Week 4 Recall Questions

Question 1

A) Nucleic Acids

What are the different types of nucleic acids?
What are their building blocks?

Answer 1

• DNA and RNA

• Building blocks:
- 5 carbon sugar
- 3 or more negatively charged phosphate groups
- nitrogenous base
—> contains 1 or 2 rings made of carbon and nitrogens.

• Carbons are numbered and if has prime symbol, means it’s from sugar ring.

Question 2

A) Nucleic Acids

What is the difference between the deoxyribose sugar found in DNA and the ribose sugar found in RNA?

Answer 2

• DNA
- C’2 (carbon 2 prime), has a H attached.
- in Nitrogenous base:
— C, T, A, Or G.
—> thymine used

• RNA

• C’2 (carbon 2 prime), has a OH attached.
• in Nitrogenous base:
  — C, U, A, Or G.
  —> uresil used

Similarities:
• phosphate group attached to 5’C
• Hydroxyl group attached to 3’C

Question 3

A) Nucleic Acids

What is the function of DNA?

Answer 3

• is a polymer
• DNA is the genetic material of the cell
  • Contains all instructions for cell structure and function
  • Directs its own replication
  •Directs RNA synthesis

Question 4

A) Nucleic Acids

What is the function of RNA?

Answer 4

• is a polymer

• Carries information in our cells
• Essential for protein synthesis

Question 5

A) Nucleic Acids

What are the two different nucleotides? What are their building blocks? (Fig F-36)

Question 6

A) Nucleic Acids

How are the monomers in nucleic acids connected?
What is the name of the bond?
What is the name of the polymer?

Answer 6

• by covalent bonds

• phosphodiester linkage (a covalent bond)

• nucleic acids(polymer) are a chain of nucleotides(monomer)

• 3’ and 5’ are in the backbone of the molecule

Question 7

A) Nucleic Acids

Which parts of the nucleotide are involved in the bond/polymerization?

Answer 7

• the 3’ -OH of 1 nucleotide attached to 5’ -P of the next nucleotide

Question 8

A) Nucleic Acids

Why are nucleic acids directional molecules?

Answer 8

• b/c of the way the nucleotides are attached together to form a nucleic acid, the 2 ends of the polymer are different.

• free P at the end that isn’t part of a phosphodiester linkage
  —> 5’ end
• free OH at other end that isn’t part of a phosphodiester linkage
  —> 3’ end

• if the molecule has this, it has direction. From the P —> OH.

Question 9

A) Nucleic Acids

How would you describe the structure of DNA e.g. shape, backbone, directionality, nitrogenous bases, bonds present?

Answer 9

• 2 strands twist around each other to forms 3D structure called a double helix.

• uniform structure

• constant diameter of 2 nanometers (nm) wide all along it’s length.

• phosphodiester backbone on outside of helix
—> contains the sugars and phosphate groups

• nitrogenous bases are on inside of helix
—> in Center of helix, the 2 nitrogenous bases are connected by hydrogen bonds, that form between the functional groups on the nitrogenous bases.

• fixed width (2nm) of double helix means a purine must pair with a pyrimidine.
— Purine + purine: too wide
— Pyrimidine + pyrimidine: too narrow

Question 10

A) Nucleic Acids

What are “antiparallel” strands?

Answer 10

There ends point in opposite directions.
5’ 3’
| |
| |
| |
V V
3’ 5’

Question 11

A) Nucleic Acids

Which bases are paired in the DNA structure and why?
What does this mean for the type of bases?

Answer 11

• Strands are specifically connected by H-bonds between bases
- Called base pairs
- are based on the presence of functional groups capable of participating in h-bonds in the nitrogenous bases in the centre of DNA.

• h-bonds requires partial negative and positive charges.

In DNA:
- 2 contacts between A & T
— Adenine only Able to form h-bonds with thymine b/c of how funct. Groups are arranged.

• therefore, form 2 h-bonds and this is called a base pair.
  — A(N•••H—N) and (N—H•••O)T
• 3 contacts between C & G
  — stronger b/c 3 bonds
  — Cytosine and Guanine.
  — G(N—H•••N), (O•••H—O) and (N—H•••O)C.

Question 12

A) Nucleic Acids

What is a base pair?

Answer 12

• a pair of complementary bases in a double-stranded nucleic acid molecule.
• consisting of a purine in one strand linked by hydrogen bonds to a pyrimidine in the other.
• Cytosine always pairs with guanine, and adenine with thymine (in DNA) or uracil (in RNA)

Question 13

A) Nucleic Acids

How would you describe the structure of RNA e.g. shape, backbone, directionality, nitrogenous bases, bonds present?

Answer 13

• RNA exists as a single strand that folds back on itself
- Each has a unique shape due to internal base-pairing.

• nitrogenous bases from different parts of the RNA hydrogen bond together to hold RNA in its own unique 3D shape.
• Still follow base-pairing rules:
  • A & U (2 H-bonds)
  • G & C (3 H-bonds)
• every RNA strand has a different shape because it has different sequences of nitrogenous bases.

Question 14

A) Nucleic Acids

What is meant by internal base-pairing in RNA?

Answer 14

• it means that the nitrogenous bases from different parts of the RNA will hydrogen bond together to hold RNA in its own unique 3D shape.

Question 15

B) Proteins

What are some common examples of proteins?

Answer 15

• In cells: Hemoglobin, collagen, insulin, etc.

• Some functions:
- Enzymes
- Transport proteins
— move nutrients in and out of cells
- Receptors
— allow things to bind to cell surface
- Motor proteins
— allow movement of material around the cell.
- Structural proteins
— important for the shape and organization of cell.

Question 16

B) Proteins

What is the difference between a polypeptide and a protein?

Answer 16

• in order to create a polymer from amino acids we need to attach them together by covalent bonds

• Polymer: Polypeptide
- Chain of amino acid monomers

• A polypeptide is a linear polymer of amino acid monomers connected by peptide bonds
• A protein is a polypeptide that has been folded into a unique 3D structure

• amino acids —> peptide —> protein

Question 17

B) Proteins

When describing a polypeptide, we often talk about the ‘backbone’.

Which parts of the polypeptide are part of the backbone, and which are not?

Answer 17

A part of backbone:
• amino groups
• carboxyl groups
• central carbons
•hydrogens
• peptide bonds

— backbone is identical, therefore contains a chain that repeat the pattern, N-C-C-N-etc.

Not part of backbone:
• side chains (the R- groups)
- this is the part that is different for each amino acid.

Question 18

B) Proteins

What functional groups from the amino acids are required to form the peptide bond?
What kind of bond type is formed?
Is this a dehydration reaction or hydrolysis?

Answer 18

• Carboxyl group of one amino acid covalently joined to amino group of the next amino acid.

• Covalent bond called a peptide bond

• formed by a dehydration rxn

• the polymer created by attaching amino acids in this way is called a polypeptide and not a protein.

Question 19

B) Proteins

How can you describe the polypeptide backbone?
Which elements are involved, is this polymer directional?

Answer 19

•

• are directional molecules (2 ends are different)
—> amino acid at 1 end has a free amino group that isn’t part of a peptide bond = amino end or n-terminus
—> amino acid at other end has a free carboxyl group that isn’t part of a peptide bond = carboxyl end or c-terminus

Question 20

B) Proteins

What are the four different types of side chains possible in amino acids?

Answer 20

Four classes:
* Non-polar
- side chains mostly composed of C-C, C-H
* Polar, uncharged
- side chains contain a O or N
* Polar, positively-charged (basic)
- side chains contain N-C, N-H
* Polar, negatively-charged (acidic)
- side chains contain Carboxyl group (COO^-)

When an amino group exists in a cell, it exists in an ionized state, where the amino groups gains a positive charge and the carboxyl group loses an H and gains a negative charge.

Question 21

B) Proteins

For each for the four types of amino acid side chains, what are their basic chemical properties (e.g. polarity, solubility, ability to form hydrogen or ionic bonds)? See table in purple pages, F-29)

Answer 21

Non-polar:
- non-polar
- poor solubility
- not able to form h-bonds

Uncharged Polar:
- polar
- generally soluble
- able to form h-bonds

Negatively charged (acidic):
- polar
- generally soluble
- able to form h-bonds

Positively charged (basic):
- polar
- generally soluble
- able to form ionic bonds

Question 22

B) Proteins

What type of chemical reaction occurs to form the peptide bond that connects the amino acids together?

Answer 22

• peptide bond is what attaches them together.

• the reaction that allows this is dehydration synthesis

Question 23

B) Proteins

What are the four different levels of protein structure?

Answer 23

• Primary (1°) Structure

• Secondary (2°) Structure

• Tertiary (3°) Structure

• Quaternary (4º) Structure

• All occur simultaneously.

Question 24

B) Proteins

What are the characteristics of primary, secondary and tertiary structure?

Answer 24

• Primary (1°) Structure:
• Unique order of amino acids in a polypeptide
• Bond type: Peptide (covalent) between amino acids
• determined by DNA sequence
  …
• Secondary (2°) Structure:
• Repetitive coiling or folding of protein
• Bond type: H-bond in the polypeptide backbone
• Between amino group of one AA and carboxyl group of another AA.
  — both contain polar bonds = lot of partial charged H (pos) and partial charge O (neg) that attract one another = h-bonds
• doesn’t involve side chains, only back bone.
• all secondary are stabilized by these h-bonds on backbone
• two types:
• a(alpha) helix
  -B(beta) sheet
  …
• Tertiary (3°) Structure:
• Overall shape of single polypeptide
• does not involve backbone
• all 4 types of bonds causes polypeptide to fold in a specific unique 3D shape
• Due to interactions between side chains:
  A) h-bonds between polar side chains
• partial charged atoms.
• helps stable bends and folds
  B) ionic bonds between oppositely charges side chains ( + <—> -)
• helps stabilize bends and folds
  C) Hydrophobic interactions:
• not actually a bond
• Non-polar side chains aggregate inside protein and exclude water
• Polar side chains exposed on protein surface and interact with water
  D) Disulfide bond:
• Covalent bond between sulfhydryl groups in the side chains of cysteine (AA)
• helps stabilize as well
  …..
• Quaternary (4º) Structure:
• Multiple polypeptides folded together
• Each has its own 1°, 2°, and 3° structure
• Stabilized by same 4 types of side chain interactions as 3° structure.
  — H-bonds
  — lonic bonds
  — Hydrophobic interactions
  — Disulfide bonds
• Protein may contain:
• Multiple copies of same polypeptide; (like in collagen) OR
• several different polypeptides (like hemoglobin)

Question 25

B) Proteins

What is the difference between tertiary and quaternary structure?

Answer 25

T:
- Overall shape of single polypeptide
- all 4 types of bonds causes polypeptide to fold in a specific unique 3D shape

Q:
- Multiple polypeptides folded together
- Each has its own 1°, 2°, and 3° structure
- Some proteins have subunits that are made up of multiple polypeptide chains. The quaternary structure of the protein is formed when these subunits come together.

Better explained:
- Tertiary structure is the overall 3D structure of the protein. Quaternary structure is the overall structure that arises when separate protein chains aggregate with self or with different proteins to form heteropolymers.

Question 26

B) Proteins

What is the difference between the hydrogen bonding in the secondary and tertiary or quaternary structure?

Answer 26

S:
- packing of polypeptide chain into α-helices and β-sheets due to h-bonds between peptide bond – central carbon backbone.

T:
- h-bonds between side chains of amino acids.

Q:
- The subunits of multiple polypeptide chains are held together by hydrogen bonds

Question 27

B) Proteins

What parts or the nucleotide are involved in the interactions determining the tertiary or quaternary protein structure?

Answer 27

T:
- The interactions between the R groups (side chains) of the amino acids are the primary reason for the tertiary structure of a protein.
–> h-bonds between polar side chains
–> ionic bonds between oppositely charges side chains
–> Hydrophobic interactions: amino acids orient selves towards center to avoid water
–> Disulfide bond: Covalent bond between sulfhydryl groups in the side chains of cysteine (AA)

Q:

Question 28

B) Proteins

What bond types or interactions determine the tertiary or quaternary protein structure?

Answer 28

— H-bonds
— lonic bonds
— Hydrophobic interactions
— Disulfide bonds

Question 29

B) Proteins

What is the difference between an α-helix and a β-pleated sheet?

Answer 29

• a(alpha)-helix:
• Repetitive coiling
• H-bonds between every 4th amino acid in helix.
  —> causes coiled shape and keep it in place.

-B(beta)sheet:
- Repetitive folding
- 2 regions of peptide chain lie side-by-side and are connected by H-bonds between backbone atoms
-(carboxyl and amino group)
- the pattern of h-bonds causes the 2 parallel chains to fold back and forth and that creates the repetitive pattern seen.

• these can occur In the same protein.

Question 30

B) Proteins

What are important functions of proteins?

Answer 30

• Some examples of protein functions:
- Enzymes
- Transport proteins
- Hormones
- Receptors (for binding to things)
- Motor proteins (for movement)
- Structural proteins
- Storage proteins (to store energy and carbon)
- Defensive proteins (antibodies)

Question 31

B) Proteins

What is determining the different function of proteins?

Answer 31

• the shape is.

• Protein shape is directly related to function
- All polypeptides have the same backbone.
- Each has a different order of amino acids in its primary structure —> controls shape —> controls function

Question 32

B) Proteins

What determines the variety of shapes in proteins?

Answer 32

• All polypeptides have the same backbone.
• Each has a different order of amino acids in its primary structure —> controls shape —> controls function

Question 33

B) Proteins

How does the primary structure relate to protein function?

Answer 33

• Changes to the primary structure of a protein (due to a mutation) can alter or eliminate protein function

• Not all primary sequence changes (mutations) will alter protein function

Question 34

B) Proteins

What is the consequence of a change in Amino Acid sequence (polypeptide)?

Answer 34

• Different amino acid in primary sequence
  —> different side chain —
  — diff side chains—
  —> forms different bonds (in tertiary structure)
  — diff bonds—
  —> changes overall shape—
  —> change enough—
  —> different shape—
  —> different shape = different/no function

Question 35

B) Proteins

What is a conformational change?

Answer 35

The adjustment of a protein’s tertiary structure in response to external factors (e.g. pH, temperature, solute concentration).

• Anything that breaks interactions between side chains will cause a protein to denature:
— high temperature
—> increases molecular movement and that can break non covalent weak bonds such as h-bonds and hydrophobic interactions.
— change in pH
—> affects charge on the amino acids in the side chains. In turn will affect whether the side chain will be in an ionic bond or h-bonds.
— organic solvents
—> are likely to be hydrophobic and want to interact with nonpolar side chains that are in the centre of the protein. These solvents will cause protein to unfold in order to bond.
— chemicals that disrupt bonds
—> like chemicals that can break the disulfide bonds between cysteine side chains

Question 36

B) Proteins

What is a conservative change?
Does it change the shape or function of the protein?

Answer 36

• Conservative change: New AA (that replaces old AA) has same properties as old AA
  • Similar bonds can form
  • Change has minimal effect on function

• it does not change the function largely because they’d have the same side chains and therefore make the same type of bonds during protein folding.
— protein will still be functional or a little less functional.

Question 37

B) Proteins

What is a con-conservative change?
Does it change the shape or function of the protein?

Answer 37

• Non-conservative change: New AA (replaces old AA) has different properties than old AA
  • Different bonds form
  • Protein function is affected

• this will affect shape because the new AA will form different bonds than the old AA, and therefore, cause the polypeptides function to change.

Question 38

B) Proteins

What is protein denaturation?
What are the effects?
Is it reversible?

Answer 38

• Denaturation: When a protein unfolds and loses its normal shape

• Causes a loss of function b/c losing 3D structure.

• The level of structure that is lost:
— secondary, tertiary, quaternary

• primary structure remains

• sometimes reversible.
— if it protein refolds and restores it’s 3D shape, it’ll restore its function.
—> this process is called renaturation.

• the bonds that it breaks:
- h-bonds
- ionic
- disulfide
- hydrophobic interactions

Question 39

B) Proteins

What is protein degradation?
What are the effects?
Is it reversible?

Answer 39

• When a protein’s peptide bonds between AA are broken and loses its shape.

• primary structure is lost
• there is no structure left b/c the protein turns back into amino acids monomers.
• the protein can no longer function.

• no the protein is destroyed.