1) Molecules and Fundamentals of Biology

any substance that takes up space and has mass

matter

A pure substance

• Has specific physical and chemical properties

• Can’t be broken down into a simpler substance

element

the smallest unit of matter

• retains all the chemical properties of an element

atom

can an atom break-down into something smaller, while still retaining the properties of the original element?

no

two or more atoms join together

Molecule

molecules that contain more than one element

compounds

strong attractive forces that hold atoms within the a molecule

intramolecular forces

an attractive force that exists between separate molecules

intermolecular forces

Type of force determines physical properties

intermolecular force

Are single molecules with the capability of polymerizing

• molecules that have the potential of bonding to other identical molecules through chemical reactions

monomers

The process by which monomers bond together

polymerization

Substances made of many monomers linked together

polymers

polymerization reaction that results in loss of H2O

• Two molecules are joined together into one molecule

Dehydration (condensation) reaction

Depolymerization reaction which utilizes water to break bonds

• water is added

• One molecule is broken into 2 molecules

Hydrolysis

• fuel

• structural support

Uses of Carbohydrates

Carbon, Hydrogen, oxygen

All carbohydrates contain

3 categories of carbohydrates

monosaccharides; disaccharides; polysaccharides

Energy storage polysaccharide of glucose monomers used by plants

strach

Energy storage polysaccharide of glucose monomers used in animals

glycogen

structural support polysaccharides made of many glucose monomers.

• important component of plant cell walls

• structural support deters cell lysis

cellulose

ribose is a _____ (shape) sugar

pentose (five carbon)

glucose and fructose are _____ (shape) sugars

hexose (six carbon)

glucose and fructose are of each other

isomers

What carbohydrate results when 2 monosaccharide monomers bond/join together?

disaccharide

monosaccharide monomers join together via what type of reaction?

dehydration/condensation reactions

what type of bond is formed and what is released in a dehydration/condensation reaction?

covalent bond formation; release of H2O

what is the opposite of a condensation/dehydration reaction - why?

A hydrolysis reaction; adds H2O to a covalent bond and splits monomers apart

what is the name of the bond that forms when a carbohydrate attaches to another molecule?

glycosidic

which disaccharide contains 1 glucose and 1 fructose?

sucrose (table sugar)

which disaccharide contains 1 galactose and 1 glucose?

lactose

which disaccharide contains 2 glucoses linked together?

maltose

polysaccharides are long polymers of _____

monosaccharides

_____ may or may not have branching

polysaccharides

some polysaccharides are for _____, and others are for _____.

storage, structure

_____ is a crucial storage polysaccharide in plants

starch

starch contains many _____ monomers in linear forms as well as branched forms

glucose

linear plant starch is called _____

amylose

what is amylopectin?

branched form of plant starch

_____ is a storage polysaccharide found in humans

glycogen

glycogen contains many _____ monomers

glucose

is amylopectin or glycogen more branched?

glycogen

what type of bonds does glycogen have?

α-1,4-glycosidic (linear)

many α-1,6-glycosidic (branches)

name two alpha-glucose polysaccharides

starch (ex. amylose, amylopectin); glycogen

_____ is a structural polysaccharide

• found in plant cell walls, wood, and paper

cellulose

cellulose is a polymer made up of what monomer?

glucose

what type of bonds does cellulose contain

Beta-1,4-glycosidic bonds;

cellulose has high ____ due to its structure

rigidity

chitin is a polysaccharide used for?

structural

chitin is found in the cell walls of _____

fungi

chitin is found in the exoskeletons of ____

insects

chitin is a structural polysaccharide with _____ added to each monomer

Nitrogen

what type of bonds are in chitin?

β-1,4-glycosidic

proteins contain polymers called _____, and each of these polymers contain monomeric subunits called ______.

polypeptides; amino acids

in an amino acid, what 4 things is the central (alpha) carbon bonded to?

hydrogen atom (H), amino group (NH2), carboxyl group (COOH), and an "R group"

how many amino acids are there?

20

amino acids in a polypeptide are linked together via a covalent bond called a ______ bond

peptide

how do amino acids form peptide bonds with one another?

dehydration/condensation reactions

which type of reactions separate the amino acids of a polypeptide?

hydrolysis

polypeptides have an _____ terminus and a _____ terminus

amino (N-); carboxyl (C-)

the _____ structure of a protein is its amino acid sequence

primary

all proteins have _____ structure

primary

the _____ structure of a protein are folds that occur in a polypeptide chain due to intermolecular forces between atoms of the polypeptide backbone

• Alpha Helix

• Beta Pleated Sheet

secondary

the _____ is the amino acid structural features other than the R-group

polypeptide backbone

does the secondary structure include interactions between R-group atoms?

no

which level of protein structure includes alpha helices and beta-pleated sheets?

secondary

the _____ structure is the 3D structure of larger polypeptide chains due to (usually) non-covalent interactions between amino acid R-groups

tertiary

what are the common interactions between R-groups in tertiary structure?

ionic bonding; hydrogen bonding; dipole-dipole interactions; London dispersion forces; hydrophobic interactions; disulfide bonding

usually tertiary structures involve non-covalent interactions; however, ______ bonds are the "covalent exception"

disulfide

which amino acids allows disulfide bond formation?

cysteine

the _____ structure refers to large proteins that have multiple subunits (i.e. contain multiple polypeptide chains)

quaternary

while there are multiple polypeptide chains in a quaternary structure, the entire structure is considered to be _____

1 protein

_____ causes proteins to lose their secondary, tertiary, and quaternary structures

protein denaturation

denatured proteins retain their _____ structure

primary

Composed of amino acids and non-protein components

Conjugated Proteins

Metalloproteins

Proteins which contain a metal ion cofactor

Glycoproteins

Proteins that contain a carbohydrate group

loss of _____ leads to a loss of protein function

shape

(denaturation)

what are some causes of protein denaturation?

excess temperature, chemicals, pH changes, radiation

_____ are molecules that increase reaction rates

catalysts

despite speeding up reactions, catalysts do not affect the _____ of a reaction

spontaneity

_____ are not used up by the reactions they manipulate, meaning the reaction does not change them

catalysts

catalysts lower _____ to speed reactions

activation energies/transition state energies

_____ do not change energy absorbing reactions to energy releasing ones, or vice versa

catalysts

catalysts do not affect the energy of _____ or _____

reactants; products

_____ are biological protein catalysts

enzymes

substrates bind to enzymes at the _____ (location)

active site

the _____ measures how efficient an enzyme is in converting substrate to product

specificity constant

enzymes bind at the active site via the _____ model

induced fit

not all enzymes are proteins - give an example of an RNA enzyme:

ribozymes

______ are non-protein molecules that assist enzymes

cofactors

________ are organic cofactors (e.g. vitamins)

coenzymes

inorganic cofactors are usually _____

metal ions

e.g. iron (Fe2+) or magnesium (Mg2+)

_____ refer to enzymes that are bound to their cofactor

holoenzymes

what is an apoenzyme?

an enzyme that is lacking (not bound to) its cofactor

cofactors that tightly/covalently bind to their enzyme in a holoenzyme are known as _____

prosthetic groups

Protein enzymes have optimal _____ and _____ ranges in which they have the highest enzymatic activity.

pH; temperature

(temperature ranges at the upper end of a normal physiological range generally increase enzyme function)

_____ is a form of enzyme regulation, where inhibitors compete with substrates for active sites

competitive inhibition

we can outcompete a competitive inhibitor by adding more _____

substrate

what is enzyme saturation?

all active sites are occupied

_____ is when an inhibitor binds to the allosteric site of an enzyme

noncompetitive inhibition