Chapter 5 Part II

Question 1

Enzymes

Answer 1

• a catalyst
• accelerates/ speeds up chemical reactions without themselves being consumed
• can be proteins
• “molecular motors” that perform cellular work
  1) highly specific
  2) accelerate chemical reactions
  3) are not consumed in the reactions they catalyze

Question 2

Protein Structure

Answer 2

structurally complex molecules known, exhibit a specific 3-D structure or conformation, and may consist of one or more polypeptides

Question 3

Polypeptides

Answer 3

polymers that are constructed from the 20 aa monomers

Question 4

Amino Acids

Answer 4

organic molecules possessing both carboxyl and amino groups

• differ in their properties due to differing side chains, called “R” groups or functional groups
• building blocks of proteins (monomer)
• about 20 essential aa

Question 5

4 types of macromolecules

Answer 5

1) Sugar/ Carbohydrates
2) Lipid/ Fats
3) Protein
4) Nucleic Acid

Question 6

proteins

Answer 6

most diverse (macro)molecule on the face of the planet

Question 7

dehydration (hydrolysis)

Answer 7

removes a hydroxyl group from the carboxyl end of one aa and a hydrogen from another aa

Question 8

Peptide bond

Answer 8

-link aa together from a dehydration reaction (O=C-NH)

Question 9

Protein conformation

Answer 9

• 3D shape or conformation determines how it functions

- i.e. lysozyme: a “clamp” shaped protein that cuts proteins

Question 10

Four levels of protein structures

Answer 10

• hierarchical
  1) Primary Structure
  2) Secondary
  3) Tertiary
  4) Quaternary

Question 11

What ultimately determine the protein structure?

Answer 11

sequence and type of aa of a polypeptide

Question 12

Primary Structure

Answer 12

unique sequence of aa in a polypeptide that is determined by the genetic sequence

Question 13

Secondary Structure

Answer 13

the (local) folding or coiling of the polypeptide into a repeating configuration and is stabilized by intramolecular hydrogen bonding
-extremely versatile and strong

Question 14

2 types of secondary structures

Answer 14

1) Alpha helix

2) beta pleated sheet

Question 15

Alpha Helix

Answer 15

• single helical structure

- stabilized by hydrogen bonding between aa in the protein itself

Question 16

Beta Pleated Sheet

Answer 16

• stabilized through hydrogen bonding
• backbone of the polypeptide
• get layers of protein, like a fabric or mess
• hydrogen bonding in (side to side?) direction (very strong)

i.e. collagen, spider webs

Question 17

Tertiary Structure

Answer 17

• overall three-dimensional (3D) shape of a polypeptide (probably in an aqueous solution)
• Results from interactions between amino acids R groups, hydrogen bonding, and hydrophobic interactions (associations)
• help 3D (globular) protein/bonding; bonding between and among the aa

Question 18

Quaternary Structure

Answer 18

• the overall structure that results from the aggregation of two or more polypeptide subunits
• protein formed from 2 distinct polypeptides
• not all proteins have this structure
• i.e. collagen: 3 distinct polypeptides (3 a helix fibers; found in tissues, bone, cartilage, muscle)
• i.e. hemoglobin: 4 distinct polypeptides; major O transport protein

Question 19

Overview: 4 levels of protein structure

Answer 19

a polypeptide chain of a given aa sequence can spontaneously arrange itself into a 3D shape by the interactions responsible for secondary and tertiary structure

Question 20

Protein folding may also be determined by the…

Answer 20

protein’s environment

i.e. pH, temperature, the solution

Question 21

What determines protein conformation (shape)

Answer 21

depends on the physical and chemical conditions of the protein’s environment

Question 22

Denaturation

Answer 22

when a protein unravels and loses its native conformation

Question 23

Most proteins probably go through…

Answer 23

several intermediate states on their way to a stable confirmation

Question 24

Chaperonins

Answer 24

protein molecules that bind unfolded proteins and assist in their proper folding
-has a cap and a hollow cylinder

Question 25

Steps of Chaperoning Action

Answer 25

1) an unfolded polypeptide enters the cylinder from one end 2) the cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide 3) The cap comes off, and the properly folded protein is released

Question 26

Genes

Answer 26

- units that store and transmit heredity information and are made of DNA - determine or program the aa sequence of polypeptides and proteins - the substance of heredity

Question 27

DNA

Answer 27

- a polymer of nucleic acids | - stores information for the synthesis of specific proteins, RNA, and the synthesis of protein through RNA

Question 28

2 types of nucleic acids

Answer 28

1) DNA (deoxyribonucleic acid) | 2) RNA (ribonucleic acid)

Question 29

the flow of molecular information in a cell

Answer 29

DNA --> RNA --> protein 1) DNA can be synthesized into RNA within a nucleus 2) RNA can leave the nucleus of a cell (if eukaryotic) 3) RNA can be translated by the ribosomes (enzyme that reads RNA) which synthesizes the growing polypeptide (protein)

Question 30

Polynucleotide

Answer 30

- a polymer strand that makes up nucleic acids - consists of monomers called nucleotides - are made up of nucleotides linked by the X--OH group on the 3' carbon of one nucleotide and the phosphate on the 5' carbon on the next

Question 31

Nucleotide

Answer 31

monomers that make up a polynucleotide | - consist of 3 parts: nitrogenous base, pentose sugar, phosphate group

Question 32

Nucleoside

Answer 32

consists of a nitrogenous base and a pentose sugar

Question 33

2 types of nucleotide monomer nitrogenous bases

Answer 33

1) Purines | 2) Pyrimidines

Question 34

Purines

Answer 34

adenine (A) or guanine (G)

Question 35

Pyrimidines

Answer 35

cytosine (C) or thymine (T, DNA) or uracil (U, RNA)

Question 36

Difference between DNA and RNA structures

Answer 36

DNA is deoxygenated at C2; in RNA, there is a hydroxyl group

Question 37

Sequences of bases along a nucleotide polymer is...

Answer 37

unique for each gene

Question 38

Cellular DNA molecules contain (structure)

Answer 38

- 2 polynucleotides that spiral around an imaginary axis and form a double helix that consists of two antiparallel nucleotides strands - sugar-phosphate backbone -nitrogenous bases buried in the inside means they are hydrophobic

Question 39

The double helix was proposed by

Answer 39

in 1953 by | Watson, Crick, Franklin and Wilkins

Question 40

form hydrogen bonds in a complementary fashion

Answer 40

A with T only (or with U) C with G only help hold DNA together to create one molecule