Biochemistry Exam 2

H covalently bonded to OH (hydroxyl) or NH2 (amino group)

How do you know if a functional group can be a hydrogen bond donor?

Enzymes, hormones, storage proteins, transport proteins, structural proteins, protective proteins, contractile proteins

What are the seven classes of proteins?

Enzymes

Proteins that are natural catalysts

Hormones

Proteins that are natural messengers that regulate the body

Ex) Insulin - regulates glucose metabolism

Storage proteins

Proteins that reserve resources so they’re immediately available when needed

Ex) Ovalbumin - Nutrient in egg whites that’s eventually hydrolyzed when needed

Transport proteins

Carry substances through the bloodstream and membranes

Ex) Hemoglobin - Carries O2 in blood

Structural proteins

Provides support and shape to cells

Ex) Fingernails

Protective proteins

Proteins that defend against invaders

Ex) Anti-bodies

Contractile proteins

Responsible for generating force and enabling movement. Essential for locomotion, heartbeat.

Ex) Actin - thin filaments in muscle fibers; Myosin - Thick filaments

Amine, carboxylic acid, R

Amino acids are made up of a positive ______ group on one end and a negative __________ on the other end. The _______ group on the alpha carbon makes it unique.

Stereoisomers

Atoms bonded in the same order, but in different arrangements

Enantiomers

Mirror images cannot be superimposed - complete mirrors of one another

Diastereomers

Stereoisomers that aren’t complete mirrors of one another

Nonpolar, neutral polar, acidic, basic

Name the four classes of amino acids

Positive, amino

Lowering pH means ________ charge in ________ group

Negative, carboxyllic acid

Higher pH means _________ charge in ________ group

Zwitterionic

The amino acid has a pH of 7, no matter if it’s deprotonated (lower pH) or protonated (higher pH).

Peptide bond

Amide bond (C-NH) that covalently links two amino acids

Covalent, amino acids

Primary: ________ bonds between atoms of ___________ _____

Hydrogen bonds, backbone amine groups (-NH) of different amino acids

Secondary: _______________ ___________ b/t _______________

Hydrophobic

Tertiary: Folding of secondary structures due to _________ nature; 1 chain

Covalent, non-covalent (electrostatic/salt bridges) + disulfide bonds

Quaternary: Has more than 1 protein chain, held together by _____ and _____ bonds

Secondary alpha-helix structure

N donates H to stabilize amide groups

Peptide bonds create curling

Only involves backbone atoms, no side chain interaction

Stabilized by H-bonds forming between peptide bonds

Secondary beta structure

Peptide bonds between residues

H bonds between adjacent strands

Disulfide bonds, hydrogen bonds, VDWF, salt bridges

Tertiary structures are stabilized by what forces to fold

Salt bridges

Acidic and basic side chains

Amino and carboxyl termini

N-/C-termini

Glycine

No organic side chain, flexible - located in turns

Proline

Secondary amine (side chain attached to Ca and backbone N)

Forms tertiary amide upon formation of peptide bond

Ridged structure, found at end of helix and beginning of turns

Cysteine

Thiol (-SH) group forms disulfide bonds in extracellular proteins, binds metal

Globular

Forms a globe-like structure, typically water soluble as

hydrophilic residues are on the surface (eg. Enzymes)

Fibrous

Insoluble sheets or fibers containing small hydrophobic residues that pack tightly together in layers; either all a-helical or b-sheet

(Hair, teeth, finger nails)

Collagen

Stabilized by H-Bonds = Insoluble

Sickle Cell Anemia

Genetic disorder where acidic residue changes to hydrophobic residue in red blood cells (2 glutamate mutated into valine). Now, mutated cell is more (+) due to loss of O-

Chaperones

Proteins that assist in holding onto hydrophobic regions serving as shelter. Assist in folding, keep from hanging around and being nonfunctional

Prions

CNS proteins that cause properly folded proteins to fold incorrectly. Can form holes in the brain.

Protein Digestion

Proteins into amino acids by adding water

Occurs in lysosomes, proteasomes, stomach, and small intestine

Proteasomes

Degrade unneeded proteins by unfolding

Heat

Mechanical agitation/lack of water

Detergents (Unfolds side chains)

Organic compounds (Polar solvents disrupt H-bonds)

pH change

Inorganic salts (disrupt salt bridges)

What six things cause protein denaturation?

Turnover number

Number of substrates converted to product at given time

Cofactor

Nonprotein substance that binds to the protein and is required for catalysis (is under or over the arrow)

Coenzyme

Organic cofactors typically found in Redox enzymes

Apoenzyme

Non-active version of an enzyme that lacks its cofactor or coenzyme

Holoenzyme

An activated enzyme with its cofactor or coenzyme

Proximity effect

Bring reactants together

Orientation effect

Hold reactants at the required distance

for the reaction

Energy effect

Lower activation energy by inducing a strain on the bonds of the substrate

Catalytic effect

Provide acidic, basic and other types of functional groups that are

required for catalysis

Highly specific enzyme

Active site catalyzes one type of reaction for a single substrate

Nonspecific enzyme

Catalyzes a single reaction for a group of similar substrates

Induced fit

Substrate binding triggers a conformational change in the enzyme itself. Scale of change may vary.

Four factors that affect enzyme activity

Substrate concentration

Enzyme concentration

Temperature

pH

Neutral, only made up of hydrocarbons

Nonpolar side chains are _____

Neutral, not made up of only hydrocarbons

Neutral polar side chains are ______

Positively charged

Basic side chains are ______

Negatively charged

Acidic side chains are _________

2 rings - 1 six carbon, 1 five carbon

Purine has ______

Single six-membered ring

Pyrimidine has ________

Phosphate anhydride

What bonds bond together phosphates in nucleic acid 

Covalent, peptide bonds

Bonds in primary structure

Hydrogen bonds between backbones

Bonds in secondary structure

Everything but covalent bonds

Tertiary bonding

All bonds (covalent, disulfide, salt bridges, hydrogen bonding)

Quaternary bonding

Hemoglobin

Has 4 polypeptide chains

Transports oxygen from the lungs to tissues (transport protein)

Allosteric regulator

Can cause sickle cell anemia

Myoglobin

Single polypeptide chain

Stores oxygen (storage protein)

High affinity for oxygen

In muscle cells

Allosteric regulation

Binding a molecule to a site other than the active site to either increase or decrease a reaction (ex. of noncompetitive inhibition)

Feedback control

Product becomes an allosteric regulator

Electrophoresis, anode, cathode

Proteins separated by charge and size: positive side - ____________; negative side - ___________

Function: Quaternary, tough protein that provides strength in bone and tissue
Subunit: Tropocollagen

Covalent, disulfide bonds between strands
Location: Bones, muscle, other tissue

Define collagen in terms of its functions, structures and cellular location.

Brittle bone disease

Disease related to collagen deficiency

Abundance of glycine

What allows for collagen to be so compact?

Disulfide, heat, hydrogen bonds, van der waals forces

Perms breakdown ______ bonds, and a curling iron adds _____ to break ________ and build new ________________

Insoluble

Fibrous proteins, like collagen, are…

Proteasomes

Agents that degrade unneeded proteins by unfolding them

Alpha helix

More single-chain interactions

Coiled, warp around itself

Intrachain H-bonds between C=O and N-H

Flexible

B pleated sheet

Multiple chains lying side by side

Flat

Inter or intra h-bonding

Parallel or antiparallel strand running

Rigid