BIO13 Exam #1

Name the 5 characteristics of life

Made of cells (multicellular/unicellular)
Metabolism, takes in energy and nutrients to maintain homeostasis
Replicates/reproduces
Has genetic info
Product of evolution, populations continue to evolve

Name NASA’s definition of life

Self-sustaining
Darwinian evolution (natural selection)
Includes viruses, cells, genes

Correlate the # of covalent bonds an atom can make based on its valence number (1, 4, 5, 6, 7)

1 valence - 1 bond
4 valence - 4 bonds
5 valence - 3 bonds
6 valence - 2 bonds
7 valence - 1 bond

Correlate hydrogen, oxygen, nitrogen, and carbon to the number of bonds they make

H - 1
O - 2
N - 3
C - 4

Why is water polar?

Oxygen is more electronegative, causing electrons to share unequally; oxygen is partially negative while hydrogen is partially positive
It is a bent molecule, so its dipoles do not cancel

Water can form hydrogen bonds because

Oxygen has lone pairs and a partial negative charge, while hydrogens are partially positive

Hydrophilic molecules are

polar and charged

Hydrophobic molecules are

nonpolar

What feature allows water to form hydrogen bonds with polar/hydrophilic molecules?

Partial charges

What feature allows water to dissolve charged molecules and ions (ionic compounds)?

Water’s full dipole/partial charges

What feature allows water to exclude nonpolar/hydrophobic molecules?

High cohesive hydrogen bonding network between water molecules

Explain London dispersion forces

In nonpolar molecules, the constant movement of electrons creates small dipoles, resulting in weak electrostatic attractions between adjacent nonpolar molecules

Stronger London dispersion forces have

Longer carbon chains, more electrons/surface area

How does shape affect the strength of London dispersion forces?

Straight hydrocarbon chains have more surface area compared to kinked chains

What does boiling do to molecules joined together?

The thermal energy overcomes the noncovalent attractions between separate molecules only

Stronger London dispersion forces mean

more energy, higher boiling point

Weaker London dispersion forces mean

less energy, lower boiling point

Name the monomer and bonds for each macromolecule

Proteins - amino acids/peptide bonds
Carbs - monosaccharides/glycosidic linkages
Nucleic acids - nucleotides/phosphodiester bonds
Lipids - fatty acids/ester linkages

Hydrolysis _______ water

Consumes/splits

Condensation/dehydration synthesis _______ water

produces

Tertiary structure

Overall 3D structure of a single polypeptide chain, stabilized by side chain interactions

Quaternary structure

Overall 3D structure and assembly of multiple separate polypeptide chains, held together by the same interactions as tertiary structure but instead between the contact surface of subunits

How can a mutant subunit of a dimer fold normally but fail to form a dimer?

A mutation that alters charge, polarity or size destroys the noncovalent attractions between subunits; still folds normally because the mutation is on the exterior and the protein retains its tertiary fold

Conservative amino acid disruptions

Replaced with amino acid that has similar charge, polarity, size, or shape; can do same noncovalent interaction

Non-conservative amino acid disruption

Replacing amino acid with one from a completely different chemical class

Electrically charged, acidic (negative at physiological pH) amino acids contain

Carboxyl (-COO-); forms ionic bonds with positively charged groups
aspartate, glutamate

Electrically charged, basic (positive at physiological pH) amino acids contain

Amino/amine (-NH3+); forms ionic bonds with negatively charged groups
lysine, arginine, hystidine

Polar uncharged (hydrophilic, neutral) amino acids contain

Hydroxyl (-OH) or Amide (C=0 + amine); possess partial charges and form hydrogen bonds

Nonpolar (hydrophobic) amino acids contain

Hydrocarbons (C-H) and sulfur (thiol/sulfhydryl); interact through vdWs (London dispersion forces) and cluster away from water

-COO-

Carboxyl

-NH3+

Amine/amino

-OH

Hydroxyl

(C=O + -NH3+)

Amide

C-H

Hydrocarbon

-SH

Sulfhydryl

Shifting pH alters ionizable acidic and basic functional groups

Altering charges in ionic bonds (salt bridges) disassociates subunits into monomers

Heating/boiling/detergents will

denature and unfold both tertiary and quaternary proteins

Reducing agents…

break through covalent disulfide bonds

Acidic (-1)

Carboxyl (-COOH) → (-COO-)
Phosphate groups
Donate protons

Basic (+1)

Amino/amine (-NH2) → NH3+
Accepts H+ from solution at physiological pHnchU

Uncharged (0)

Amides (C=O + amine) do not accept protons
Hydroxyl (-OH), carbonyl (C=O), sulfhydryl (-SH), methyl and hydrocarbons do not form full charges

N-terminus

Beginning, -NH3+ or -NH2

C-terminus

End, -COO- or -COOH

Peptide bonds are

Covalent amide linkages (C-N) between carbonyl carbon and amino nitrogen

Tetrapeptide is

4 amino acid residues, 3 peptide bonds

SDS-PAGE separates polypeptides by

Size/weight, smaller proteins are faster

What does SDS-PAGE do to proteins?

Denatures proteins and coats them with negative charge

What does boiling do to proteins?

Disrupts all noncovalent interactions

What do reducing agents (BME or DTT) do to proteins?

Cleave disulfide bonds between cysteine side chains

If there is a disulfide (covalent) bond, without the reducing agent the protein

remains a single band

If there is a disulfide (covalent) bond, with the reducing agent the protein

will have two bands

If there are noncovalent bonds, and boiling and SDS disrupt all noncovalent interactions of the protein

there will be 2 bands

A sample taken halfway through activation reaction will have a mixture of starting materials and products, including

Unprocessed pro-H protein, mature H complex/fragments (N and C terminus), and a released middle segment

If a sample taken halfway through activation reaction has been reduced, the mature H will

be split into two bands, the overall mixture will have 4 pieces

If a sample taken halfway through activation reaction has NOT been reduced, the mature H will

be linked, the overall mixture will have 3 pieces

Difference between DNA and RNA base pairs

DNA has thymine, RNA has uracil

Double stranded DNA and RNA have

complementary strands, A=T/U, C=G

Single-stranded DNA and RNA have

non-equal base pairs

Describe the two ends of DNA

5’ unbound phosphate → 3’ free hydroxyl group; complementary strands run antiparallel

How do you classify sugars by counting carbons?

triose, tetrose, pentose, hexose

In linear form monosaccharides contain

One carbonyl (C=O) and all other carbons bear a hydroxyl group

A carbonyl at the end means

aldose

A carbonyl in the middle means

ketose

What is the first step to determining aldose or ketose?

Locate the intra-ring oxygen and examine the 2 carbons bonded to it, then identify which is attached to -OH.

If the carbon is attached to -H and -OH

it is at the end of the chain (C1) and is aldose

If the carbon is attached to -CH2OH

it is in the middle of the chain (C2) and is ketose

How do carbohydrates function as energy storage polysaccharides?

Starch (plants) and glycogen (animals) store monosaccharides that have been broken down for later ATP energy
They feature alpha glycosidic linkages that produce flexible, helical structures
They allow for a high degree of branching, with many free ends for enzymes to hydrolyze and release glucose for energy

How do carbohydrates function as structural support polysaccharides?

Cellulose in plant walls, chitin in fungal cell walls, and peptidoglycan in bacterial cell walls
Parallel linear strands via hydrogen bonds form tough, insoluble structural sheets
Few organisms produce enzymes that can hydrolyze these, instead they break down in digestive tracts

How do carbohydrates function in cell identification and surface signaling?

Oligosaccharides attach covalently to glycoproteins or glycolipids on the exterior interface of the cell membrane
These aid in cell identification communication, as well as protection

Describe steroid structure and diffusion

Lipid made up of nonpolar hydrocarbon rings and tails; small, nonpolar, hydrophobic nature allows for simple diffusion

What molecules pass through a membrane easily?

Small, nonpolar molecules

What molecules pass through a membrane slowly?

Small, uncharged polar molecules

What molecules cannot pass through a membrane without assistance?

Large uncharged polar or charged molecules/ions

Attaching what to a steroid would make it unable to cross a membrane on its own?

A polar, charged, or large hydrophilic group would alter the steroid to become polar/charged/hydrophilic

What would attaching a large hydrophilic, charged/polar group to a steroid do to its biological function?

It cannot cross the membrane on its own anymore, therefore it cannot enter the cell to bind to its target receptor and its intended biological response is blocked

When salt washes into soil

the Na+ and Cl- make the water a high solute concentration solution

High solute concentration on the outside is

hypertonic

Low solute concentration on the outside is

hypotonic

High solute concentrated soil water would be _____ relative to the cytoplasm of roadside plant cells

hypertonic

Osmosis is

net diffusion of water across a selectively permeable membrane, water moves to a high concentration

When salt washes into soil, water would move ______ plant cells

Water would move out of plant cells into the higher solute concentration; the loss of turgor pressure would cause the cells to shrink and even lead to plant damage or death

How do the double bonds/kinks in unsaturated fatty acids affect vdWs, membrane fluidity, and melting point?

The kinks prevent packing and surface contact, resulting in weaker vdWs. The membrane will be more fluid at lower temps due to lower melting point

How do the single carbon-carbon bonds and straight hydrocarbon chains in saturated fatty acids affect vdWs, membrane fluidity, and melting point?

The straight chains are able to pack together more easily, resulting in stronger vdWs. The membrane is less fluid and more rigid, as well as less permeable due to its higher melting point

Short tails in fatty acids mean

less surface contact, weaker vdWs and more fluidity

Long tails in fatty acids mean

more surface contact, stronger vdWs, more rigidity

How do organisms adapt in cold temperatures to prevent lipid slowness, packing, rigidity, and freezing?

They synthesize phospholipids with a higher percentage of unsaturated fatty acids/shorter hydrocarbon tails

How do organisms adapt in warm temperatures to prevent fluid/leaky lipid membranes?

They synthesize phospholipids with higher percentage of saturated fatty acids/longer hydrocarbon tails

A species with more unsaturated fatty acids and shorter chains will be in a

cold environment

A species with more saturated fatty acids and longer chains will be in a

warm environment

Entropy is

the amount of disorder/even spread

An increase in disorder is

positive delta S, drives a process to be spontaneous

A decrease in disorder is

negative delta S

Dissipating a concentration/ion gradient decreases or increases entropy?

Increases; diffusing increases spread

Osmosis when a cell is placed in a hypotonic solution increases/decreases entropy?

Increases; water will move into the cell, evening out solute distribution

Macromolecule hydrolysis increases or decreases entropy?

Increases; cleaving the polymer into monomers increases free movement

The phase change of ice melting increases or decreases entropy?

Increases; ice melting from solid to liquid state increases molecular movement

Establishing a concentration gradient increases or decreases entropy?

Decreases; ions/solutes are all pumped to one side

Dehydration synthesis/condensation (polymerization) increases or decreases entropy?

Decreases; joining the monomers restricts the free units

Protein assembly/folding increases or decreases entropy?

Decreases; this constrains polypeptide chains into structured complexes

For delta G to be negative (reaction is spontaneous/favorable), delta S must be

greater than 0 (positive)