bio 211 - exam 1

atomic structure and bonding

nucleus with protons (positive) and neutrons (neutral)

• - surrounding orbitals contain negative electrons

• - number of bonds an atom can form is based on the number of spaces in its valence shell

covalent bonds

sharing electrons between atoms

nonpolar: electrons shared equally

polar: electrons are unequally shared because one atom attracts electrons stronger than the others

electronegativity

the strength an atom pulls electrons with

• if two atoms have similar electronegativity, they form nonpolar bonds, otherwise, polar bonds are formed

ionic bonds

electrons are transferred from one atom to another

• typically found between metals and nonmetals

hydrogen bonds

from between and H atom (with a slightly positive charge) and an atom with a partial negative charge

van der Wall interactions

form between hydrophobic molecules when they create opposing charges in each other, causing attraction

• - occurs when nonpolar molecules are in close proximity to each other

isomer

compounds with the same molecular formula but different arrangements of atoms

hydroxyl group

-OH

ketone group

carbonyl in the middle of a carbon chain

aldehyde group

carbonyl at the end of a carbon chain

amine group

NH2

carboxy group

COOH

macromolecule

large organic (contain carbon) molecules that carry out specific functions

what are the four classes of macromolecules?

carbohydrates, nucleic acids, proteins, lipids

monomer

building blocks that make up molecules

polymer

long molecules made up of repeating monomers

dehydration synthesis/condensation reactions

connects two monomers, water molecule is formed (OH from one monomer, H from the other)

• - endothermic reaction because energy is stored in the bond formed

hydrolysis reaction

polymer breaks up into two monomers using a water molecule

• -exothermic reaction (energy from bond is released)

what is the carbohydrate monomer and bond that connects them?

monosaccharides, connected by glycosidic bonds

what is the nucleic acid monomer and bond that connects them?

nucleotides, which are connected by phosphodiester bonds

what is the protein monomer and bond that connects them?

amino acids, which are connected by peptide bonds

what is the protein monomer and bond that connects them?

no monomer, various single and double bonds connection portions (ester linkages connect triglycerides)

amino acid structure

• alpha carbon in the center

• amine group to the left

• R group below the alpha carbon

• carboxy group to the left

end amine group is the N-terminus, C terminus is the carbon end

what are the three main chemical properties of r groups?

electrically charged, polar, or nonpolar

Electrically charged r groups

can be acidic or basic

• - acidic groups will have a COOH bonded to some CH..

• - basic groups will have CH bonded to one or more NH

polar r groups

allow r groups to form hydrogen bonds with water

• - have CH or OH, or CH-C-O-NH2

nonpolar r groups

don’t interact with water

• - have H, CH, S, NH, can be long or short

peptide bond formation

oxygen form carboxyl group combines with two hydrogens from an amine group, forming water and a —

• - lone pairs on N give this bond the characteristics of a double bond and make it more stable

• - R groups face away from the backbone

• - single bonds make backbone flexible for folding

levels of protein structure

primary, secondary, tertiary, quaternary

primary protein structure

refers to the polypeptide chain, which is held together by peptide bonds

secondary protein structure

formed by hydrogen bonding between portions of the polypeptide chain (no R groups involved)

• - forms alpha helices and beta pleated sheets

tertiary protein structure

formed by interactions between R groups, including ionic, hydrogen, disulfide, hydrophobic, and van der Waal bonds/forces

• - occurs over long ranges to form intricate structures

• occurs between beta sheets, alpha helices, and disulfide bonds

quaternary protein structure

occurs when multiple polypeptide subunits interact, forming, dimers, trimers, etc.

• - can be between the same or different subunits

• - same bond types as tertiary structure

factors affecting protein folding

• - can be denatured by acids, bases, heat, salt, reducing agents

• - may undergo confirmational changes in response to environmental conditions or to interact with other proteins

nucleotide structure

made up of:

• one phosphate group that gives it a negative charge

• one five carbon sugar (ribose or deoxyribose)

• a nitrogenous base (A, T, G, C, or U)

aka NTP (— triphosphate monomers)

nucleotide base pairing

a forms double bonds with t

g forms triple bonds with c

purines

have a two ring structure

• guanine and adenine

pyrimidines

have a one ring structure

• cytosine, thymine, and uracil

how are phosphodiester linkages formed

the hydrogen atom of a hydroxyl group on 3’ carbon combines with hydroxyl from phosphate group to form a water molecule

• linkage forms from 3’ carbon to a phosphate and a phosphate to a 5’ C of the next sugar

• - the 5’ end has a terminal phosphate, whereas the 3’ end has a terminal hydroxyl group

features of DNA

• exhibits antiparallel orientation (one strand runs from 3’ to 5’, the other from 5’ to 3’)

• one helical turn is about 10 base pairs long

• helix is 2nm wide, with .34 nm between base pairs

• helix has alternating major and minor grooves (proteins use H bond donors and acceptors to find binding site on major groove

• g forms triple bonds with c and a forms double bonds with t

• h bonds and van der Waal forces help to strengthen attraction between bases

• is right handed

What are the differences between RNA and DNA

— uses a, g, c, t whereas — uses a, c, g, u

— uses deoxyribose, which doesn’t have a hydroxy group on the second carbon, whereas — uses ribose

— is double stranded, whereas — is single stranded but can fold to become double/triple stranded

why is RNA unstable

it can undergo self-hydrolysis of its sugar backbone

• the 2’ OH attacks phosphate, breaking the bond between the phosphate and the other sugar its bonded to, breaking the chain

evidence for an RNA world

riboenzymes are — molecules that can catalyze reactions requiring enzymes, meaning there could be a world where — was self sufficient (genetic material and could catalyze reactions, forming life)

monosaccharide structure and numbering

made up of carbonyl and OH groups

• if the carbonyl is at the end of the C chain, its an aldose

• if the carbonyl is in the middle of the C chain, its a ketose

• C’s are numbered starting with the one closest to the carbonyl group

• 3 C = triose, 5 = pentose, 6 = hexose

how do sugars go from linear to ring structure

carbonyl group on one carbon reacts with a hydroxyl group of another

eg: hydroxyl group on C5 attacks carbonyl on C1

C5 bonds with oxygen from C1

Hydrogen is removed from C5 and added to C1’s oxygen, forming a new hydroxyl group

simple sugar

mono or disaccharide

oligosaccharide

made up of 3-10 sugar units

complex sugar

made up of 3-1000 linked sugar units

alpha linkages

bons between carbons from sugar groups that are below the rings

• forms compact alpha helices and allows for branching, increasing energy storage

beta linkages

bond between two carbons in sugar found above the rings

• straight, parallel chains (formed by second sugar being flipped) allows for the formation of cross linkages that are formed by H bonds in adjacent strands, offering structural support

• look at carbon to the left to determine type of linkage