Bio U2

Polar

Polar

water is this

one end is slightly positive while the other end is slightly negative

nonpolar

same charge on each end

no opposite charges

hydrogen bond

when H and O are attracted to each other because H is positive and O is negative and form a hydrogen bond

not very difficult to break

cohesion

bonding of a molecule to itself

sticking of alike molecules

ex. water molecules attracted to other water molecules

adhesion

when two different substances come together due to attractive forces

hydrophobic

afraid of water

molecules that do not mix with water

hydrophilic

loving water

attracted to water

can mix and interact with water

macromolecules

make up cells

proteins

nucleic acids

carbohydrates

lipids

4 major elements

• CHON

not all macromolecules have CHON but they all have CHO

CHON elements

nucleic acids

proteins

CHO elements

carbohydrates (polysaccharides)

lipids

organic molecules

made of carbon and hydrogen

some define it as just being made of carbon

need to have carbon atoms covalently bonded to hydrogen atoms (C-H bonds) or can be carbon bonded to carbon

can include other elements

CHONSP elements

CHO: lipids and carbohydrates (polysaccharides)

CHONS: proteins

CHONP: nucleic acids

polypeptide

chain of amino acids that can be shaped into a protein

formed by multiple peptide bonds between amino acids

forms proteins

• diverse structures and many functions

• ex. structure, storage, transport, hormones, contractions, receptors, defense, enzymes

polysaccharide

carbohydrates

made of monosaccharides bonded by glycosidic linkage

• fuel and building material

• CH2O ratio

• Carbonyl group

• multiple hydroxyl groups

compromised of sugar monomers put together by dehydration synthesis

lipid

has a hydrophilic head and a hydrophobic head

used to create walls and barriers in cells

not polymers

do not form long chains

ex. of lipids are fats

• are glycerol (3 hydroxyls) + fatty acids (carboxyl groups) at one end w/hydrocarbon chains

• energy rich - 2x calories as carbs because made of hydrocarbon bonds which store lots of energy

• sometimes called triglyceride

nucleic acid

biological info is encoded into a sequence of nucleotide monomers

have directionality - DNA is built from 5’ to 3’ direction

store and transmit hereditary information - type of polymer

polymer b/c - have a nucleotide covalently bonded to other nucleotides - known as sugar phosphate backbone

examples of nucleic acids

• DNA

• RNA

amino acid

monomers - building blocks of proteins

contain (KNOW EACH ONE!!!!)

• an amino group

• alpha carbon

• carboxyl group

• R side chain - this is what makes amino acids vary from each other can determine how a protein folds and behaves in a cell ex. can be hydrophobic or hydrophilic

amino acids are linked together through dehydration synthesis and covalent peptide bonds

bonded amino acids are called a polypeptide chain

protein synthesis

diff structures

primary

secondary

????

add more

monosaccharide

smallest carbohydrates - building blocks

two bonded monosaccharides form a disaccharide

the way the monosaccharides are connected can impact if they can be broken down

ex. with starch vs. cellulose

cellulose has alternating bonds —> humans can break them but other organisms can

fatty acid

makes up lipids with glycerol

can be saturated or unsaturated

saturated: only single bonds in a long chain of hydrogens and carbons that make up the long fatty acid chain

Unsaturated: If there is a double bond (not just a single covalent bond) that will cause a kink/change of direction in the chain

saturated fatty acids can be packed closely together ex. butter

unsaturated fatty acids can not be packed closely together ex. vegetable oil

glycerol

3 hydroxyls

makes up lipids with fatty acids

phospholipid

make up the phospholipid bilayer of the cell membrane

contain polar and nonpolar regions

nucleotide

makes up - building blocks of nucleic acids

monomers of nucleic acids

structural components

• 5-carbon sugar (deoxyribose or ribose)

• phosphate

• nitrogenous base (ATCGU)

always added to the 3’ end because it targets the hydroxyl to add in the phosphate of the new base

nucleic acids are polymers because they have a nucleotide covalently bonded to other nucleotides - known as a sugar phosphate backbone

covalent bonds

shared electron between atoms - stronger bond than hydrogen bonds - peptide bonds are this type

hydrolysis

use of water to disassemble a polymer

dehydration synthesis

also known as condensation reaction - lose hydrogen (H) and hydroxyl (HO) to form water (H2O) and then the unpaired electrons will bond to form a longer chain

can link together amino acids & form peptide bonds

monomers

make up polymers

to join monomers you undergo dehydration synthesis

“building blocks”

polymers

long chains of monomers ex. carbs

deoxyribose

5 carbon sugar

makes up nucleotides

means missing one oxygen in deoxyribonucleic acid

1 less oxygen than in ribose

ribose

5-carbon sugar

can make up a nucleotide

has 2 hydroxyls

3’ and 5’ orientation

DNA & RNA are built from 5’ to 3’ direction

DNA strands are antiparallel

adenine guanine thymine cytosine uracil antiparallel primary secondary tertiary & quaternary structures

nitrogenous bases

AT or U

CG

antiparallel

DNA runs antiparallel - the backbone go opposite

primary structure (in protein synthesis)

amino acids link together through dehydration synthesis (covalent peptide bonds) - polypeptide

secondary structure

called alpha helix or beta pleated sheets - the polypeptides fold over on themselves and can be hydrogen bonded to itself - when the backbone starts to interact

tertiary structure

can have hydrogen bonding

disulfide bridges can be formed (2 cysteines can have their sulfurs form a covalent bond)

this happens with R groups start to interact

• ionic & disulfide bridges

• acid base interactions

overall 3d shape of the protein

quaternary structure

tertiary structure hydrogen bonded with other tertiary structures

when multiple subunits of a protein (polypeptides) come together & interact —> results in the quaternary structure

protein synthesis

Proteins have primary structure determined by the sequence order of the amino acids, secondary structure arises through local folding of the amino acid chain into elements like alpha-helices and beta-sheets, tertiary structure is the overall 3d shape of the protein and minimizes free energy, and quaternary structure arises from interactions between multiple polypeptide units

These 4 elements of protein structure determine the function of a protein

enzymes

almost always proteins

biological catalysts

• can speed up the rate of a reaction while not being used up

• rearranges the substrate in a particular way

• can lower the activation energy needed to start the reaction to go from the substrate to the product

• allows reactions to take place in living systems at temperatures that are appropriate for those living systems

changes in temperature can result in different enzyme shapes

at lower temps

• fewer interactions between enzymes and substrate

• fewer collisions between active site and substrate

at warmer temps

• kinetic energy of molecules increase

• but if too warm —> thermal stress on protein —> denaturing —> active site can lose shape —> lose activity

at low pH

• acids contain hydrogen ions

• can bind to negative areas on the enzyme & disrupt bonds —> break them

• causes the enzyme to lose its shape

the folding of proteins influenced by R groups in the chain

• as it folds there will be pockets with certain chemical properties or chemical attractions that allow for certain substrates to fit

with a substrate and enzyme

• it is both a shape and charge interaction that binds the two

enzymes provide torsional stress on the molecules

active site

amino acid side chains in the active site determine the interaction between the enzyme and substrate

for an enzyme-mediated chemical reaction to occur - shape and charge of the substrate must be compatible with the active site of the enzyme

normally very polar

• certain amino acids that line the active site are polar

site where the substrate binds to the enzyme

substrate

the substance that the enzyme acts upon

catalyst

a substance that increase the rate of a chemical reaction without itself undergoing any permanent chemical change

activation energy

energy required to break bonds in the reactant molecules

enzymes lower activation energy

denaturation

when an enzyme loses its shape —> loses activity

the substrate can no longer bind to the active site

conformational change

when the enzyme provides a torsional stress on the molecules

the enzyme can change shape a bit

the substrate can also undergo a change and be broken apart or combined together

competitive inhibitors

when an inhibitor binds into the enzyme instead of the substrate because they may bind more closely than the substrate and blocks the activity of the enzyme by preventing the substrates from interacting with the active site

activity rate of the enzyme will decrease

the enzymes still work though - its just that their reaction rates are slowed

noncompetitive inhibitors

when there is another area on the enzyme separate from the active site where an inhibitor could bind

as it binds it changes and has an allosteric effect on the whole shape of the enzyme

this change in shape can close off the active site

inhibits the substrate from binding to the active site —> decreases activity rate of the enzyme —> since the active site no longer works they stop functioning completely

allosteric site

the site where the other molecule can bind to which changes the shape of the active site

allosteric enzymes

change their shape in response to a molecule that alters their active site

these enzymes are the ones affected by noncompetitive inhibitors

enzyme inhibition