Chapter 4

Question 1

What is an amino acid?

Answer 1

They are biological molecules that allow for the creation of proteins, cells, horomones, antibodies, transporters, basically everything we need to survie on a biological basis

Question 2

Basic Structure of an amino acid?

Answer 2

Question 3

What are the classifications of Amino Acids?

Answer 3

Polar, Non Polar, Acidic, Basic

Question 4

How many amino acids are there?

Answer 4

There are a total of 20 amino acids in the human body.

Question 5

What are the two acidic amino acids? What are their structures?

Answer 5

Aspartic Acid and Glutamic Acid

They both have carboxylic acid functinoal group in their side chain with a PKA of 4

Rember glutamic acid glues on an extra CH2 to aspartic acid

Question 6

What are the Basic Amino Acids? And their structures?

Answer 6

Lysine, Argeine, Histidine

Question 7

hydrophobic (nonpolar) amino acids

Answer 7

Glycine, Alanine Valine Leucine Isoleucine phenylalanine tryptophan

GLY G, ALA A, VAL V, LEU L, Ile I, Phe F, Trp W

Question 8

Polar Amino Acids and structures

Answer 8

Serine Threonine Tyrosine Asparagine Glutamine

Ser S, Thr T, Tyr Y, Asn N, Gln Q

Question 9

Sulfur containg amino acids

Answer 9

Cysteine, Methionine

Cys C, Met M

Question 10

Proline

Answer 10

Proline is unique the amino group is covalently bound to its non polar chain, which creates a secondar alpha amion group and ring structure. It causes kinks in protein folding due to this structure.

Pro P

Question 11

what is the henderson hasselbalch equation?

what is this equation used for ?

Answer 11

Ph=pka+log [H-]/[HA] = PKA + log baseform/acidform

This equation is used to describe relationship between ph and pka and the postion of equilibirum.

Question 12

what happesn when PH of soloutin is less than the pka of an acid group.

Answer 12

the acidic group will be in its protonated form.

Question 13

what happens when the ph of the soloution is more than the pka of the acidic group?

Answer 13

the acidic group will be in its deprotonated form

Question 14

What is the isoelectric point?

Answer 14

The isoelectric point is considered the zwitterion. This is when the PH is considered uncharged. It is designated by pI where there is a postive and negative charge.

Zwitter in german means hybrid

Question 15

How do you calculate the zwitter ion?

Answer 15

add the first pka with the second pka and divide by two

pKa1 + pKa2 /2 = pI

Question 16

What are the two common types of covalent bonds between amino acids?

Answer 16

Peptide bonds and disulfide bridges

Question 17

What is the peptide bond? How is this bond formed?

Answer 17

The pepetide bond links amino acids to one another. This bond is formed though a dehydration rxn with the loss of water. It is formed between the caroxyl group of one amino acid and the alpha amion group. Pictured is the rxn

Question 18

What is the polypetide bond pattern for the formation ?

Answer 18

n c c n cc

Question 19

What is an individual amino acid called?

Answer 19

Residue

Question 20

What is it called when a protein hydrolysis another protein?

Answer 20

This is called proteolysis or porteolytic cleaveage.

Question 21

What is the protein called that cleaves another protein

Answer 21

Protease , or Proteolytic enzyme

Question 22

Disulfide Bond

Answer 22

Disulfide bonds are formed between two cysteine amino acides to make a cystine. This is done through a oxidation rxn. with the loss of hydrogen on both cysteine amino acids.

Question 23

What is it called when a protein is broken down.

Answer 23

The term is dentauration

Question 24

What are the ways that a protein can be denatured?

Answer 24

Increase in heat, decrease in pH, chemical

Question 25

Primary structure 1

Answer 25

This is the first structure in creation of proteins, this is the polypetide backbone of the protein. refered to as a sequene

Question 26

Secondary Structure

Answer 26

This is the intial folding of the chain, which folds into shapes to stabilze. This is done with hydrogen bonding. Two common alpha helix and beta pleated sheats

Question 27

How does proline cause an issue in peptide chain?

Answer 27

Forces the chain to kink, due to the bonding of one hydrogen on the nitrogen not being able to complete the chian.

Question 28

Tertiary Structure

Answer 28

Concerns with distant amino acids interactions This is done through van der walls forces between nonpolar side chains, hydrogen bonds between polar sidechians and cysteing disulfide.

Question 29

What is the hydrophobic effect concering proteing folding?

Answer 29

The hydrophobic effect concering proteins, has to do with the folding during the tertiary stages. The exterior of the protein becaums hydrophili, while they hydrophobic R groups fold inwards.

Question 30

Quaternary Structure

Answer 30

Is the interaction between various polypetide subunits. Example is hemoglobin which is 4 proteins together. Forces stabilizing the are similar to teritary, besides the peptide chain which only is in primary.

Question 31

# Define each Term Hydrolase Isomerase Ligase Lyase

Answer 31

Hydrozels chemical bonds rearranges bonds withing a molecule to form an isomer Forms ca chemical bond (glue) Breaks a chemical bond by means other than oxidation or hydrolsis

Question 32

# Define each term Kinase Oxidoreductase Polymerase Phophsatase

Answer 32

transfers a phosphate group to amolecule from a high energy carrier such as ATP runs redox rxns polymerization additon of nucleotids to the leading strand of dna by dna polmerase 3 removes a phosphate group

Question 33

# Define Each Term Phopshorlylase Protease

Answer 33

transfers a phosphate group to a molecule from inorganic phosphate hydrolyzes pepetide bonds

Question 34

Reaction Coupling

Answer 34

This allows for thermodynamically unfavorbale rxns to occur through coupling with ATP hydrolsis. ATP to ADP + PO 4 2- ^G -12 the properties are additve so by adding the ATP hydrolsis it can push a rxn to the negative Delta G

Question 35

Active Site Model (Lock and Key)

Answer 35

Binding no conformation change

Question 36

Induced fit model

Answer 36

Active site and substrate are different,and they go through a conformational change