Bio Exam 2: Chemistry and Macromolecules

Protons

define an element (the same element cannot have a different number of protons), has mass, has positive charge

Neutrons

neutral, same element can have different numbers of neutrons

Electrons

negative charge, virtually no mass, number changes

Atomic mass

number of protons and neutrons (weight)

Atomic number

number of protons

Electrons in each orbital

2 (think box diagram in 103)

1st shell holds - electrons

2

2nd shell holds - electrons

8

Valence electrons

electrons that fill outermost shell (trying to get to 8 by forming bonds)

Covalent bonds

2+ atoms shares electrons

Ionic bonds

atoms steals/gives electrons

Nonpolar bonds/ diatomic molecules

sharing is equal (neither side is stronger than the other) (Hydrogen and Carbon are very nonpolar molecules)

Polar bonds

sharing is not equal (one atom holds bonds closer to themselves)

Two elements that mainly form polar bonds (bullies)

Nitrogen and oxygen

Ionic bonding

stealing/giving of electrons, always results in a charge (molecule that gain electron has negative charge and molecule that gave electron has a positive charge)

Water is (non/polar)

POLAR

Hydrophilic (polar)

attracted to water (because water is also polar and polar and polar attract)

Hydrophobic (nonpolar and nonionic)

Repels water (because polar does not like nonpolar)

How can you have polar bonds but a nonpolar molecule

If the polar bonds equal out on both sides EX: O=C=O the oxygen pulls the carbon towards it equally so the force equals out and makes the molecule SYMMETRICAL

Polar molecules are

asymmetrical EX h2o is bent because oxygen has a strong pull on both hydrogens

Ionic bonds are different from covalent bonds because

ionic bonds do not share electrons like covalent, they steal them

How are hydrogen bonds different from covalent and ionic bonds

hydrogen bonds form when a hydrogen gains a slightly positive charge from being attracted to a very negative element (like O or N). Hydrogen bonds are weaker than covalent or ionic bonds

Water properties

cohesion, surface temp, density, solvent

Water cohesion

Hydrogen bonds form between water molecules causing water to “stick together” which allows for water to travel up the roots and stems of plants

Water density

density decreases as water freezes (turns to ice) because of the crystalline lattice formed between molecules having a lot of space between them. This makes ice float which means things living in water bodies do not freeze when the temperature drops

Water as a solvent

the charges of water molecules allow for them to dissolve many substances helping with transport of nutrients (transported as aqueous solutions)

Water surface tension

water b

Hydrophobic molecules in water

group together so hydrophilic heads are exposed but hydrophilic tails are not (think circle or double layered line of molecules)

Ionization

when water molecules break apart H2O←→

Acid

High H+ concentration

Base

OH- concentration (combines w H+)

pH scale

scale from 1-14 that measures how basic/how many OH- (8-14), neutral (7), or acidic/how much H+ (1-6) something is/has

pH equation

-log[H+]

A lower pH means

Higher [H+] EX: 10^-3 is a low, acidic pH of 3

A higher pH means

Lower [H+] EX: 10^-8 is the high, basic pH of 7

A solution with pH 6 has how many more H+ ions than a pH of 7

10 times as many

Dehydration synthesis (condensation rxn)

removal of water molecules to bring other molecules together/form bond

Hydrolysis

breaks bonds using water (reverse of dehydration synthesis)

Hydroxyl group

OH EX: -OH

Methyl Group

CH3 EX:

Carbonyl

C=O EX:

Carboxyl

O-C-OH EX:

Amino Group

NH2 or NH3 (one H will have positive charge (H+)) EX:

Phosphate

PO3-?

Sulfhydryl

-SH EX:

Hydrogen v.e.-

1

Oxygen v.e.-

2

Nitrogen v.e.-

3

Carbon v.e.-

4

Carbohydrates characteristics

C and H2O, polar, dissolves in water

Monosaccharides

quick energy and used in DNA or RNA

Disaccharide

quick energy in diet EX: glucose

Polysaccharides

energy storage EX: glycogen or starch

Nucleic Acid (nucleotide)

contains phosphate group, sugar, and NITROGEN

Lipids (fats and steroids)

energy storage, long chains of hydrophobic regions (H and C) EX cell membrane

Saturated fat (lipid)

all bonds are H-C (no bend)

Unsaturated fats (lipids)

has double bonds (=)

Phospholipid

C and H tail (nonpolar and saturated) but polar and unsaturated head

Proteins (amino acids)

1) Central carbon 2) amino group 3) carboxyl group 4) side chain (r group)

How to classify protein hydrophilic of hydrophobic

look at side chain

Triglycerides

type of lipid involved in energy storage (1 molecule of glycerol and 3 fatty acids)

Steroid hormones

type of lipid that can pass through membranes formed by phospholipids

Nucleic acids

long chains of nucleotides that contains phosphate group, sugar, and nitrogen

Similarities between ATP and nucleic acids

ATP has a single nucleotide but is a protein and nucleic acid contains multiple nucleotides

Proteins role

found in cell membrane and is responsible for transport across membranes, structure, signaling, and storage

protein synthesis

DNA → mRNA → Amino acids → Protein

• DNA contains the instructions.

• mRNA carries the instructions.

• tRNA brings the building blocks (amino acids).

• Ribosomes assemble the amino acids into a protein.

Primary structure of protein

covalent peptide bonds between a carboxyl and an amino group formed through dehydration synthesis (chain of amino acids)

Secondary structure of protein

folding of the polypeptide backbone due to hydrogen bonds (causes sprials)

tertiary protein structure

overall shape of polypeptide chain (includes all the sidechains and has a nonpolar inside polar outside) because side chains are included the spirals fold into different shapes

quaternary protein structure

multiple tertiary structures together as one

Sketch of protein structures

Why cells need a biological membrane

controls what enters and exits cell, protects cell, maintains internal balances (pH, concentration, etc.), holds cell together, allows for communication between other cells

How do lipids come together to form membranes

polar heads come together to encase nonpolar tails and protect them from water (circle or bilayered) because of 2nd law of thermodynamics

Weak interactions between lipids in membranes

hydrophobic sticks with hydrophobic (tails by tails) and hydrophilic wants to be by other hydrophilic (heads by heads) which causes water and the hydrophilic parts of the cell to be by each other forming H bonds. because most of cell has weak bonds or attraction it remains fluidlike

Water excludes lipids by

forcing lipids (which are typically nonpolar) to group together (imagine oil in water) reducing amount of space lipids take up so it does not decrease entrophy

membrane fluidity

the ability of molecules to be able to flow through or within the lipid bilayer

unsaturated lipids and fluidity

unsaturated lipids have double bonds, causing their tails to have bends, which means they are not able to pack as closely together, causing them to be more flexible/fluidlike

cholesterol and fluidity

at high temps cholesterol reduces the movement of phospholipids so the membrane is not too fluid and at low temps it prevents them from packing too close together and causing the membrane to be too rigid

membranes are semi permeable meaning

they allow some molecules to pass through while others cannot depending on things like shape, size, polarity, and charge

Simple diffusion

molecules pass straight through membrane needing no energy (passive) and no protein transporter (nonpolar molecules and very small polar molecules)

facilitated diffusion 1

molecules pass through a channel protein but require no extra energy (passive) or interaction from protein (ions)

facilitated diffusion 2

molecules (polar) pass through a transporter protein but still require no extra energy to do so

Active transport

polar molecules pass through transporter protein to go AGAINST concentration gradient (so they require extra energy to do so) (ions or polar)

passive transport

no extra energy required

active transport

requires extra energy

facillitated diffusion

requires protein channel

simple diffusion

molecules pass directly through membrane

osmosis is

diffusion of water down its concentration gradient (moves to high solute concentration so it can dilute more)

tonicity is

comparison of hypotonic (less concentrated) hypertonic (more concentration) and isotonic (equal concentration) inside and outside of cells

prokaryotic cell

bacteria cells, NO nucleus or membrane bound organelles, small, binary fusion reproduction

eukaryotic cell

has membrane bound organelles and nucleus, plants and animal cells

Plant cells specific

cell wall for support, choloroplasts (photosynthesis), central vacuole (storage)

animal cell specific

lysosomes (break down)

cytoplasm

fluid and organelles

cytosol

fluid component of cytoplasm

cytoskeleton

proteins in cytoplasm that have structural support (animal cell specific (plant have cell wall))

nucleus

stores DNA and has pores to let out RNA

mitochondria

powerhouse-performs respiration, breaks down glucose/metabolism; has its own DNA (mom), double membrane, own ribosomes

chloroplast (PLANTS ONLY)

performs photosynthesis, green, has own DNA and ribosomes

bacteria and mitochondria+chloroplasts

double membrane, free ribosomes+DNA, independent