Fundamentals of Biology

any substance that takes up space and has mass is called \_____

matter

an \______ is a substance that has specific chemical and physical properties

element

an \_____ is the smallest unit of matter that still 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

molecules result whenever \_____ atoms join together

2 or more

\_____ are molecules that contain more than one element

compounds


(ex: H2O is a molecule/compound)

what are the strong attractive forces that hold atoms within a molecule?

intramolecular forces

which type of force exists between molecules?

intermolecular forces

which type of force (intra-/intermolecular) determines physical properties?

intermolecular

\_____ are molecules that have the potential of bonding to other identical molecules through chemical reactions

monomers

\_____ is the process when monomers bond together, and it forms \_____

polymerization; polymers

\_____ are substances that have a large \# of monomers bonded together

polymers

what are the 3 varieties of carbohydrates?

monosaccharides; disaccharides; polysaccharides

monosaccharides have a ratio of precisely \_____ carbon per water molecule, and they have the empirical formula \_____

1; (CH2O)n

ribose is a \_____ sugar (monosaccharide)

pentose (five carbon)

glucose and fructose are \_____ sugars (monosaccharides)

hexose (six carbon)

glucose and fructose are \_____ of each other

isomers

what type of 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

glucose

what type of bonds does cellulose contain - what do they do?

β-1,4-glycosidic bonds; allows cellulose to form linear strands that pack together in parallel

cellulose has high \____ due to its structure

rigidity

chitin is a \_____ polysaccharide

structural

chitin is found in the cell walls of \_____ and in the exoskeletons of \____

fungi; 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

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 (van der Waal) forces; hydrophobic interactions; disulfide bonding

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

disulfide


(these are covalent)

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

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

what is an allosteric site?

a different location that is not the active site of enzyme catalysis

a noncompetitive inhibitor binding to the allosteric site modifies the \_____ so that the substrate has reduced binding or cannot bind

active site

we cannot \_____ allosteric inhibitors by adding more substrate

outcompete

the rate of enzyme catalysis is unaffected by increasing the substrate concentration in \_____ inhibition

noncompetitive

\_____ is the substrate concentration [X] at which the velocity is 50% of the Vmax

Michaelis Constant (Km)

a \_____ Km indicates that Vmax is reached at low substrate concentrations because enzyme ability/function is high

small

a \_____ Km indicates that Vmax is reached at high substrate concentrations because enzyme availability/function is low

large

in competitive inhibition, Km increases and Vmax \_____

remains the same

this enzyme cleaves a phosphate group off of a substrate molecule

phosphatase

this enzyme adds a phosphate group to a substrate molecule using inorganic phosphate

phosphorylase