02

Question 1

What is the structure of the amino acid

Answer 1

alpha carbon
amino group, carboxylic acid, hydrogen, unique side chain (R)

Question 2

What are zwitterions

Answer 2

state when amino acids exist at physiological pH
- pH 7.35-7.45 in blood
- amino and carboxylic groups ar charged
- molecule is neutral

depending on pKa of each functional group, it may be charged or uncharged at physiological pH

Question 3

Which part of the amino acids do peptide bonds form
How do they occur

Answer 3

between the carboxylic acid group of one amino acid and the amino acid of the amino group
- condensation reaction
- catalyzed by ribosomes

Backbone formed by nitrogens and carbons

Question 4

What is a nonpolar, aliphatic molecule

Answer 4

have mostly hydrophobic side chains
- shared electrons, no charges to interact with the polar water molecules

Question 5

What is an aromatic molecule

Answer 5

have aromatic rings in their side chains
- have different polarities (could be non polar or polar)

Question 6

What is a polar, uncharged molecule

Answer 6

have side chains containing electronegative O and N atom
- electrons are not shared equally
- side groups are not charged at physiological pH
- can form hydrogen bonds and participate in chemical reactions

Question 7

What is a sulfur-containing molecule

Answer 7

S bonded to C

methionine and cysteine (can form SS bonds)

Question 8

What is a charged molecule

Answer 8

carry (or can carry) a charge on their side at physiological pH

Question 9

When are buffers most effective

Answer 9

when pH=pKa
- equal amount of acid and base are present
(in blood, when pKa = ~7)

Question 10

What are disulfide bonds

Answer 10

sulfhydryl groups of two cysteines are oxidized and bound together
- spontaneous, doesnt require an enzyme
Strong covalent bond because the sulfur atoms share the electrons equally

conformational stabilizer - holds different parts of a proteins molecule together or 2 or more chains that make up a protein molecule

Question 11

What are electrostatic (ionic) interactions

Answer 11

charged groups on amino acids interact with each other

when pH changes, more H+ starts to bond –> no more charge, cannot participate in the interaction and starts to unfold

Question 12

what are the types of post-translational modifications

Answer 12

can alter the structure or function of a protein –> allow other molecules to interact with them or altering the location of the protein in the cell
- accesorizing a protein to recognize self and doesn’t illicit immune response

1. carbohydrate addition
   - o-glycosylation (OH)
   - N-glycosylation (NH2)
2. regulation (uncharged to charged or charged to uncharged)
   - phosphorylation
   - acetylation
3. modified amino acids
   - oxidation
   - carboxylation

Question 13

What is the N and C terminus

Answer 13

N-terminus: has NH3

C terminus: has COOH

Question 14

What is sickle cell disease

Answer 14

point mutation in the gene for B-globin protein
- mutation changes the 6th amino acid in the B-globin chain of hemoglobin from glutamate to valine

(changes the structure of the RBC –> changes function (more rigid))

Question 15

What is the heterozygotic pattern of hemoglobin

Answer 15

1 good allele, 1 altered allele
- mixture of normal and altered hemoglobin
- usually asymptomatic unless under stress
- protects against malaria

Question 16

What is a homozygotic pattern of hemoglobin

Answer 16

either 2 good allele or 2 altered alleles
- both copies encode the sickle cell allele (homozygous), all the hemoglobin will be the altered version

Question 17

What does homologs mean

Answer 17

similar protein that have arisen from a common ancestor, often by gene duplication

Question 18

What are the types of general protein structure

Answer 18

globular protein: balls of polypeptide

fibrous protein: long linear (repeating structures)

Transmembrane proteins: embedded in plasma membrane

DNA binding proteins: bind to DNA

Question 19

What type of bonds hold protein shapes

Answer 19

non covalent bonds
- electrostatic (ionic) interactions
- hydrogen bonds
- hydrophobic interactions (non-polar amino acids)

Question 20

What are the protein structure rules

Answer 20

3d structure must be flexible enough to function properly

stable enough that it will not convert to another conformation

exposed amino acids must be compatible with the environments the protein will function in

Question 21

What is primary structure of protein

Answer 21

sequence of aa in the polypeptide chain determined by genetic code
- connected through peptide bonds
- rigid and stable
- Rchains are on opposite sides of the bond
- direction from n-terminal to c-terminal

Question 22

What is secondary structure

Answer 22

a-helix
- maintained by h bonds
- H in N-H forms a Hbond with the O=C of the amino acids 4 residues away in the peptide chain
- no proline “helix breaker” because no hydrogen on nitrogen
- R groups radiate out to stabilize

B-sheets
- AA in a flat plane
- can be parallel or anti parallel
- more rigid than a-helix
- can form B-barrels –> transport hydrophobic substances or form pores in membranes

Question 23

What is tertiary structure

Answer 23

secondary structures combine with irregular elements (loops and turns)
- AA from primary structure define which secondary structure will be adopted and which tertiary conformation every molecule of the protein will take

Question 24

What is quarternary structure

Answer 24

proteins that are made up of more than one polypeptide subunit (eg. dimers, trimers, tetramers…)

Question 25

What are immunoglobulins

Answer 25

antibodies –> defense functions

2 light and 2 heavy chains held together by disulphide bonds
- form a Y shape
- antigens are bound at the ends of the Y

Question 26

What are the factors that contribute to protein denaturation

Answer 26

1. temperature
2. pH (changes the protonation of side chains – impact HB and IB)
3. protein modifications (cause new folding)
4. binding to other proteins

Question 27

What is unintended protein modification

Answer 27

higher concentration of glucose in blood = glycation

Question 28

What are the steps of ABG analysis

Answer 28

1. look at pH (acidosis or alkalosis or nomal)
2. Look at CO2 and HCO3- (one abnormal = no compensation, both abnormal = some compensation)
3. compare the pH and pCO2 to determine where the H+ are coming from or going (tells you which direction it is moving)