Bio I: Chapter 3 -- Biological Molecules

hydrolysis

A chemical reaction in which the bond between two molecules is split by the addition of a water molecule--the process that breaks down polymers and monomers. The reverse is dehydration synthesis. Literal translation: "water to break apart"

dehydration synthesis

A chemical reaction in which two molecules covalently bond to each other with the removal of a water molecule; Remove water to join monomers and form a polymers. Literal translation: "removing water to put together"

helix

A coil, springlike secondary structure of a protein.

glycerol

A three-carbon alcohol to which 3 fatty acids are covalently bonded to make fats and oils--this structure give fats and oils the chemical name triglycerides.

amino group

An -NH2 group. Organic compounds which have this group...

Four Organized Levels of Protein Structure

Interactions among amino acids R groups cause twists, folds, and interconnections that give proteins their 3D structure. There are up to four organized levels of of protein structure: primary, secondary, tertiary and quaternary.

Why is Carbon So Important in Biological Molecules?

Organic molecules have a carbon backbone. They are so diverse because the carbon atom is able to form bonds with up to four other molecules. This allows organic molecules to form complex shapes, including branched chains, helices, pleated sheets, and rings. The presence of functional groups produces further diversity among biological molecules. [Table 3-1]

peptide

a chain of two amino acids joined by a peptide bond. This term is used for relatively short chains.

lipid

a diverse group of biological molecules that contain regions of composed almost entirely of hydrogen and carbon with non-polar C-C and C-H bonds. Non-polar regions make this group insoluble in water (hydrophobic). Some can store energy--some form waterproof coverings for animal bodies or on plants--some serve as primary component of cellular membranes--others are hormones. There are 3 major groups: 1. Oils, fats and waxes 2. phospholipids and 3. steroids.

oil, fat and waxes

a major group of lipids--they are built from only 3 types of atoms: carbon, hydrogen and oxygen. Each contains one or more fatty acid subunits. Formed by dehydration synthesis linking 3 fatty acid subunits to 1 molecule of glycerol (a 3-carbon molecule)--this structure give fats and oils the chemical name triglycerides.

nucleotide

a molecule with a three-part structure: a five-carbon sugar, a phosphate functional group, a an nitrogen-containing base. They fall into two general classes: deoxyribose nucleotides and ribose nucleotides--depending on which type of sugar they contain. They may function as energy-carrier molecules, intracellular messenger molecules or as subunits of polymers called nucleic acid.

denatured

a protein that has different properties and will no longer perform its functions--its normal 3D structure is altered while leaving the primary structure intact. Think egg being cooked--heat changes it ability to carry its job.

adenosine triphosphate (ATP)

a ribose nucleotide with three phosphate functional groups. ATP stores energy in bonds between its phosphate bonds groups and releases energy when the bond linking the last phosphate to the ATP molecule is broken. The energy is then available to drive energy-demanding reactions such as linking amino acids to form proteins.

glycogen

similar polysaccharide to starch--stored by animals in the liver and muscles (including humans). It is a chain (polymer) of glucose subunits but is more highly branched than starch.

phospholipids

similar to an oil, except that one of the 3 fatty acids is replaced by a phosphate group attached to any of the several polar functional groups that typically contain nitrogen. Can be found in the plasma membrane that surrounds each cell. They have 2 dissimilar ends. At one end--they are 2 nonpolar fatty acid "tails" which are insoluble (hydrophobic)--and the other end--has the phosphate nitrogen "head" that is polar and water soluble (hydrophilic). This property is crucial to the structure and function of the cell membrane (chapter 5).

nucleic acid

single nucleotides (monomers) that may be strung together in long chains by dehydration synthesis, forming these polymers--consists of an oxygen atom, in the phosphate functional group of one nucleotide is covalently bonded the sugar of the next.

ribonucleic acid (RNA)

single-stranded chains of ribose nucleotides are copied from DNA and direct the synthesis of proteins (see Ch.11 &12)

disulfide bonds

Chemical side bonds that are formed when two sulfur type chains are joined together--the amino acid cysteine has the R group that allows for this bond with another cysteine molecule.

synthesize

Combining or bringing together two or more elements to produce something more complex--in complex molecules it is preassembled molecular subunits and hooking them together. Just as trains are made by joining a series of train cars, small organic molecules (i.e. sugars or amino acids) are joined to form larger molecules (i.e. starches or proteins).

triglycerides

Formed by dehydration synthesis linking 3 fatty acid subunits to 1 molecule of glycerol (a 3-carbon molecule)--this structure give fats and oils this chemical name.

oils

Used mainly for energy storage and contain more than twice as many calories per gram as carbs and proteins. The difference between fats and this type lies in the structure of fatty acid subunits, which are joined by double bonds with between some carbon and has fewer hydrogens. Remains in liquid form at room temperature. Described as unsaturated.

base

all have carbon and nitrogen atoms linked in rings, with functional groups attached to some of the carbon atoms.

amino acids

all share the fundamental structure: a central carbon bonded to a hydrogen atom, a nitrogen-containing amino group (-NH2), a carboxylic acid group (-COOH) and a R group that varies among different amino acids. Twenty are commonly found in proteins of organisms. The R group gives each amino acid distinctive properties.

deoxyribose nucleotide

bases for this class of nucleotides are: adenine and guanine (both have double rings), cytosine and thymine (both have single rings).

ribose nucliotide

bases for this class of nucleotides are: adenine and guanine (both have double rings), cytosine and uracil (both have single rings).

carbohydrate

biological molecules that are composed of carbon, hydrogen and oxygen in the appropriate ratio 1:2:1--which explains the origin of the word "carbon plus water". All are either small, water-soluble sugars or polymers of sugar, such as starch. There are 2 types: Soluble small bonds that dissolve easily & unsoluble small bonds that don't dissolve easily--Includes monosaccharides, disaccharides, and polysaccharides (most do not dissolve in water).

carbon backbone

carbon atoms bind readily together with each other forming long chains, branched molecules, rings and other shapes. The presence of functional groups produces further diversity among biological molecules.

polymers

chains of monomers--"poly" meaning many--of the synthesizing process--, A large molecule consisting of many identical or similar molecular units, called monomers, covalently joined together in a chain.

waxes

chemically similar to fats, except humans and most animals do not have the appropriate enzymes to break them down. Highly saturated and solid at normal temperatures. Can form a waterproof coating over the leaves and stems of plants--animal fur and insect exoskeletons.

starch

commonly found in roots and seeds, consists of branched chains of up to a million glucose subunits. It is a polymer (polysaccharide) of glucose molecules. Plants use this as an energy-storage molecule.

functional groups

commonly occurring combinations of atoms that are attached to the carbon backbone of organic molecules--*Seven important examples are shown in Table 3-1*

steroids

composed of four rings of carbon atoms [figure 3-16a] the rings share one or more sides with various functional groups protruding from them. Cholesterol, Testosterone and Estrogen are some examples.

organic

describes molecules that have a carbon backbone bonded to hydrogen atoms. The term is derived from the ability of organisms to synthesize and use this general type of molecule.

unsaturated

fatty acids that are double bonded between some carbon and has fewer hydrogens. The double bonds in the fatty acids produce kinks in the chains. Remains in liquid form at room temperature because these kinks prevent it from packing closely together.

saturated

fatty acids that contain as many hydrogen atoms as possible--joined by single bonds with hydrogen bonding sites--these fatty acid chains are straight and can pack closely together, thus forming solid form at room temperature.

carbon atom

has four electrons in its outermost shell, which can accommodate eight electrons. Therefore, a this type of atom can become more stable by bonding with up to four other atoms or with fewer by forming double or even triple bonds. As a result, organic molecules can assume complex shapes--chains, rings, sheets and helices.

enzymes

proteins that promote specific chemical reactions--most cells contain hundreds of different kinds. Works in close association with other molecules. They have very precise roles to play, their highly organized 3D structures help ensure that they interact only with other molecules of particular shapes--much like a key fits a lock.

peptide bond

in proteins, the nitrogen in the amino group (-NH2) of one amino acid is joined to the carbon in the carboxylic acid group (-COOH) of another amino acid by a single covalent bond and water is liberated (dehydration synthesis). The resulting chain of two amino acids is called a peptide.

fatty acid

long chains of carbon and hydrogen with a carboxylic acid group (-COOH) at one end. Connects with one glycerol molecule to form triglycerides.

trans fat

made artificially when hydrogen atoms are added to oils to make them solid at room temperature. This process alters the attachment points of hydrogen near the remaining double bonds, causing kinky tails of oil to straighten. These fats are not metabolized in the same way as naturally occurring fats. Increases risk for heart disease.

disaccharide

meaning "di" for two--a carbohydrate that consists of two monosaccharide linked together by dehydration synthesis is called this and is commonly called sugar. This type of sugar can dissolve in water.

polysaccharide

meaning "many" sugars--a carbohydrate that consists of a polymer of many monosaccharides is called this and is commonly called starch. Most of this type of sugar do not dissolve in water (at body temperature).

polypeptide

meaning "more" of...long chains (polymers) of amino acids bonded by peptide bonds and ranging up to thousands per length. Primary protein structure.

monosaccharide

meaning "one" and "sugar"--a carbohydrate that consists of just one sugar molecule is called this and is commonly called sugar. This type of sugar dissolves in water. Has a carbon backbone of 3 to 7 carbon atoms.

proteins

molecules composed of chains (polymers) of amino acids--the human body has 100,000 different types of proteins that play important and diverse roles. Formed by dehydration synthesis (water is liberated by single covalent bond) and consisting of one or more polypeptide chains (3D structure). There can be up to four organized levels of structure: primary, secondary, tertiary and quaternary.

inorganic

molecules that lack carbon atoms (examples are water and salt) or lack hydrogen atoms (carbon dioxide). They are far less diverse and generally much simpler than organic molecules.

sugars

molecules that make up Carbohydrates--they have one or two monosaccharide units and have a sweet taste.

cellulose

one of the most important structural polysaccharides--makes ups most of the walls of the living cells of plants, the fluffy bolls of cotton plants and about half of the bulk of tree trunks. Like a starch--it is a polymer of glucose but every other glucose is upside down. It is the most abundant organic molecule on Earth.

tertiary structures

one of up to four organized levels of protein structure--in addition to secondary structures, many proteins are contorted into this...their origami folds are determined both by the secondary structure and by its environment.

primary structure

one of up to four organized levels of protein structure--it is the sequence of amino acids.

quaternary structure

one of up to four organized levels of protein structure--occurs in certain proteins that contain individual polypeptides linked by hydrogen bonds, disulfide bonds, or by attractions between oppositely charged portions of different amino acids. *Hemoglobin consists of four polypeptide chains held together by hydrogen bonds.*

secondary structure

one of up to four organized levels of protein structure--the specific amino acid sequences (genetic instructions from cell's DNA) causes polypeptides to assume simple, repeating shapes: a helix or pleated sheet. It is maintained by hydrogen bonds between polar portions of amino acids.

biological molecules

organic molecules that comprise the structure and function of all living organisms. Most fall into four general categories: carbohydrates, lipids, protein and nucleic acids.

fats

such as butter and lard are produced primarily by animals. Used mainly for energy storage and contain more than twice as many calories per gram as carbs and proteins. The difference between this and oils lies in the structure of fatty acid subunits, which are joined by single bonds with hydrogen bonding sites. Takes solid form in room temperature. Described as saturated.

pleated sheets

the folding of a polypeptide chain in secondary structure held together by hydrogen bonds.

monomers

the individual subunits are called this--"mono" meaning one--of the synthesizing process--a small unit that can join together with other small units to form polymers.

glucose

the most common monosaccharide in organisms and the primary source of energy source of cells. It has 6 carbons. Slightly different structures are fructose ("fruit sugar") and Galactose (part of lactose or "milk sugar")--but fructose and galactose must be converted to glucose before cells can use them as a source of energy.

deoxyribonucleic acid (DNA)

the polymer of deoxyribose nucleotides that can contain millions of nucleotides. It is found in the chromosomes of all cells. Consists of two strands of nucleotides entwined in the form of a double helix and linked by hydrogen bonds. Its sequence of nucleotides, like the letters of a biological alphabet, spells out the genetic info needed to construct the proteins of each organism.

chitin

the supportive outer coverings (exoskeletons) of insects, crabs and spiders are made of this polysaccharide, in which the glucose subunits bear a nitrogen-containing functional group. Also stiffens the cell walls of many fungi, including mushrooms.