BIO EXAM1

What is the importance of water?

can’t have life without it

• biochemical reactions require an aqueous environment

  • humans are mostly 55-60% water

• important means of transport

  • blood is 50% water

  • plant transport

• resistant to temperature change

  • acts as temperature buffer for organisms and ecosystems

water is a _ molecule

polar

how is water a polar molecule

1. held together by covalent bonds

2. O₂ is much more electronegative than H+ (polar covalent)

3. causes partial charges, and partial-positive H+ allows water to create hydrogen bonds

how does water form hydrogen bonds

1. need hydrogen donor and hydrogen acceptor

2. electrostatic attraction between partial-positive H+ & a partial-negatively charged atom

in water, how many bonds can each H or O participate in? how many H-bonds can water form?

• H: 1 H-bond

• O: 2 H-bonds

• water: up to 4 H-bonds

can water have ionic bonds

No (no ions = no ionic bond)

what does H-bonding allow water to do

be liquid at room temperature

polar molecules are _ in water and nonpolar molecules are _ in water

soluble; insoluble

hydrophillic vs hydrophobic, w examples for both

• water-loving (ex. ammonia)

• water-fearing (ex. oils/lipids)

when molecules have both polar and nonpolar features

amphipathic

bronsted lowry definition of acid

donates protons (H+)

bronsted lowry definition of base

accepts protons (H+)

how does hydrochloric acid (HCl) interact in water

ionizes into H+ and Cl-

how does sodium hydroxide (NaOH) interact in water

ionizes into Na+ and OH- & H+ (forming H2O)

pH

negative log of H+ concentration in solution (mol/L) (-log[H+])

as proton conc. _, pH _ and vice versa

increases; decreases

scale of pH: what is basic, neutral, acid

0-14: 0 is acidic, 7 is neutral ([H+] = [OH-]), 14 is basic

a _ unit change in pH = a _ change in H+ and vice versa

1; 10-fold

biological macromolecules (BNM)

large and biologically important molecules

• they are polymers (large molecules made up of multiple subunits (monomers that are covalently bound)

• each category of BNM is defined by their monomers

condensation reactions

link monomers together via covalent bonds to form a polymer

• water formed as a product

• also known as dehydration/synthesis reactions

• needs specific enzymes

hydrolysis reactions (water-lysis)

water used as reactant to break polymers back into individual monomers by breaking covalent bonds

carbohydrates

molecules with general formula (CH₂O)_n

• H’s and O’s present in 2:1 ratio like water

• have monomers (simple sugars)

  • monosaccharides (MS): individual (ex. glucose, fructose)

    • glycosidic linkages: covalent bonds that link MS together; many specific types

complex carbohydrate levels

1. disaccharides: carbs w/ 2 MS covalently bound together (ex. sucrose, fructose)

2. oligosaccharides: 3-15 MS (ex. raffinose w/ 3 MS)

3. polysaccharides: carb MACROMOLECULES, >15 MS (ex. cellulose, starch, glycogen)

cellulose

• provides shape and rigidity to plant walls

  • primarily a structural polysaccharide (PS)

• important to people (ex. buildings, heat, tools, e.t.c.)

  • wood is mostly cellulose

what is cellulose in terms of chemistry

polymer of beta-glucose monomers held together by beta-linkages

why can’t humans digest cellulose but cows and other herbivores can

• humans don’t make the digestive enzyme cellulase that breaks beta-linkages, so they can’t hydrolyze cellulose into beta-glucose monomers for energy

• cows and other herbivores have microorganisms that can produce cellulase to hydrolyze cellulose (endosymbiotic relationship)

starch/glycogen

polymers of alpha-glucose monomers

• function as energy storage molecules

• animals have the enzymes to break alpha-linkages

plants only make _ and what is _

starch: energy storage molecule in plants

• later broken down for energy

animals only make _ and what is _

glycogen: energy storage molecule in animals

• later broekn down for energy

cellulose is a _ molecule

linear unbranched

starch is a _ molecule

moderately branched

glycogen is a _ molecule

highly branched

branching allows what

more glucose to be stored

where does the word proteins come form

greek word proteios which means primary/of first importance

examples of protein functions

• enzymes: speed up chemical reactions

• movement: motor proteins

• structural: cytoskeletal proteins, ECM

• signaling molecules: hormones/neurotransmitters

• signaling receptors: cell signaling

monomers

amino acids (20 common ones)

covalent bonds that link aminao acids together are called

peptide bonds

polymers of amino acids

• peptides: AA polymers w/ 2-49 aa (ex. endorphins have 16-30 aa)

• polypeptides/proteins: aa polymers w/ 50+ amino acids (macromolecules, ex. titin has 35k aa)

amino acid structure

amino group, alpha carbon, carboxylic acid (left, center, right)

• r group gives each aa their unique characteristics

amino acids form _

proteins

amino terminus

amino group attached to first aa added to protein

carboy-terminus

carboxylic acid group attached to last aa added to protein

why is nucleic acid named that

nucleic: nucleus and acid: acidic nature of the molecule

what are monomers and what are the covalent bonds that link them together

nucleotides; phosphodiester bonds

nucleic acid polymers and functions

• DNA: polymer of DNA nucleotides; stores genetic info

• RNA: polymer of RNA nucleotides; involved in regulating flow of genetic info

difference between prokaryotes and eukaryotes

• Prokaryotes: no-membrane nuclei with circular DNA, smaller/simpler organisms (ex. bacteria)

• Eukaryotes: membrane-bound nucleus with linear DNA inside, mitochondria, ER, plant and animal cells

difference between the typical habitats of Eubacteria and Archaea?

• eubacteria: common everyday environments (ex. soil, water, inside or on surfaces of other organisms)

• archaea: harsh, extreme environments (ex. hot springs, deep-sea hydrothermal vents, acidic or anaerobic conditions) (however, can also live in moderate soils or oceans)

In terms of shape, what are the three major categories of Bacteria?

1. cocci: spherical/round shaped

​2. bacilli: rod-shaped

3. spirilla: spiral/corkscrew-shaped

What is the major difference between autotrophic and heterotrophic bacteria?

• autotrophic: make own organic foods using light (photosynthesis) or chemical energy (chemosynthesis)

• heterotrophic: cannot make own food, must absorb or consumer organic nutrients from other living or dead organisms

What is the major group of photosynthetic bacteria?

Cyanobacteria

nucleotide structure

nitrogenous base, phosphate group, and pentose sugar

what is RNA

single-stranded polymer of RNA nucleotides

• held together by phosphodiester bonds

• contains nitrogenous bases and sugar-phosphate backbone

what is DNA

polymer of DNA nucleotides

• has 2 s-phosphate backbones (double-stranded), which bond to each other through hydrogen bonding between the nitrogenous bases

origin of word lipid

greek word “lipos” (fat) and suffix “id” (denotes a group of something)

characteristics of lipids (loosely defined group)

• hydrophobic or ampipathic

• contains nonpolar, carbon-hydrogen bonds (hydrocarbons)

lipid various biological roles

• energy storage

• membrane structure

• cell signaling

• protection/insulation

lipid structure

different lipids have different monomer compositions; don’t fit simple monomer/polymer structure

2 types of lipids

• triglycerides: energy storage molecules

• phospholipids: primary component of cell membranes

triglyceride structure

monomers:

• 1 glycerol molecule (3-carbon molecule; backbone)

• 3 fatty acids (carboxylic acid group attached to long hydrocarbon chain)

• glycerol and fatty acid monomers held together by ester bonds

fatty acids

FA hydrocarbon chains can be saturated or unsaturated

• saturated: all C-C single bonds/long straight chains (hydrogen-saturated)

• unsaturated: C=C double bonds / mono/poly-unsaturated (bends in FA chain)

saturation effects at room temp

saturated FA pack well (solid (fats))

unsaturated FA don’t (liquid (oils))

cis and trans double bonds in FAs

• H on same side = cis; H on opposite sides = trans

  • trans double bonds in FAs DONT significantly change shape of hydrocarbon chain

  • trans double bonds in FAs are artifically generated as byproduct of partial hydrogenation process

  • consuming FAs with trans double bonds (trans fats) has negative health effects

phospholipids

• monomers: glycerol, 2 FA chains, and phosphate group held together by ester bonds

• amphipathic: polar hydrophilic head and nonpolar hydrophobic tail

phospholipids in an aqueous environment

phospholipid bilayer; structural basis for cellular membranes

rank these in size from biggest to smallest: viruses, eukaryotic cells, atoms, macromolecules, prokaryotic cells

eukaryotic cells, prokaryotic cells, viruses, macromolecules, atoms

what are atoms

building blocks of life

elements

each is an individual type of atom

structure of an atom

• central nucleus: contains most of the atom’s mass (protons and neutrons)

• outside nucleus: electrons: very little mass, found in orbitals

charges in the atom structure

• in the nucleus, protons have charge +1 and neutrons have charge 0

• electrons have charge -1

• for an atom to be electrically neutral, # of protons = # of electrons

ions

atoms or molecules with a net + or - charge

• some atoms tend to lose electrons, others tend to gain

ionic bonds

electrostatic attraction between oppositely charged ions

covalent bonds

when atoms share electrons

• carbon can have 4 covalent bonds

types of covalent bonds

• nonpolar: electrons shared equally

• polar: unequally; electrons spend most of their time closer to one nucleus than the other

electronegativity (en)

how strongly an atom attracts electrons

• varies between atoms

• determines if covalent bond will be polar/nonpolar

  • if difference in ENs is <0.5: nonpolar covalent bond (equal sharing)

  • if difference in ENs is >=0.5: polar covalent bond (unequal)