group

What does protein folding do?

dictates the function of the protein

Primary structure of proteins

sequence of amino acids bound together by peptide bonds (polypeptitide)

Secondary structure of proteins

folding of polypeptide chains, stabilized by hydrogen bonds (alpha-helix, beta-pleated sheets, and loop), rotations of bonds around alpha carbons

Tertiary Structure of proteins

forms when the R groups of the amino acids begin to interact, further folding and twisting secondary structures, sometimes can be final structures, “ribbon” traces the path

quaternary structures of proteins

2 or more tertiary structures (subunits) combine to fold together into a final active protein

What bond types occur in secondary structure of a protein?

Hydrogen bonds

What bond types occur in tertiary structure of a protein?

Hydrogen bonds, ionic bonds, hydrophobic interactions, disulfide bridge, covalent interactions

Why do proteins fold?

to hide hydrophobic (non-polar) parts

Enzyme

biological catalyst, speeds up reaction without being consumed

Proteins can be altered through the process of ________, which adds a phosphate group to the enzyme

phosphorylation

Some enzymes have a 2nd site where compounds can bind called?

allosteric site

Cell Membrane

selectively permeable membrane most commonly made up of phospholipids

Phospholipids contain?

hydrophilic head group and 2 hydrophobic tails

lipid bilayer

phospholipids will spontaneously arrange themselves into this in the presence of water, 2 layered sheet only a few nanometers thick

Hydrogen is composed of?

1 proton, 1 electron, 0 neutrons

What are some elements that are necessary for life but typically not found in much abundance

Calcium, Chloride, Sodium, Iron, Cobalt, Magnesium, Potassium

Example of polar bonds but nonpolar molecule

CO2, bond dipoles cancel eachother out

Hydrogen bond donor

molecule that contributes the partially charged hydrogen atom

hydrogen bond acceptor

molecule that has the partially negative charge

Water is a _______ to other polar molecules and ionic compounds

solvent- things can dissolve in it

Hydration layer/shell/sphere

layer of partially contsrained waters surrounding a solute particle

Dissociation

occurs when atoms or groups of atoms break off from molecule and form ions

dipole-dipole interactions

interaction between 2 permanent dipoles, repulsive (same charge) or attractive (separate signs)

Van der Waals Forces

all molecules experience, interaction found when molecules get very close together 4-5 angstroms

pi Interactions

involvement of pi bonds, specific type of covalent bond between 2 atoms in which neighboring electron orbitals are close enough to overlap

pi bonds are found where?

aromatic ring structures like amino acids, vitamins, cofactors, and nucleic acids

Examples of lipids

fats, oils, waxes, phospholipids, steroids

Lipids and water

due to the abundance of nonpolar functional groups lipids are hydrophobic and most have low solubility in water

Triglyceride

hydrophobic, best known for roles in body fat and plant oils

Triglyceride composition

polar head group- a single glycerol molecule which is composed of 3 carbons, 5 hydrogens, and 3 OH groups

nonpolar fatty acid tail- 3 hydrocarbons, polar carboxyl group

What are the physical properties that vary fats

number of carbons in hydrocarbon chain and number of desaturations, double bonds in hydrocarbon chain

Desaturated fats

introduces a double bond and causes a kink