biol1000 unit 2-3

organic compound

Compounds that contain carbon

carbon

basis of almost all molecules important for life

carbon skeleton

chain of carbon atoms

Isomers

compounds with the same chemical formula but have different structural arrangements (e.g. glucose, fructose)

hydrocarbons

molecules with only C and H, major component of petroleum (fossil fuels)

structure determines function: how does the structure of carbon allow it to function in a way that it can form extremely complex molecules? how does the shape of a molecule determine its function?

Carbon has four valence electrons, enabling it to form four covalent bonds with a variety of atoms, including hydrogen, oxygen, nitrogen and halogens... enabling specific physical and chemical interactions, such as fitting into enzyme active sites or receptor bindings

how do double bonds affect the structure of a molecule compared to a single bond?

double bonds create shorter, stronger, and more rigid, planar structures... single bonds are often tetrahedral, longer and flexible

In what ways can a carbon skeleton be arranged?

varies in length, may have double bonds differing in locations, branched/unbranched, may be in a ring form

why do isomer structures determine what the molecule does?

despite having the same molecular formula, they possess different structural arrangements, leading to distinct physical, chemical, and biological properties

chemical group

atoms attached to the carbon skeleton, affects the function of a molecule (e.g., testosterone and estradiol are the same molecule with differences in chemical groups)

hydroxl group

-OH, alcohols

carbonyl group

C=O, simple sugars

carboxyl group

-COOH, donate H+ to a solution making it acidic

amino group

-NH2, pick up H+ from solution and are called amines

phosphate group

-OPO3^2-, often ionized because O atoms are negative

methyl group

-CH3, affects gene expression

functional groups

6 groups that affect a molecule's function by participating in chemical reactions

hydroxyl, carbonyl, carbozyl, amino, phosphate, methyl

polar group

hydrophilic, includes hydroxyl, carbonyl, carboxy, amino, and phosphate groups

non-polar group

hydrophobic, includes only methyl group ; not reactive ; affects shape of the molecule

hydrophilic vs. hydrophobic

Hydrophilic- water loving
Hydrophobic- water fearing

what makes each group hydrophilic or hydrophobic?

hydrophilic: able to form hydrogen bonds with water
hydrophobic: lack significant charge or the ability to form hydrogen bonds

Macromolecules

very large complex molecules composed of large polymers

polymers

small, long molecules consisting of many identical or similar building blocks all strung together in a chain

monomers

building blocks of polymers

dehydration reaction

removes a molecule of water as 2 molecules become bonded together

hydrolysis

digestion of polymers into monomers, opposite of dehydration reaction

how are dehydration reactions and hydrolysis reactions opposites of each other?

Dehydration reactions remove a water molecule to join monomers into polymers, while hydrolysis uses a water molecule to break polymers apart into monomers

purpose of dehydration and hydrolysis reactions

To construct macromolecules (polysaccharides, proteins, lipids, nucleic acids) from smaller subunits.

4 types of macromolecules

carbohydrates, lipids, proteins, nucleic acids

unity of life: all life uses the exact same monomers to form polymers and macromolecules. what monomers are used to make each type of macromolecule?

carbohydrates: monosaccharides
lipids: fatty acids + glycerol
protein: amino acids
nucleid acids: nucleotides

Carbohydrates

sugars, saccharides, can be small or large molecules, most are hydrophilic (many hydroxyl groups)

what do our bodies use carbohydrates for?

energy

monosaccharides

monomers of carbohydrates, simplest of sugars (e.g. honey is made up of two monosaccharides, glucose and fructose), forms a ring shape, main fuel for cells (releases energy when broken down)

chemical formula of monosaccharides

generally a multiple of CH2O (e.g. glucose is C6H12O6)

sugars typically contain what kind of chemical groups?

carbonyl and multiple hydroxyl

most sugar names end in "___", enzymes that break sugars apart end in "___"

sugar names end in OSE, sugar breaking enzymes end in ASE

disaccharides

2 monosaccharides linked together, linked during dehydration reaction (e.g. maltose, sucrose)

polysaccharides

hundreds or thousands of monosaccharides linked together… function: stores molecules and structural compounds

4 common types of polysaccharides

starch, glycogen, cellulose, chitin

starch

storage of polysaccharides in plants (used as carbohydrate bank)… helical branched or unbranched shape, most animals have the enzymes to hydrolyze starch (into amylase), mainly found in potatoes + grains

glycogen

glucose storage molecule in animals, highly branched, hydrolyzed by liver and muscle cells to release glucose when needed

cellulose

polymer of glucose, cable-like microfibrils (layers of strings), most abundant organic compound on earth (in tough walls in plant cells), cannot be broken down by animals

chitin

used by insects and crustaceans to build their exoskeleton, found in cell walls of fungi

what type of cells can the 4 types of polysaccharides be found in?

starch: plant cells
glycogen: animal + fungal cells
cellulose: plant cells
chitin: fungal + animal cells

which of the 4 polysaccharides can we digest and why?

starch, glycogen, and chitin can be digested because we have enzymes that can break them down to release energy... cellulose cannot be digested because humans lack the enzymes to break them down

lipid

second type of macromolecule… all hydrophobic (with small hydrophilic regions), smallest of macromolecules, NOT polymers made of monomers

3 important types of lipids

fats, phospholipids, steroids

fat

large lipid made from glycerol and 3 fatty acids… AKA triglyceride

fatty acid

carboxyl group bound to a hydrocarbon chain (non-polar)… can be saturated or unsaturated

glycerol

Combines with fatty acids to make lipids… small sugar

unsaturated fatty acid

hydrocarbon chain that has one or more double bond… causes the chain to have fewer hydrogen atoms… causes kinks or bends in hydrocarbon chain

saturated fatty acid

a hydrocarbon chain that has only single bonds… chain will have the maximum possible number of hydrogen atoms

partially hydrogenated oils

unsaturated fats that have been converted to saturated fats

why are saturated fatty acids solid at room temperature and unsaturated fatty acids liquid at room temperature?

most saturated animal fats are saturated … lacking double bonds = pack closer together = solid at room temperature

most plant and fish fats are unsaturated … kinks in tail ends prevent a tightly packed structure = liquid at room temperature and referred to as oils

why do animals store energy in the form of fats and plants store energy in the form of carbohydrates?

animals store anergy in the form of fats by using ADIPOSE TISSUES, plants store energy in the form of carbohydrates using STARCH

Phospholipids

major component of cell membranes, similar in structure to fats; arranged in double layer sheet, fatty acid tails in the middle, glycerol heads outside

difference between fat and phospholipids in structure

phospholipids are structurally similar to fats, except that phospholipids contain only two fatty acids attached to glycerol instead of three

difference between fat and phospholipids in polarity

fats are entirely nonpolar and hydrophobic (water-fearing), while phospholipids possess both a polar/hydrophilic (water-loving) head and a nonpolar/hydrophobic tail.

difference between fats and phospholipids in uses in our bodies

fats are used for long-term energy storage and insulation, while phospholipids are used for building cell structures and managing transport across membranes.

steroid

carbon skeleton of 4 fused rings, different steroids vary in the chemical groups attached to them (e.g. cholesterol)

proteins

third macromolecule, made of polypeptides, which are made of amino acids, almost all bodily functions depend on proteins

role of proteins

enzymes, transport, defense, signalling, receptor, contractile, structural, storage

why does the function of the protein depends on its structure?

each protein has a specific unique shape… proteins must recognize and bind to other molecules to function

globular proteins

spherical, water-soluble proteins, most enzymes and many other proteins are globular (e.g. lysozyme)

fibrous proteins

long, insoluble, structural proteins (e.g. in hair, tendons, ligaments)

how do phopholipids form a membrane

they have a water-loving (hydrophilic) head and water-fearing (hydrophobic) tails.

placed in water = arrange into a bilayer, with the heads facing the water and the tails pointing inward toward each other = stable barrier that forms the cell membrane

Denaturation

loss of normal shape + function of a protein due to heat or other factor

incorrectly folded proteins can lead to…

diseases like Alzheimers and Parkinsons

prions

infectious misshapen proteins associated with degenerative brain diseases (e.g. mad cow disease)

Amino Acids

building blocks of proteins, 20 standard amino acids all have an amino, carboxyl, and a variable chemical group (R group)

R group

R can be a single hydrogen atom (simplest amino acid, glycine), R can be additional carbon atoms bound to various functional groups

peptide bond

dehydration reaction between the carboxyl group of one amino acid and the amino group of the other amino acid

dipeptide

molecule (or peptide) made of two amino acids

polypeptide

a chain of amino acids, most proteins are at least 100 amino acids long

in what condition must a polypeptide be in to make a protein?

a polypeptide must be coiled and folded into its final shape to make a protein

what determines a protein's shape?

hydrogen + ionic bonds between hydrophilic R groups

covalent bonds called DISULFIDE BRIDGES between sulfur atoms in some R groups

basic structure of an amino acid

central carbon atom bonded to 4 groups: amino group (-NH2), carboxyl group (-COOH), a hydrogen atom (-H), and a unique variable side chain (R group)

where in the amino acid structure do the OH- and H+ ions come from for a dehydration reaction to bind the amino acids together?

in a dehydration reaction that links amino acids, the HYDROXYL group (OH-) comes from the CARBOXYL group of one AA, while the HYDROGEN ION (H+) comes from the AMINO group

in a globular protein why do hydrophobic amino acids cluster in the center and hydrophilic amino acids face the outside?

hydrophobic amino acids cluster in the center because they REPEL WATER and avoid contact with watery environments

Hydrophilic amino acids face the outside because they are ATTRACTED TO WATER, which makes the protein more stable in an aqueous environment.

primary structure

sequence of amino acids in a polypeptide chain; determines shape of the protein

secondary structure

segments of the polypeptide chain coil and fold into regional patterns

tertiary structure

overall 3D shape of the folded polypeptide; polypeptide is now considered to be a fully formed protein

quaternary structure

some proteins consist of more than 1 polypeptide chain (subunits)

what do subunits do in quaternary structure

subunits interact with each other in the quaternary structure to form the completed protein, a protein will not be functional until all subunits come together

nucleic acids

4th macromolecule… 2 types: DNA and RNA

gene

the unit of inheritance that determines the amino acid sequence of a polypeptide

DNA

the nucleic acid that a gene is made of… one or more chromosomes

RNA

nucleic acid that assembles the polypeptide according to the instructions in DNA

nucleotides

monomers that make up nucleic acids… 5 carbon sugar, in phosphate group

nitrogenous base

structure that contains nitrogen and carbon

what are the nitrogenous bases in DNA and RNA?

DNA: ATGC = adenine, thymine, guanine, cytosine

RNA: AGCU = adenine, guanine, cytosine, uracil

polynucleotide

polymer built from nucleotide monomers

how are nucleotides bound together using a dehydration reaction?

sugar of one nucleotide binds to the phosphate group of the other nucleotide

result of polynucleotide dehydration reaction

a repeating sugar-phosphate backbone in the polymer, nitrogenous bases are outside of the backbone

difference between RNA and DNA in structure

RNA: 1 polynucleotide strand

DNA: 2 polynucleotide strands wound into a DOUBLE HELIX

what nitrogenous bases pair with each other in a DNA double helix

A pairs with T, G pairs with C, pairs are held together by hydrogen bonds, and each strand is complementary

inheritance

DNA is the genetic material we inherit from our parents, arranged in chromosomes that can each carry hundreds of genes

how can DNA provide directions for its own replication

complementary base pairing

gene expression

the production of proteins using the instructions found in DNA

similarities and differences between DNA and RNA

similarities: both made of nucleotides, contain a sugar phosphate backbone, uses the ACG bases to store genetic info

differences: DNA has deoxyribose sugar, uses T (thymine) and double stranded, while RNA has ribose sugar, uses U (uracil), and single stranded