BISC 1111: Exam 1

7 chemical groups most important in biological processes

1. hydroxyl group

2. carbonyl group

3. carboxyl group

4. amino group

5. sulfhydryl group

6. phosphate group

7. methyl group

cabonyl group

(=C=O)

compound name: ketone aldehyde

ex. acetone

# of molecules in a sample measured in

moles

water freely dissociates into

- hydrogen ion (H+): the hydrogren atom leaves it's electron behind

-hydroxide ion (OH-): the molecule that has lost the hydrogen ion

-hydronium ion (H30+): the moleculre that gained the hydrogen ion (H+)

what determines ph

changes in the relative concentration sof hydroxide and hydronium (amount of H+)

Acids

- substance that INCREASES the H+ concentration of a solution

- HCl --> H+ CL- (dissociates in liquid water, more H+ in water)

- ph values LESS than 7

Bases

- substance that REDUCES the H+ concentration of a solution

- NaOH --> Na+ + OH-

- Basic solutions have Ph GREATER than 7

Ph scale

- concentration of H+ and OH- are equal in pure water

- adding acids or bases modifies these concentrations

- ph is used to describe if a substance is acidic or basic

buffers

- weak acids or bases that can react with strong acids or bases to prevent sharp, sudden changes in pH

- minimize changes in concentrations of H+ and OH-

- combine reversibly

ex. ammonia

three classes of macromolecules that are polymers

1. carbohydrates

monomer: glucose

2. proteins

monomer: amino acids

3. nucleic acids

monomer: nucleotide

hydroxyl group

(-OH)

compound name: alcohol

ex: ethanol

carboxyl group

(-COOH)

compound name: carboxylic acid or organic acid

ex. acetic acid

Amino Group

(-NH2)

compound name: amine

ex. glycine

sulfhydryl group

(-SH)

compound name: thiol

ex. cysteine

phosphate group

(-OPO3^-2)

compound name: organic phosphate

ex. glycerol phosphate

methyl group

(-CH3)

compound name: methylated compound

ex. 5-Methyl citosine

gene expression

The process by which information encoded in DNA directs the synthesis of proteins or, in some cases, RNAs that are not translated into proteins and instead function as RNAs.

molecular mass

The sum of the masses of all the atoms in a molecule

Molarity

the number of moles of solute per liter of solution

Avagadro's number

6.02 x 10^23, the number of atoms or molecules in 1 mol

Polymer

A long molecule consisting of many similar or identical monomers linked together.

monomer

small chemical unit that makes up a polymer

Four macromolecules

carbohydrates, lipids, proteins, nucleic acids

enzymes

specialized macromolecules that speed up chemical reactions

dehydration reaction

when two monomers bond together through the loss of a water molecule

hydrolysis

process by which polymers are dissasembled into monomers, the reverse of the dehydration reaction

natural polymers

rubber, starch, protein, and DNA

synthetic polymers

man made polymers

nylon, polyester, teflon, epoxy

simplest carbohydrates

Monosaccharides or simple sugars

Carbohydrate macromolecules

polysaccharides, polymers composed of many sugar building blocks

monosaccharides molecular formula

usually multiples of CH2O

(1C:2H:1O)

How are monosaccharides classified?

The location of the carbonyl group (as aldose or ketose)

The number of carbons in the carbon skeleton

Disaccharide

formed when a dehydration reaction joins two monosaccharides

glycosidic linkage

A covalent bond formed between two monosaccharides by a dehydration reaction.

The architecture and function of a polysaccharide are determined by

its sugar monomers and the positions of the glycosidic linkages

starch

A storage polysaccharide in plants consisting entirely of glucose monomers

simplest form of starch

amylose

how do plants store starch?

in granules called plastids which include chloroplasts

glycogen

storage polysaccharide in animals

where is glycogen mainly stored?

liver and muscle cells

hydrolysis of glycogen

releases glucose when the demand for sugar increases

cellulose

A substance (made of sugars) that is common in the cell walls of many organisms

the most abundant polymer

can cellulose be broken down to formulate ATP?

no, with the exception of bacteria in cows stomach or termites gut bacteria

cellulose vs starch

different glycosidic linkages:

- alpha (α) ring form

- beta (β) ring form

they are isomers of each other but their difference defines their availability to be used

Chitin

Polysaccharide found in arthropod exoskeletons and fungal cell walls.

Lipids are not polymers (true or false)

true

unifying feature of lipids

hydrophobic (not soluble in water)

most biologically important lipids

fats, phospholipids, steroids

fats (tryglycerides) building block molecules

glycerol and fatty acids

Glycerol

A three-carbon alcohol to which fatty acids are covalently bonded to make fats and oils.

fatty acids

carboxyl group attached to a long carbon skeleton

Fats separate from water because

water molecules form hydrogen bonds with each other and exclude the fats (they are NOT repellant of each other)

ester linkage

three fatty acids joined to glycerol

triacylglycerol

A lipid consisting of three fatty acids linked to one glycerol molecule

fatty acids vary in

length (number of carbons) and in the number and locations of double bonds

saturated fatty acids

have the maximum number of hydrogen atoms possible and no double bonds

- solid at room temp b/c shape is linear so molecules can be packed closer together

unsaturated fatty acids

A fatty acid possessing one or more double bonds between the carbons in the hydrocarbon tail. Such bonding reduces the number of hydrogen atoms attached to the carbon skeleton.

- liquid at room temp b/c shape is bent and non linear, more space and less dense

trans fats are a subtype of:

unsaturated fat

Mono-unsaturated Fats

have one double bond

Poly-unsaturated Fats

have many double bonds

Hydrogenenation

the process of converting unsaturated fates to saturated fats by adding hydrogen -- creates trans fats

major function of tryglecerides

energy storage in animals

adipose cells

cells that store fat

adipose tissue

cushions vital organs and insulates the body

white adipose tissue

white fat, in which excess calories are stored in the body

- more white adipose as you age

- less mitochondria

- purpose: resoivar of fat molecules in times of food scarcity

brown adipose

- metabolizes fats so you can produce ATP

- more in babies

why are seeds and nuts full of fats?

- starch is a long time energy storage carb molecule in plants

- sometimes seeds need to be fueled by a more energy dense molecule -- tryglicerides

amphipathic molecule

one side hydrophillic, one side hydrophobic

phospholipids:

a lipid consisting of a glycerol bound to two fatty acids and a phosphate group.

Steroids

lipids characterized by a carbon skeleton consisting of four fused rings

Cholesterol

a type of fat, is a component in animal cell membranes and a precursor from which other steroids are synthesized

Enzymatic Proteins

Function: Selective acceleration of chemical reactions

Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules

defense proteins

Function: Protection against disease

Example: Antibodies inactivate and help destroy viruses and bacteria.

storage proteins:

Function: Storage of amino acids

Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo.

transport proteins

Function: Transport of substances

Examples: Hemoglobin, the iron-containing

protein of vertebrate blood, transports

oxygen from the lungs to other parts of the

body. Other proteins transport molecules

across membranes, as shown here.

hormonal proteins

Function: Coordination of an organism's

activities

Example: Insulin, a hormone secreted by the

pancreas, causes other tissues to take up

glucose, thus regulating blood sugar,

concentration.

recpetor proteins

function: response of cell to chemical stimuli

ex. the receptors built into the membrane of a serve cell detect signaling molecules released by other nerve cells

contractile and motor proteins

Function: Movement

Examples: Motor proteins are responsible

for the undulations of cilia and flagella.

Actin and myosin proteins are responsible

for the contraction of muscles.

structural proteins

Function: Support

Examples: Keratin is the protein of hair,

horns, feathers, and other skin

appendages. Insects and spiders use silk

fibers to make their cocoons and webs,

respectively. Collagen and elastin proteins

provide a fibrous framework in animal

connective tissues.

different groups of amino acids

- hydrophobic R-groups linearly arranged (non-polar)

- polar side chains; hydrophilic

- electrically charged side chains; hydrophillic

- acidic (negative charge)

- basic (positivly charged)

peptide bond

The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid

primary structure of proteins

sequence of amino acids

secondary structure of protein

the coils and folds result from hydrogen bonds between repeating constituents (amino and carboxyl groups) of polypeptide

alpha α helix

beta β pleated sheet

no r group interactions

Terciary structure of a protein

: the overall shape of a polypeptide results from interactions between R groups (hydrogen bonds, ionic bonds, hydrophobic interactions, and van der waals interactions)

- disulfide bridges: strong covalent bonds that reinforce structure

tertiary structure can change if chemical environments is changed b/c structure is never fixed.

disulfide bridges

covalent bonds that may further reinforce the shape of a protein

Van Der Waals attraction

Weak noncovalent interaction, due to fluctuating electrical charges, that comes into play between two atoms within a short distance (DISTANCE DEPENDANT) of each other.

-collectivly van der waals interactions can be strong -- but not individually

ex. gecko's toe hairs and wall surface

Quaternary Structure

- result of two or more polypeptide chains bound together to form one macromolecule

- not always present in proteins

ex. hemoglobin, collegen (abundant in mammals)

Structure = function example (sickle cell anemia)

sickle cell = singular change in primary structure (one amino acid difference) that has cascading effects and creates misshapen red blood cell

Factors affecting protein structure

primary structure but ALSO physical and chemical conditions:

- alterations in Ph, salt concentration, temperature, or other environmental factors can cause protein to unravel

denaturation

loss of a protein's native structure

(ex. frying an egg changes the temperature of the environment

- proteins in egg white provide viscosity in the aqueous solution

- frying pulls apart the proteins from the evaporating water

- linearization of protein creates closely packed together = solid egg white)

cells fold proteins in several stages (true or false)

true

Diseases associated with misfolded proteins

Alzheimer's, Parkinson's, and mad cow disease

Enzymes

proteins that act as catalysts to speed up chemical reactions

- can perform their functions repeatedly, functioning as workhorses that carry out the processes of life

- even a single mistake in its primary structure can have a domino effect on all other orders of structure

The process/cycle of enzymatic activity

1. substrate enters the active site; the enzyme changes shape such that the active site enfolds the substrate

2. substrate held in the active site by weak interactions such as hydrogen bonds and ionic bonds

3. the active site lowers the activation energy and speeds up the reaction

4. substrates are converted to products

5. products are released

6. active site is available for two new substrate molecules

What determines the amino acid sequence of a protein?

genes

Gene

sequence of DNA that codes for a protein and thus determines a trait

DNA

a nucleic acid made of monomers of nucleotides

nucleotides

the building blocks of nucleic acids consisting of a five-carbon sugar, a nitrogenous base, and a phosphate group.

DNA provides directions for its own replication (true or false)

true

How does DNA control protein synthesis?

DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis