AP BIO UNIT 1: BIOCHEMISTRY + WATER

A water molecule is

polar

Hydrogen bond strength

Individually, hydrogen bonds are weak. But together, they are strong enough to give water unique properties.

Liquid water

hydrogen bonds are breaking, reforming, moving around

solid water (ice)

bonds become less flexible, causing the water to expand, H-bonds are fixed in an interconnected network. The expansion of water causes ice to be less dense than water.

Cohesive properties

2 water molecules form H-bonds with each other. Allows water to form droplets and is responsible for the surface tension that many small organisms rely on.

surface tension

Water has an element of surface tension due to the increased hydrogen bonding forces in water at the surface which allows insects to walk on water or for plants to transfer water from the roots to the leaves

adhesive properties

2 different molecules form h-bonds with each other. Water is attracted to other molecules because of its polar nature. Water will form thin films and "climb" up surfaces when the molecular forces between them (adhesive forces) are greater than the cohesive forces.

example: Adhesion enables capillary action.

solvency of water

water's polarity/adhesive property allows it to dissociate ions in salts and bond to other polar substances (alcohols, acids), dissolving them. Non polar substances like fats and oils won't dissolve.

example: Blood plasma in humans and other animals is largely water and transports many water soluble substances

specific heat capacity of water

water has the highest specific heat capacity of all liquids, so it takes a lot of energy before it will change temperature.

example: large bodies of water will maintain a relatively stable temperature.

latent heat vaporization of water

water has a high latent heat vaporization of water, so it takes a lot of energy to transform from the liquid to gas phase

example: high heat of vaporization makes sweating a very effective cooling mechanism.

Four Main Macromolecules of Living Organisms

carbohydrates, nucleic acids, lipids, protein

All macromolecules contain the elements…

carbon, hydrogen, oxygen

carbohydrates

form structural components of cell, provide usable as glucose, energy storage, cellular recognition

proteins

several structural and functional roles (enzymes, structural materials like collagen, transport, movement

nucleic acids

encode information for the construction and functioning of an organism (DNA, RNA), ATP (energy of the cell) is derived from this

inorganic ions

participate in metabolic reactions, components of larger organic molecules

water

major component of cells, many substances dissolve in it and metabolic reactions occur in it

why is carbon so important for building the molecular components of an organism?

• carbon is able to form up to four valence bonds with other atoms while also being able to combine with other elements to form other large number of molecules.

• can form many different structures which makes it very useful for molecular components of an organism.

Miller-Urey experiment

Two scientists attempted to reproduce the condition of the (assumed) earth's primitive ocean's under a reducing atmosphere. They produced some of the key molecules to life (amino acids and nucleotides).

Abiogenesis

The idea that long ago, very simple life forms spontaneously appeared through chemical reactions.

STRUCTURE affects

FUNCTION

methyl group

-CH3, depending on where methyl is put, it will change function of sex hormone, also plays a role in gene expression

double bond makes molecule

ONE plane

versatility of carbon means…

it can create long chains

different shapes -->

.. different structure --> different function

isomers

Compounds with the same formula but different structures.

cis-trans isomers (geometric isomers)

have the same covalent bonds but differ in spatial arrangements

cis isomers

the two Xs are on the same side

trans isomers

the two x's are on opposite sides

enantiomer

shape is the same, isomers that are mirror images of each other

hydroxyl group

-OH, will make things polar, can form H-bonds

carbonyl group

C=O , keytone (C is in the middle), aldehyde (C on the end)

amine group

-NH2, a basic group where the amino part of amino acid comes from

amino acid

carboxyl + amine group + side chain

sulfhydryl group

-SH, thiol, can make disulfide bridge between amino acids which will switch structure

phosphate group

-OPO3^2-, ATP! phospholipid bilayer, nucleic acids (DNA, RNA nucleotides like adenine)

polymer

long chain of building blocks bonded together

monomer

building blocks

enzymes

speed up reactions to build polymers or break them down

dehydration synthesis

polymerization, one molecule of water (1 O, 1 OH) is removed to bond monomers

hydrolysis

Add water to break down (hydrolyze) a polymer

monosaccharide

monomer of a carbohydrate, ex: glucose

polysaccharide

using dehydration synthesis to bond many monosaccharides together

monosaccharides molecular formula

usually multiples of CH2O

linear carbs become

rings in aqueous solutions

disaccharide

two monosaccharides joined together

glycosidic linkage

a covalent bond formed between 2 monosaccharides by a dehydration reaction

storage polysaccharides

starch (plants) and glycogen (animals)

plastids

organelles involved in storage, chloroplast, amyloplast

simplest form of starch is

amylose

glycogen

storage polysaccharide in animals.

muscles, liver cells

glycogen is hydrolzed as more glucose is needed

structural polysaccharides

cellulose and chitin

cellulose

major component of the tough wall of plant cells, provides fiber to humans (insoluble fiber)

like starch, it is a polymer of glucose, but the glycosidic linkages differ

chitin

structural polysaccharide in exoskeleton of anthropods, also exist in fungi, fungi cell wall

lipids

• not polymers, no real repeating units bonded together

• provide a concentrated source of energy, cellular membranes (phospholipids)

• main thing in common: don't solublize well in water (hydrophobic)

fats, phsopholipids, steroids

fats

glycerol, fatty acid, triacylglyercol, adipose tissue

glycerol

backbone

fatty acid

varying lenghts, dif number of carbon, always a carbyoxyl group at the end

truglyceride/triacylglycerol

glycerol with 3 fatty acids

proteins account for

more than 50% of the dry mass of most cells

dry mass: mass without liquids

functions of proteins

1. catalyze/speed up reactions (enzymes)

2. transport materials (hemoglobin, protein channels/pumps)

3. protect your body (immune system, antibodies)

4. storage (can store amino acids --> nourishing embryos --> Casein [milk] and ovalbumin [for egg embryos])

5. communication/cell signaling --> hormones, receptors (proteins)

6. movement (myosin, actin --> these are muscle proteins)

7. structural support (keratin, collagen --> in connective tissue)

catalysts

enzyme --> biological catalysts

polypeptides vs proteins

polypeptides --> polymer of a.a.

protein --> polypeptide that is functional, a functional molecule

peptide bonds

covalent, join two a.a. together

polypeptides have directionality, meaning:

free amino group free carboxyl group

polypeptide

three dimesnional shape of protiens

makes it functional determines its function

the sequence of amino acids determiens a protein's

three dimensional structure

the function of a protein…

usually depends on its ability to recognize and bind to some other molecule

four levels of protein structure

primary structure, secondary structure, tertiary structure, quatemary structure

primary structure

sequence of amino acids determined by genetic code

secondary structure

H-bonds between backbone

(a helix, B pleated sheet) --> H bond interactions between amino acid backbone

a helix: coils