Biology Molecule Essay, Research Paper

Unit 1 -man is high 50?s to 60% water -distribution in body divided into 3

compartments: 1) intracellular – 28 litres 2) intercellular/interstitial fluid -

11 litres – 80% 3) blood plasma – 3 litres – 20% -women contain less water than

men -organisms can contain 60-80% water -bacteria have lots of water -fat cells

have little -water?s properties result from its structure and molecular

interactions -water is polar -polar covalent bonds and asymmetrical shape give

it opposite charges on opposite sides -electrons spend more time around O giving

H a slight positive charge -hydrogen bonds form between the oxygen of one

molecule and the hydrogen of another -cohesion: substance being held together by

hydrogen bonds -hydrogen bonds are transient yet enough is always held together

to give water more structure than almost any other liquid -beads and meniscus

formed by cohesion (also helps upward transport of water in plants) -adhesion

counteracts downward pull of gravity -water has greater surface tension than

most liquids -surface molecules are hydrogen bonded to molecules below and

around them -surface tension can hinder life (i.e. beading in the alveoli of

lungs) -makes water ?unwettable? -surfactants used to counteract this -water

has a high specific heat which allows it to resist extreme temperature changes

-has a high heat of vaporization that causes it to require alot of energy to

change states -when sweating, heat energy is utilized to change states from

liquid to gas, causing a drop in temperature -as a solid water is less dense

than as a liquid and will float -charged regions of molecules have an electrical

attraction to charged ions -water surrounds ions separating and shielding them

from one another -polar compounds are generally soluble -charged regions of

water are attracted to oppositely charged regions of other polar molecules

-polar molecules are miscible in other polar liquids -most water molecules

don?t dissociate (~ 1/554 million do) -hydrogen atom in hydrogen bond between

the two water molecules may shift from the oxygen atom it is covalently bonded

to the unshared orbitals of the oxygen that it is hydrogen bonded to -hydrogen

ion is transferred creating a hydronium ion and leaving a hydroxide ion -the

solvent is water itself -at equilibrium water is not dissociated -at equilibrium

in pure water at 25oC [H+] = [OH-] -pH of this solution is 7 (neutral) -high pH

= low acidity -acids are substances that increase the relative [H+] and remove

OH- because it tends to combine with H+ to form water – if [H+] * [OH-] , it is

acidic and has a pH between 0 and 7 -bases are substances that reduce the

relative [H+] in a solution -it may increase the [OH] -if [H+] * [OH-] , it is

basic and has a pH greater than 7 -buffers are important in the body to keep the

pH range between 6 and 8 -pH of blood is between 7.34 and 7.44 -mustn?t shift

below 7.2 or acidosis will occur -some body zones may have a pH as low as 0.5 or

as high as 10 -buffers minimize sudden changes and are a combo of hydrogen

donors and hydrogen acceptors -ions are accepted when in excess and donated when

in short supply -in biological systems an example is the bicarbonate buffer -in

response to a rise in pH, the carbonic acid dissociates to form a carbonate ion

and a hydrogen proton -if there is a drop, it is reversed (pH up = to right, pH

down = to left) -equilibrium is established but it is always moving to the left

or the right -a balance is the optimum pH -other body buffers include protein

molecules which donate and accept amino acids to stabilize pH -most of the rest

of organisms is made up of carbon based compounds like carbs, lipids, proteins,

nucleic acids -carbon compounds are known as organic -vitalism is the belief in

a life force outside the control of chemical laws -this has been disproved as

water, ammonia, hydrogen and methane have been combined in a lab to form organic

substances -C+O+H = carbohydrates -C+H+N = amino acids, urea, proteins, lipids

-carbon atoms are the most versatile building blocks -each has 4 valences where

bonds can form -carbon chains form the skeleton of most organic molecules -may

be straight or branched, long or short, or in closed rings -hydrocarbons contain

only hydrogen and carbon -they form when organic matter decomposes and

functional groups break off leaving a skeleton -hydrocarbon chains, branches,

and rings can be modified by other elements which are joined on in a particular

matter -these are components of organic molecules that are often involved in

chemical reactions -they replace 1 or more hydrogens in a hydrocarbon

Carbohydrates: -sugars and starches -nonsugars: plant starch, animal starch,

cellulose, chitin -come from pasta, rice, flour, fruit, syrups -important source

of energy, can be oxidized to release energy, improves your mood -contain C, H,

and O, with generally 2 times as much H as O -sugar names usually end with -ose,

and are named depending on the number of carbons in them (e.g. triose, pentose)

-6 carbon sugars, hexoses, are most important -general formula is C6H12O6, and

in living systems, the state is aqueous -solids exist in chains, and liquids as

rings -the molecular formula is the same for different hexoses, but the

structural formula differs -other isomers of glucose can be reorganized by cells

into alpha glucose, and then oxidized -glucose is the major nutrient for cells

and its carbon skeleton is raw material for the synthesis of other organics

Disaccharides: -2 hexose sugars-most common are: sucrose, lactose and maltose

-glucose + glucose = maltose + water -glucose + fructose = sucrose + water

-glucose + galactose = lactose + water -this process is known as condensation or

dehydration synthesis -synthesis of disaccharides doesn?t happen in the human

body, but usually they are eaten and digested, through a process known as

hydrolysis or disaccharidases Polysaccharides: -these are macromolecules that

are made by condensation when monosaccharides are joined -general molecular

formula isC6H12O5 -common polysaccharides are amylose, amylopectin (plant

starch), glycogen (animal starch), cellulose (cell wall material), chitin

(leathery covering of invertebrates) -plants use glucose to grow, and extra is

stored in the roots in a soluble form which is then reactivated in the spring -

this reactivates the growing process year after year -animal starch is stored in

special cells (average person has a 24 hour supply) and can readily be converted

into glucose for use -cellulose and chitin are structural carbohydrates -amylose

is formed when glucose molecules join in a 1-4 linkage pattern -first carbon of

one glucose links to the fourth carbon of another -this is a covalent bond or a

glycosiolic link -bond is angular and forms a spiral called an alpha helix -if

it branches, amylopectin is formed -cellulose is a 1-4 linkage of beta glucose

-this creates a straight strand and not a helix -these bonds are rigid and

require special enzymes (cellulase) to break them -the position of the beta

glucose molecules alternates Lipids: -humans rarely eat pure lipids -cell

membranes are primarily lipid and lipids can easily enter cells, carrying a

food?s flavor with them -a diet should have less than 30% fat, 55-65% carbs,

and 10-15% protein -lipids are important as a source of energy, insulation

(adipose tissue), cushions for the internal organs, as a lubricant, as an

emulsifying agent (cholesterol in bile), as a structural component of cells (1/6

of brain is fat), cholesterol as a precursor molecule for vitamin D, cortisone,

testosterone, progesterone, and estrogen -lipids are simplest biological

molecules and are composed mostly of C, H and a few Os -they are energy rich

because of the high C to H ratio -fat consists of a glycerol molecule connected

by ester bonds to a 3 fatty acid molecule (this is a tryglyceride) -if the bonds

between the carbons are single bonds, the fatty acid is saturated (fat formed is

a saturate) -if they have multiple bonds, it is an unsaturated fat -a

polysaturate is more than one fatty acid held together by single bonds -multiple

bonds can be broken and extra hydrogens added through hydrogenation -short

chained fats of unsaturated fatty acids are soft with a low b.p. -long chained

fats of saturated fatty acids are harder with a high b.p. -length of chains

affects boiling point the most -to make an oil from a solid, you must

hydrogenate it Steroids: -saturated fatty acids can be converted to the steroid

cholesterol -triglycerides are monitored more closely in the blood than

cholesterol -the amount of saturates converted to cholesterol is genetic

-abnormal genes can cause excessive production (1 gene = severe heart disease, 2

= shortened life span) -liver produces cholesterol -steroids have a 5 ring shape

-examples are androgens, estrogens, and cortisone Proteins: -there are 20 amino

acids, 8 of which are essential and can be converted into any of the other 12

-protein rich foods are digested into amino acids and the body absorbs them to

make their own proteins -liver cells convert them into absent aminos =

transaminofication -proteins are synthesized on ribosomes in the cytoplasms of

cells or on polysomes (ribosome chains0 -DNA codes proteins by copying its info

onto a shorter strand known as mRNA (m = a message to synthesize a protein) -the

message is received and a protein is synthesized -for synthesis all 20 are

required -number, sequence and type of amino acids making up the protein is the

primary structure – this is determined by DNA -secondary structure is the

coiling or pleating of amino acid chains, caused by rigid peptide bonds which

are bent by strong intermolecular attraction between hydrogens and oxygens of

every fourth amino – this results in a regular, repeating twist or an alphahelix

-chains lie parallel to one another and form hydrogen bonds between themselves -

this is a beta sheet but is not very common -secondary structure is determined

by intermolecular bonds -tertiary structure refers to the folds in the coiled

chain -this is called by a thiol called cysteine – this can form a bridge when

it meets another cysteine -when 2 cysteines meet, a disulfide link is formed

-insulin has 6 cysteine amino acids and forms 3 bridges and a slightly globular

protein -the more cysteine amino acids there are, the more folds or joints that

result and the more globular the protein is -globular proteins are the

?doers? that function because they have a particular shape due to the

cysteine-cysteine sulfur bridges -some proteins may be a bunch of polypeptide

chains close together -this is quaternary structure, which very few proteins

have -all proteins have a primary and secondary structure, but few have a

tertiary structure, and even fewer a quaternary -proteins can be 50-50,000 amino

acids long -amino acids are joined by peptide bonds, a covalent bond between the

C of one amino acid and the N of a neighbour -a polypeptide chain is a string of

aminos not long enough to be a protein -amino acids are so named because of

their two functional groups, the amine group and the carboxylic acid group

Nucleic Acids: -all living cells contain DNA and RNA -these carry instructions

for making proteins and specify the sequence in which amino acids should be

linked together -DNA and RNA are polynucleotides, polymers of nucleotides

-nucleotides consist of a phosphate group + a pentose + a nitrogenous base -they

can be linked together by condensation to form a polynucleotide -if a nucleotide

contains ribose, it becomes Ribo Nucleic Acid -these are always just a single

strand, but may be looped into 3 dimensional shapes -if the nucleotide contains

deoxyribose, Deoxyribo Nucleic Acid results -DNA molecules are far longer than

RNA molecules, and can never contain Uracil -4 possible bases are adenine,

guanine, cytosine, and thymine -DNA molecules contain two polynucleotide

strands, held together by hydrogen bonds between the bases -hydrogen bonds can

only be formed between specific base pairs: Adenine – Thymine Cytosine – Guanine

-a sense strand is a sequence of bases that tells the order in which to string

together the amino acids -a length of DNA coding the sequence for a polypeptide

is called a gene -three bases, a codon, specify an amino acid -there are 64

possible arrangements of bases in a codon -polypeptides are made when 2 strands

of DNA split up and an RNA molecule builds up against the sense strand -base

sequence of RNA must match that of the DNA molecule -a complete RNA molecule

then peels off and travels to the location where polypeptides are made -sequence

of bases on a DNA molecule is the same for a human or a bacteria Other

Nucleotides: -a slightly different version of one of the nucleotides that forms

RNA is ATP -ATP contains ribose, adenine and 3 phosphate groups instead of 1

-phosphate groups may be lost one at a time to make ADP (di) or AMP (mono) -all

living cells make ATP as an energy currency, it is produced constantly -ATP

molecules usually last less than a minute before being broken down -~40 kg is

produced in a day -if a cell needs energy, it hydrolyses ATP and releases energy

in small packets NAD: -contains ribose sugar, adenine and 2 nucleotides -one

nucleotide does not contain any of the 5 bases, but instead a nicotinamide ring

-they can accept hydrogens and become NADH -hydrogens are accepted or passed on

during respiration or photosynthesis.