biochem exam 1

Most common elements in life

Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur

size of an average bacterial cell

2 microns

central dogma of biology

DNA -\> RNA -\> Protein

\___ is the medium for life

water

biochemical reactions occur in

aqueous solutions

water is a critical determinant of

structure and function of proteins, nucleic acids, and membranes

hydrogen bond

weak electrostatic attraction between one electronegative atom and a hydrogen atom covalently linked to a second electronegative atom

water forms hydrogen bonds with

polar solutes

competition from water molecules

disrupts hydrogen bonds in other molecules

Why do nonpolar molecules not dissolve in water?

they do not make hydrogen bonds

hydrophobic effect

clustering of hydrophobic molecules in water

membrane formation is powered by

hydrophobic effect

covalent bonds are \___ than noncovalent bonds

stronger

equilibrium of the ionization of water

strongly to the left (most molecules remain un-ionized)

extent of water dissociation depends on

temperature

pH

-log[H+]

pH scale is

logarithmic

A 1 pH unit change \=

10x change in [H+]

Extent of dissociation is determined by

acid dissociation constant (Ka)

buffers

mixtures of weak acids and their conjugate bases

buffers resist

changes in pH

buffering capacity is greatest when

pH \= pKa

buffering zone

+/- 1 pH unit from pKa

what amino acid isomers are present in proteins

only L isomers

alpha amino acid

the alpha carbon is linked to an acidy carboxyl group, a basic amino group, a hydrogen, and an R group

all alpha amino acids are chiral EXCEPT

Glycine

amino acids can act as

weak acids and weak bases

the carboxyl group of amino acids is protonated at

a low pH

the amino group of amino acids is protonated at

a high pH

can the R groups of amino acids ionize

yes, some

Charge of amino acids at low pH

positive

charge of amino acids at high pH

negative

zwitterion

both positive and negative charge

When do zwitterions predominate?

At pH values between the pKa values of the amino and carboxyl groups

amino acids carry a net charge of zero at

the isoelectric point

at the isoelectric point amino acids

least water soluble, do not migrate in electrical field

pI \=

(pK1 + pK2)/2

Nonpolar, aliphatic amino acids

glycine, alanine, proline, valine, leucine, isoleucine, methionine

aromatic amino acids

phenylalanine, tyrosine, tryptophan

polar uncharged amino acids

serine, threonine, cysteine, asparagine, glutamine

positively charged amino acids

lysine, arginine, histidine

negatively charged amino acids

aspartate, glutamate

primary protein structure

sequence of amino acids

secondary protein structure

occurs when the sequence of amino acids are linked by hydrogen bonds

what are the most common types of secondary structures

alpha helix and beta sheet

how do your read amino acid sequences

amino terminal to carboxyl terminal (left to right)

pattern of polypeptide backbone

NCC

peptide bonds have

partial double bond character

the resonance of peptide bonds make them

rigid and planar

disulfide bonds

Strong chemical side bonds formed when the sulfur atoms in two adjacent protein chains are joined together.

disulfide bonds form by oxidation of

2 cysteines

are the peptide bonds of an alpha helix parallel or perpendicular

parallel

are the side chains of an alpha helix parallel or perpendicular

perpendicular

strong helix formers

Alanine and Leucine

Helix breakers

glycine and proline

side chains in beta sheets extend

above and below the plane

parallel beta sheet

all of the N-termini of successive strands are oriented in the same direction

antiparallel beta sheet

strands run in opposite directions

the hydrogen bonds of parallel beta sheets are

bent (weaker)

the hydrogen bonds of antiparallel beta sheets are

linear (stronger)

what is an example of beta sheets

fibroin in spider webs

examples of alpha helices

keratin (horns and hair), collagen

beta turn

A short U-shaped secondary structure in proteins where beta sheets change direction

how many amino acids make up a beta turn

4

amino acids common in beta turns

proline and glycine

tertiary protein structure

spatial arrangement of amino acids that are far apart in the primary structure

tertiary structures are stabilized by

weak interactions between side chains (disulfide bonds, hydrophobic, polar interactions)

globular proteins

these are compact, generally rounded, and soluble in water.

interior of globular proteins

consists mainly of hydrophobic amino acids

exterior of globular proteins

consists of charged and polar amino acids

quaternary protein structure

protein consisting of more than one amino acid chain

why is hemoglobin necessary?

because O2 has a low solubility in water

globins

oxygen binding proteins

myoglobin

stores oxygen in muscle cells

how many subunits does myoglobin have

one

hemoglobin

An iron-containing protein in red blood cells that reversibly binds oxygen.

How many subunits does hemoglobin have?

4 (2 alpha and 2 beta)

heme

iron containing prosthetic group

what form of iron is found in heme

ferrous (Fe2+)

The iron of heme is in the middle of

protoporphyrin

how many bonds does the iron of heme form

6 (4 in the porphyrin plane, 2 perpendicular)

how many bonds does iron from with nitrogen in the heme

4

how many bonds does heme form with oxygen

1

what residue does iron bond to in heme

histidine

oxygenation of heme causes the iron to

shift into the porphyrin plane

prosthetic groups are

nonprotein components permanently associated with the protein

hemoglobin is a tetramer composed of

2 identical dimers

hemoglobin dimers

1 alpha 1 beta

hemoglobin subunits are structurally similar to

myoglobin

positive cooperativity of hemoglobin

when first heme unit is oxygenated, O2 affinity of second heme unit is increased and so on

T state of hemoglobin

tense, low affinity for oxygen

R state of hemoglobin

relaxed, high affinity for oxygen

CO has a \_____ affinity for Hb than O2

higher

CO is a \___ for O2

competitive antagonist

the oxygen-binding curve of hemoglobin is what shape

sigmoidal

the shape of the oxygen binding curve of hemoglobin indicates what

cooperativity between subunits

2,3 BPG

binds to the "donut hole"; favors T-state - release of oxygen

fetal hemoglobin

has a higher affinity for oxygen than adult hemoglobin, lower affinity for 2,3-BPG

what molecules are produced by respiring tissues that enhance oxygen release by hemoglobin?

CO2 and H+

Bohr effect

the effect of carbon dioxide concentration on the uptake and release of oxygen by
hemoglobin