BIO2: Unit 1

define: hydrophobic interactions

forcing of nonpolar/hydrophobic groups together in the presence of water

which 2 particular molecules are very electronegative?

oxygen (O) and nitrogen (N)

define: nonpolar covalent bond

an equal sharing of electrons due to similar electronegativities

define: polar covalent bond

an unequal sharing of electrons due to different electronegativities

place the 5 bonds/interactions in order of strongest to weakest

1. covalent bonds
2. ionic bonds
3. hydrogen bond
4. hydrophobic interactions
5. van der waals interactions

what are the 4 emergent properties of water

1. cohesion/adhesion
2. moderation of temperature
3. lower density of ice
4. versatility as a solvent

what makes water cohesive?

hydrogen bonding allows water molecules to stick together

cohesion vs. adhesion

* cohesion: water sticking to other water
* adhesion: water sticking to other polar substances

why is ice less dense than water?

when water freezes, the molecules form stable H-bonds and therefore less densely packed as ice

what kind of compounds can water dissolve?

water can only dissolve polar/hydrophilic compounds

define: pH

tells us how out of balance a solution is by \[OH-\] and \[H+\]

what does a change in pH value represent?

a 10 fold increase or decrease in \[H+\]

define: acid

a molecule that can donate a proton (H+) to solution

define: base

a molecule that can accept a proton (H+) in solution

define: buffers

substances that minimize changes in \[H+\] and \[OH-\] in a solution

identify the functional group:

hydroxyl group (-OH)

identify the functional group:

carbonyl group

identify the functional group:

carboxyl group (-COOH or COO-)

identify the functional group:

amino group (-NH2 or NH3+)

identify the functional group:

sulfhydryl group (S-H)

identify the functional group:

methyl group (CH3)

identify the functional group:

phosphate group

which functional group contains nitrogen?

amino group

which functional group contains sulfur?

sulfhydryl group

which functional group contains phosphorous?

phosphate group

which functional group is nonpolar?

methyl group

which functional group is an acid?

carboxyl group

which functional group is a base?

amino group

what is the difference between protonated and deprotonated?

* protonated: has H+


* deprotonated: doesn’t have H+

what are the 4 classes of macromolecules?

1. carbohydrates
2. proteins
3. nucleic acids
4. lipids

what process forms polymers?

dehydration synthesis/rxns

define: hydrolysis

a rxn in which a polymer is broken apart, consumes 1 water molecule

carbohydrate:

* monomer?
* polymer?
* link?
* atoms present?

* monosaccharide
* polysaccharide
* covalent glycosidic linkages
* C,H,O (1:2:1)

protein:

* monomer?
* polymer?
* link?
* atoms present?

* amino acid
* polypeptide
* peptide bond
* C,H,O,N,S

nucleic acid:

* monomer?
* polymer?
* link?
* atoms present?

* nucleotide
* polynucleotide
* …
* C,H,O,N,P

what determines polysaccharide structure?

the sugar monomers + the position of the glycosidic linkages

what are the 3 components of a protein?

1. amino group (+)
2. alpha carbon
3. carboxyl group (-)

what forms the secondary structure of a protein?

H-bonds forming between the polar backbone

what forms the tertiary structure of a protein?

weak bonding between side chains of 1 polypeptide

what forms the quaternary structure of a protein?

multiple polypeptide chains interacting/bonding

why when a protein denatures, does the polypeptide chain not come apart into small sections?

the denaturation is only able to break the weak bonds, the bonds along the backbone are covalent bonds and are difficult to break

what are the 3 components of a nucleic acid?

1. 5 carbon sugar
2. phosphate group
3. nitrogenous base

what are the differences between DNA and RNA?

DNA:

* double stranded
* contains thymine
* has an H at C2

RNA

* single stranded
* contains uracil
* has an OH at C2

what are the 3 main types of lipids?

1. triglycerides (fats)

2. phospholipids

3. steroids

what makes lipids hydrophobic?

non-polar C-H bonds

what composes a triglyceride (fat)?

1 glycerol linked to 3 fatty acids by ester linkages

what composes a fatty acid?

a long hydrocarbon chain and a carboxyl group

which part of a phospholipid composes the hydrophobic core?

the hydrophobic tails form the core, the hydrophilic heads point outward

what are the steps of the Na/K pump?

1. 3 Na binds to the protein intracellularly

2. 1 phosphate from ATP binds to protein, rotating it to face outside the cell

3. the rotated protein releases Na outside of the cell

4. 2 K binds with the protein

5. phosphate group is release and protein rotates back

6. 2 K are released inside the cell

how does the Na/glucose co-transporter work?

2 Na bind and enter the cell, 1 glucose binds and enters the cell

what are the conditions inside and outside the cell that enable the Na/glucose co-transporter to work?

extracellularly: high [Na], low [glucose]

intracellularly: low [Na], high [glucose]

do Na and glucose go against or with their gradient with the Na/glucose co-transporter?

• glucose goes against its gradient

• Na moves with its gradient

what composes a steroid?

C-skeleton and 4 fused rings

what organelles are responsible for genetic control?

the nucleus and ribosomes

what organelles are responsible for manufacturing, distribution, and breakdown?

the endomembrane system (golgi, ER, etc.)

what organelles are responsible for energy processing?

mitochondria + chloroplast

what organelles are responsible for structural support, movement, and communication?

cytoskeleton

what are the 3 main components of the nucleus and their characteristics)?

1. nuclear envelope (bilayer with pores)

2. chromatin (includes DNA + associated proteins)

3. nucleolus (side of ribosome synthesis)

ribosome function?

protein synthesis

what are the 3 filaments of the cytoskeleton?

1. actin (microfilaments)

2. tubulin (microtubules)

3. fibrous (intermediate filaments)

actin (microfilament) function?

• cell shape

• cytokinesis

• contractability

tubulin (microtubule) function?

• intracellular transport (cell-to-cell)

• cell motility (cilia + flagella)

fibrous (intermediate filament) function?

• cell shape

• anchoring of nucleus + organelles

why do the mitochondria + chloroplasts have its own DNA?

it is believed to be linked to a eukaryote’s phagocytosis origin

what energy centers to plants have?

mitochondria AND chloroplast

chloroplast function?

converts light energy to chemical energy

what part of the chloroplast collects light for photosynthesis?

thylakoids

peroxisome function?

breaks down fatty acids for energy

rough ER function?

makes proteins + membranes for ecport

Golgi apparatus function?

modifies proteins from rough ER

what is the path a protein travels during synthesis?

ribosomes → ER → cis Golgi → trans Golgi → final destination

lysosome function?

contain digestive enzymes that break down things

• lysosomes fuse with vacuole to digest molecules

smooth ER function?

diverse functions inc manufacturing lipids, storing calcium, etc.

what types of molecules can cross membranes via simple diffusion?

small and nonpolar

what types of molecules can cross membranes via facilitated diffusion?

large, polar, or charged molecules

does facilitated diffusion require a protein?

yes, can be a carrier or channel protein

what types of molecules can cross membranes via primary active transport?

large, polar, or charged molecules

does primary active transport require a protein?

yes, a carrier protein

does primary active transport require energy?

yes, ATP is required

do molecules traveling via primary active transport move with or against the gradient?

both molecules move against the concentration gradient

what types of molecules can cross membranes via secondary active transport?

large, polar, or charged

does secondary active transport require a protein?

yes, a carrier protein

does seconadry active transport require energy?

yes, it requires indirect ATP from the Na gradient flowing from the outside of the cell in

do molecules traveling via secondary active transport move with or against their gradient?

• Na moves with its concentration gradient

• glucose moves against its concentration gradient

what is membrane potential?

a potential gradient that forces ions to passively move in one direction (+ attracted to - side and vice versa)

what is an electrochemical gradient?

a combination of concentration and electrical gradient (membrane potential)

what type of protein generates membrane potential?

carrier proteins

how does water act as a versatile solvent for ionic compounds?

the salt ionizes into its anion and cation which are then surrounded by the partial + and - end of the water molecules forming a hydration shell around them

how does water act as a versatile solvent for sucrose?

what can form hydrogen bonds with the sugar molecules (hydroxyl groups), dissolving it

what composes a phospholipid?

2 fatty acid chains attached to a glycerol; phosphate group present

starch

1. monomer

2. function

3. structure/shape

4. where in nature?

1. glucose

2. storage in plants

3. helical, branched or unbranched

4. plants (chloroplasts)

glycogen

1. monomer

2. function

3. structure/shape

4. where in nature?

1. glucose

2. storage in animals

3. highly branched

4. animals

cellulose

1. monomer

2. function

3. structure/shape

4. where in nature?

1. glucose

2. structure/protection

3. unbranched, forms microfibrils

4. plant cell walls

chitin

1. monomer

2. function

3. structure/shape

4. where in nature?

1. glucose

2. structure/protection

3. unbranched, has N containing group

4. insect exoskeleton, cell walls of fungi

main function of triacylglycerides?

long-term energy source

what type of bonds hold the nucleotide bases together in DNA?

H-bonds

how many bonds are formed between the different nitrogenous base pairs?

3 H-bonds between G and C

2 H-bonds between A and T

how is DNA arranged in a prokaryote vs. eukaryote cell?

prokaryote: single circle of DNA

eukaryote: multiple strands of DNA (chromosomes)

do both prokaryotes and eukaryotes have cell walls?

prokaryotes: yes

eukaryotes: only in plants (cellulose) and some fungi (chitin)

what cells have peroxisomes, lysosomes, and centrosomes?

all eukaryotic cells