Biochemistry - Proteins - EXAM 1

What is the central dogma?

DNA—>RNA—>unfolded protein (polypeptide chain)

What is the result of an unfolded protein?

No result: no structure = no function

What is transcription? Where does it occur?

DNA—>RNA. In cell nucleus.

What is translation? Where does it occur?

RNA—>protein (unfolded). On ribosome.

What are the simplest organisms?

Single celled organisms

Size of bacteria vs. animal cells

bacteria are smaller (1 um) and animal are larger (50 um)

Major differences between animal and plants cells (2)

animal: nucleus and compartmentalized (membrane bound organelles)

Bacteria: nucleoid and no internal membrane

Commonalities between animal and plant cells (3)

plasma membrane, ribosomes, cytoplasm

What are the 3 supramolecular complexes in the hierarchy of structure?

chromatin, plasma membrane, cell wall

What are the 3 macromolecules in the hierarchy of structure?

DNA, proteins, cellulose

What are the 3 monomeric units in the hierarchy of structure?

nucleotides, amino acid, sugars

What is the smallest unit of chromatin?

nucleotides

What is the smallest unit of the plasma membrane?

amino acids

What is the smallest unit of the cell wall?

sugars

hierarchy of nucleotides:

nucleotides—>DNA—>chromatin

hierarchy of amino acids:

amino acids—>protein—>plasma membrane

hierarchy of sugars:

sugar—>cellulose—>cell wall

What are the functions of proteins? (8)

Transport, pH balance, channels/pumps, fluid balance, antibodies, hormones, enzymes, structure+mechanics

What is life made up of? Why?

Made of carbon which can make four bonds, making a complex thing easier

Common elements that make up life (6)

C, H, O, N, P, S

Metal ions important to life (6)

Mg, Ca, K, Na, Zn, Fe

why is water the “medium for life” (4 reasons)

1) life began in water (protection from UV light)

2) organism = 70-90% water

3) chemical reactions occur in aqueous milieu

4) determines the structure of proteins, nucleic acids, and membranes

What partial charges are found within an H2O molecule

Partial positive on hydrogens, partial negative on oxygen

What kinds of bonds are observed in an H2O molecule

covalent bonds

What is the geometry of water?

distorated tetrahedron

What enables water to act as both a h bond donor and acceptor

the net dipole moment (polarity)

When are hydrogen bonds strongest

When bonding occurs in a linear pattern (electroneg, electropos,electroneg)

what kind of bonding is hydrogen bonding

either dipole-dipole or charge-dipole

Relationship between number of hydrogen bonds present and tempurature

As tempurature increases, number of hydrogen bonds decreases

What form of water has maximum hydrogen bonds

solid (ice)

What gives water such a high melting point, boiling point and surface tension?

Hydrogen bonds

How many hydrogen bonds can each H2O molecule form?

4

Which is stronger: H-O hydrogen bonds, or H-O covalent bonds

H-O covalent bonds

7 important impacts of h bonding

1) unique properties of water

2) structure/function of proteins

3)structure/function of DNA

4) Structure/funciton of polysaccharides

5) Binding of substrates to enzymes

6) Binding of hormones to receptors

7) matching of mRNA to tRNA

4 biological relevances of h bonding

1) alcohol - water

2) ketone carbonyl - water

3) peptide - peptide

4) DNA base pair - DNA base pair

common crystal form of water

hexagonal ice (6 angles)

entropy of hexagonal ice

low due to lattice formation

When entropy goes up, what happens to gibbs free energy

entropy up → delta g down (more feasible)

what is the relationship between delta g and reaction feasibility

positive g = less feasible, negative g = more feasible

does ice or water have a lower density? why?

ice is less dense than water because it’s unusually high number of h bonds creates more empty space between molecules

Charged, polar substances that water dissolves well (3)

amino acids, small alcohols, carbohydrates

non-polar substances that water is a bad solvent for (3)

aliphatic chains, non-polar gasses, aromatic moites

what is an alipatic molecule?

a molecule made up of a mixture of polar and non-polar substances

What is the make-up of polar vs. non-polar substances

polar: O and N present, nonpolar: C/H chain

rank the strength of the 4 non-covalent interactions:

ionic > dipole ~ hydrophobic effect > van der waals

are covalent or non-covalent interactions stronger?

covalent always stronger!

difference in electron sharing of covalent vs non-covalent bonding

covalent = permanent sharing of e-

non-covalent = temporary sharing of e- (21x weaker)

define ionic interactions

electron sharing between complete (+) and (-) charges

define dipole interation

electron sharing between uncharged, polar molecules (dipole moment)

define van der waal interaction

weak, universally present interaction between all atoms with an attractive (dispersion) and repulsive (steric) component

define hydrophobic interaction

how H2O orders around a non-polar substance

what happens to entropy as an ordered crystal lattice is dissolved?

entropy increases

what happens to entropy as salts are dissolved?

entropy increases initially as salts break apart (ionic interactions being broken), and then entropy decreases as water become more organized. overall, there is an increase in entropy

what is the hydrophobic effect?

an increase in the randomness of water, aka an increase in entropy of water molecules

what is the attractive force of van der waal interactions? what distance is it present at?

london dispersion forces dependent on polarizability, present at larger distances

what is the repulsive force of van der waals interactions? what distance does it occur at?

steric repulsion dependent on size, occurs over short distances

importance of van der waals in biology

steric compatibility, stabilize macromolecules (DNA), bind polarizable ligands

what does the hydrophobic effect play role in? (4)

preotein folding, protein-protein interaction, formation of lipid micelles, steroid hormone binding to receptors

is the hydrophpbic effect a force of attraction?

no, it is the increase or decrease in order of H2O molecules

Which force does not effect the attraction/repulsion of molecules

the hydrophobic effect = describes the displacement of water molecules

describe how enthalpy changes with lipid formation

initially entropy decreases as water organizes around lipids, then entropy increases as lipids aggregate (forming a micelle) and water is displaced

what would happen if water was not present as a substrate binds an enzyme?

it would take longer for binding to occur

why do hydrophobic solutes have low soluability?

because low entropy is thermodynamically unfavorable and aggregation of hydrophobic solutes displaces more water

result of micelle formation on entropy

entropy increases because more water is displaced with complete formation

colligative properties of water (3)

depend on concentration: melting point, boiling point, osmolarity

noncolligative properties of water

depend on chemical nature: viscousity, surface tension, taste, color

what is Osmotic pressure (π)

the force necessary to resist the movement of water (icRT)

identify the variables in the osmotic pressure equation: π = icrt

π = osmotic pressure

i = degree of immigration (solute)

c = concentration of solute

R = gas constant

T = tempurature

practice calculating salt concentration in order to identify osmotic pressure

examples in notes

what is the degree of immigration for a compound that does not ionize? give an example.

1. sucrose

water movement in an isotonic cell

no net movement

water movement in an hypotonic cell

water moves in → cell swells

water movement in an hypertonic cell

water moves out → cell shrinks

what happens to ionization of water when temp increases

ionization increases

are there free protons in ionized water?

no. h+ → h3o+ immediately

what is the equation for Keq of water

Keq = [H+] [OH-] / [H2O]

what is the process of water excepting an H+ to become hydronium ion called?

proton hopping

base/acids are proton acceptors/donors?

base = proton acceptor, acid = proton donor

why does water have a low Keq

because it ionizes very little, it like to stay in the form of H2O

Concentration of [H+] / [OH-] in pure water:

10e-7 M

what is the conenctration of water in pure water

55.5 M [H2O]

What is the keq of water @ 25 C

1.8e-16

what is Kw

Kw = Keq [H2O] = [H+] * [OH-] = 1e-14 M²

key eqution for pH calculations

pH = -log[H+] AND -log[H+] + -log[OH-] =14

dissociation of weak vs strong acids in water

strong: dissociate completely, weak: dissociate partially (Ka)

Ka equation

Ka = x² / [HA]

Pka calculation for weak acids

pKa = -log(ka)

in a buffer solution, when does pH = pKa?

pH = pKa when there is a 50:50 mixture of the acid and it’s anion

limitation of buffering capacity

+/- 1 pH unit from pH = pKa

where is the max buffer capacity?

where pH = pKa

what is the henderson-hasslebalch equation? (know how to work these problems both forwards and backwards)

pH = pKa + log [A-]/[HA]

What are buffer systems in vivo based on mainly?

phosphate, bicarbonate, histidine

What are buffer systems in vitro mainly based on?

sulfonic acids of cyclic amines (HEPES, PIPES, CHES)

Importance of pH to cells

enzyme catalyzed reactions have an optimal pH, equilibrium of CO2 gas and HCO3- depends on pH