Proteins, Enzymes, & Nucleic Acids

Question 1

What is competitive inhibition?

Answer 1

• inhibitors that compete with the substrate molecules for the active site
• action is proportional to its concentration; when more inhibitor is present compared to substrate, it will out-compete the substrate for the active site
• resembles the substrate structure closely
• no induced fit and no catalyze

Question 2

How many hydrogen bonds are between DNA?

Answer 2

2 hydrogen bonds between A-T
3 hydrogen bonds between G-C

Question 3

What is a phosphodiester bond

Answer 3

~the covalent bond between nucleotides
~ a result of the condensation reaction between the phosphate group of one nucleotide and a hydroxyl group on the sugar of the next nucleotide in the strand
~ one water molecule is produced

Question 4

What is the tertiary structure of proteins?

Answer 4

the helixes and sheets in a polypeptide arrange themselves according to hydrophobic ness/ hydrophilic ness, H-bonding, and electrostatic charges
~ Most of tertiary structure is determined by the hydrophobic effect; polar groups face towards the aqueous environment and non-polar groups towards the interior

Question 5

What is the active site of the enzyme?

Answer 5

region on the protein/enzyme where reactions happen

Question 6

How is a peptide bond formed?

Answer 6

2 amino acids bond, creating 1 water molecule (an oxygen from the carboxyl group and 2 H from the amino group) and a peptide bond which links a carbonyl group to N that is bonded to H

Question 7

Whats the quaternary structure of proteins?

Answer 7

various polypeptides can join together forming multi polypeptide proteins (ex. enzymes)
~ 2 or more large polypeptides interact to create a final shape that gives a protein its function

Question 8

What are nucleic acids made up of?

Answer 8

nucleotide monomers bonded together with a phosphodiester bond which creates a sugar-phosphate backbone

Question 9

Describe the lock and key mechanism regarding enzymes.

Answer 9

The enzyme is the lock and the substrate is the key
~ substrate binds to the enzyme (this is called Enzyme-substrate complex) and after the reaction is done, 2 products are produced

Question 10

What are enzymes

Answer 10

proteins that act as biological catalysts, increasing the rate of certain reactions

Question 11

What is the catalytic cycle for enzymes?

Answer 11

once the reaction is complete, the enzyme can go back to work on a new substrate molecule

Question 12

What is non-competitive inhibition?

Answer 12

• binds to a different site on the enzyme called the allosteric site, which regulates enzyme activity (they prevent the enzyme from working but do not bind to the active site)
• decreases enzyme activity

Question 13

For every 2 amino acids, how many water molecules are produced

Answer 13

1 water molecule

Question 14

What are proteins made up of?

Answer 14

amino acid monomers that are bonded together with a peptide bond forming a polypeptide

Question 15

What are the 4 different Nitrogenous bases?

Answer 15

Adenine, Thymine, Guanine, Cytosine
~ (A pairs with T, C pairs with G)

In RNA, all are the same except Thyme (Thymine) is replaced by Uracil

Question 16

What are the two types of nucleic acids? Describe.

Answer 16

DNA (deoxyribonucleic acid)
~ contains the genetic info of an organism which is decoded into particular amino acid sequences of proteins
~ contains a modified 5-carbon sugar which only has 4 oxygen atoms instead of 5 (this gives it its name of deoxy)

RNA (ribonucleic acid)
~ contains the genetic information of some virus particles and assists DNA to make proteins
~ is a large polymer that is composed of nucleotides which contain the sugar ribose (a normal 5-carbon sugar containing 5 oxygen atoms

Question 17

What are the 4 levels of protein structure?

Answer 17

Primary Structure

Secondary Structure

Tertiary Structure

• Quaternary Structure

Question 18

What are some factors that cause protein denaturation?

Answer 18

• changes in pH
• heat
• exposure to alcohol
• high salt concentrations

Question 19

What are some factors that affect enzyme activity? explain each.

Answer 19

• temperature (at high temps, proteins denature; at cold temps, the bonds are not flexible enough to allow the substrate to bind)
• pH (extreme pH levels cause protein denaturation)
• concentration of substrate & enzyme
• inhibitors (chemicals that reduce the rate of enzymatic reactions; reduce the enzyme’s ability to interact with its substrate)

Question 20

How do enzymes provide new reaction pathways?

Answer 20

by lowering the activation energy required

Question 21

What types of nitrogenous bases are pyrimidines and purines? Give examples.

Answer 21

PYRIMIDINES: single-ringed bases (Thymine & Cytosine)

PURINES: double-ringed bases (Adenine & Guanine)

Question 22

What is the secondary structure of proteins?

Answer 22

the amino acids hydrogen bond with neighbors, creating coils (alpha helix) or folds (beta-pleated sheets)
~ FOLDING: B sheets created when H-bonds form between 2 parts of the polypeptide chain layered on each other
~ COILING: alpha helix created by H-bonding between every 4th amino acid within a strand

Question 23

What does the structure of a nucleotide include

Answer 23

PSN

Phosphate Group
Sugar
Nitrogenous base

Question 24

Are enzymes recyclable?

Answer 24

Yes, they can be reused with every subsequent reaction

Question 25

What is the amino acid structure?

Answer 25

Ionized amino group on the left bonded to a C (with H bond at top and R bond at bottom) and ionized carboxyl group on the right

Question 26

What is an enzyme’s specificity determined by? What is the active site determined by?

Answer 26

the active site; active site is determined by the folding

Question 27

What are enzyme cofactors?

Answer 27

a metal ion or mineral needed by some enzymes to help the reaction
~ ex. iron, zinc

Question 28

What is induced fit for enzymes?

Answer 28

induced fit is when enzymes adjust their shapes so that the substrate fits perfectly

the enzymes “hug” the substrate

Question 29

What is protein denaturation? Give examples.

Answer 29

the breaking of many bonds within a protein molecule that disrupts its shape & stabilizes the highly ordered structure

short & simple: the breaking of bonds

ex: curling/straightening hair, curing meat, cooking

Question 30

What types of reactions can enzymes catalyze?

Answer 30

both ANABOLIC (synthesis/condensation) and CATABOLIC (hydrolysis) reactions

Question 31

What is the primary structure of proteins?

Answer 31

the linear sequence/order of amino acids
~ amino acid monomers are joined by peptide linkages, forming polypeptide strands

Question 32

What determines function when talking about proteins?

Answer 32

shape determines function

Question 33

What are hydrolase enzymes?

Answer 33

enzymes that catalyze hydrolysis reactions

Question 34

What’s the difference between RNA and DNA in terms of structure?

Answer 34

DNA has a missing oxygen on carbon 2 (hence it has 4 oxygens) and RNA has all 5 oxygens

Question 35

What are coenzymes?

Answer 35

organic molecules that assist the reaction (many vitamins are coenzymes)