L07: Biomolecules: Proteins and Nucleotides

Question 1

Which elements comprise proteins? What are examples of proteins (several were listed in the slides)?

Answer 1

Proteins (C, H, O, N, P, S) = amino acids (monomer units for proteins) polypeptides, etc.
- structural roles
- enzymes (facilitate chemistry)
- membrane transport
- hormones
- energy to make ATP

Nucleic Acids (C, H, O, N, P) = nucleotides, NAD+, FADH2, DNA, RNA, etc.
- energy conversion to help make ATP
- genomic storage and expression

Question 2

What roles do proteins play in biota (recall the 8 roles)?

Answer 2

Enzymatic proteins - selective acceleration of chemical reactions
ex: digestive enzymes catalyze the hydrolysis of bonds in food molecules

Defensive proteins - protection against disease (either make it less likely virus can replicate or they call more cells to attack) Vaccines work by getting the body to make antibodies ahead of time before getting sick.
ex: antibodies inactivate and help destroy viruses and bacteria

Storage proteins - storage of amino acids (for reproduction)
ex: casein, the protein of milk, is the major source of amino acids for baby mammals

Transport proteins - transport of substances
ex: hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body (systemic function entire body). Other proteins transport molecules across cell membranes.

Hormonal proteins - coordination of an organisms activities (deliver a signal circulating through the body through blood)
ex: insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration (decrease sugar in blood and raise internal cellular sugar)

Receptor proteins - response of cell to chemical stimuli
ex: receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells

Contractile and motor activities - movement (muscle)
ex: motor proteins are responsible for the undulations of cilia and flagella

Structural proteins - support
ex: Keratin is a protein of hair, horn, feathers, and other skin appendages. Collagen and elastin proteins provide a fibrous framework in animal connective tissue

Question 3

What are the monomers used to make proteins?

Answer 3

amino acids

Question 4

Which constituent is bonded to the four bonds of an α-carbon in an amino acid?

Answer 4

• amino group (ionized at body pH)
• carboxyl group (ionized at body pH)
• Hydrogen
• R group (a variable side chain)

Question 5

Which constituents are the same for all amino acids? Which constituent is unique among all amino acids?

Answer 5

All biota use the same 20 amino acids to make polypeptides. All amino acids have the same base but varied R groups change protein shape/function.

Question 6

Which two functional groups are found in amino acids?

Answer 6

• carboxyl
• amino

Question 7

Why are amino acids called amino acids?

Answer 7

because the carboxyl group acts as an acid when the covalent bond to H ionizes. (extra H+ from the carboxyl group)

Question 8

How many unique amino acids can biota polymerize into proteins?

Answer 8

Polymerize 20 unique amino acids in unique
sequences and you can assemble 100,000s of unique proteins.

Question 9

In which four classes are amino acid R-groups classified?

Answer 9

• polar ; hydrophilic
• non-polar ; hydrophobic
• acidic (negatively charged)
• basic (positively charged)

Question 10

How can polymerizing amino acids with different R-groups into a polymer impact the shape of the polymer? And how does shape relate to function?

Answer 10

Proteins fold up into specific shapes according to the sequence of amino acids in the polymer, and the protein function is directly related to the resulting 3D structure.

Question 11

Which kind of chemical reaction do biota use to polymerize amino acids into proteins?

Answer 11

Cells polymerize a.a. via dehydration rxn resulting in a
peptide bond between bonded a.a forming a polypeptide.

Question 12

What is the bond called that bonds two or more amino acids together in a polymer? Which functional groups are involved in this bond?

Answer 12

Cells polymerize a.a. via dehydration rxn resulting in a
peptide bond between bonded a.a forming a polypeptide.
- carboxyl
- amino

Question 13

What is a dipeptide and a polypeptide?

Answer 13

dipeptide - a molecule that consists of two amino acids joined together by a peptide bond

polypeptide - a linear organic polymer consisting of a larger number (more than 2) of amino-acids bonded together forming a protein molecule

Question 14

You should realize that protein function has everything to do with underlying structure. This structure is organized into four levels. What are the four levels of protein structure and what is responsible for/underlies each level of organization?

Answer 14

1. The sequence of a.a. from the N-terminus to the C-terminus comprises the primary (1°) structure of a polypeptide.
2. Secondary (2°) structures α-helices and β-sheets form as non-R group constituents interact via H bonding
3. Tertiary (3°) structure forms as loops link α-helices and β-sheets into a 3-D volume as a consequence of R-group interactions (e.g., disulfide bridges from –SH groups).
4. Quaternary (4°) structure forms as polypeptide subunits assemble into a protein.

Question 15

If you were given the primary structure of a polypeptide, how would you know which amino acid is in the first position and which is in the last position?

Answer 15

Amino end (N-terminus)
Carboxyl end (C-terminus)

Question 16

Hemoglobin is a quaternary-level protein. What does this mean?

Answer 16

a big protein with multiple subunits (in this case 4)

Question 17

How does protein folding relate to protein function?

Answer 17

Higher levels of organization of protein structure, often
referred to as ‘folding’, also influence a protein’s function.
A properly folded protein is important to maintain function.

Question 18

What happens when proteins denature?

Answer 18

Proteins lose their higher level organization as well as function during denaturation.

Question 19

Changes in which three factors denature proteins? How does this likely impact protein function?

Answer 19

Changes in temperature, pH, or salinity may denature proteins. It can no longer perform its function if denatured.

Question 20

What are the three components of a nucleotide?

Answer 20

• phosphate
• sugar
• nitrogenous base

Question 21

How are these three components arranged relative to each other in a nucleotide (i.e., what is bonded to what)?

Answer 21

Phosphate group and nitrogenous base are connected to sugar molecule.

Question 22

Which molecule did I give has an example of an important modified nucleotide? Why is it important?

Answer 22

ATP (adenosine triphosphate) is a modified nucleotide used as a rechargeable battery to power cellular work. Biota break the terminal phosphate to release energy to do cell work. Later, biota recharge ADP from energy extracted from food molecules during cellular respiration.

Question 23

What is a dinucleotide?

Answer 23

Dinucleotides are two nucleotides bonded together via phosphate groups.

Question 24

Which components of nucleotides are bonded together to make a dinucleotide?

Answer 24

bounded through phosphate group

Question 25

I listed two examples of important dinucleotides. What were they, in what process were they important, and which molecules are used to make these important dinucleotides?

Answer 25

NAD+ and FADH2 help recharge ATP batteries during cellular respiration.

Biota use B vitamins to make dinucleotides:
B3 (Niacin) ➟ NAD+
B2 (Riboflavin) ➟ FADH2

*ex: whole grain bread has lots of B vitamins

Question 26

What is a polynucleotide? What are the two examples of polynucleotides? What overall functional role do these polynucleotides serve?

Answer 26

Polynucleotide is a linear polymer whose molecule is composed of many nucleotide units, constituting a section of a nucleic acid molecule.

DNA and RNA are used for genomic storage/expression.

DNA and RNA have different sugars:
- Deoxyribose (in DNA) missing an oxygen in sugar molecule
- Ribose (in RNA)

Question 27

How do biota polymerize nucleotides into polynucleotides (consider chemical reaction type and with components are bonded together)?

Answer 27

Biota polymerize nucleotides into polynucleotides (e.g., DNA and RNA, left) via dehydration rxns forming sugar-phosphate bonds.

Question 28

What is the sugar-phosphate backbone?

Answer 28

The sugar-phosphate backbone organizes Nitrogen bases (A,T,C,G) into a 3´ ➟ 5´ direction.

3 to 5 prime

Question 29

If you were given a sequence of polynucleotide how would you know which nucleotide was in the first position and which nucleotide is in the last position?

Question 30

What does the following phrase mean: “DNA is organized as two antiparallel polynucleotide strands held together via Hydrogen bonding and twisted into a helix?”

Answer 30

For FNA: One strand 3´➟5´; the other is 5´➟3´. Both twisted into a
helical (spiral) orientation.

RNA tends to be organized in single strands (but can fold onto itself)

Question 31

How are DNA and RNA similar to each other? How are DNA and RNA different from each other? To answer the previous questions consider number of strands (typically), sugar, and nitrogen bases.

Answer 31

Both DNA and RNA are used for genomic storage/expression. They both have a sugar-phosphate backbone.

*DNA is 2 strands and RNA is 1 strand
*DNA and RNA have different sugars:
-
-
*Polynucleotides have different Nitrogen bases:
- DNA has A,T,C,G.
- RNA has A,U,C,G.

Question 32

Why is DNA/RNA so important to biota?

Answer 32

DNA is so essential to life that every cell must make a copy
of it to pass onto to its descendant cells.
Nucleotides in DNA determine how to organize amino acids to make proteins. RNA facilitates gene expression/protein synthesis.

Question 33

What is a genome?

Answer 33

Each cell needs a genome to stay alive. A genome is the set of all genes of a species. Genes are written in DNA language.

Question 34

What is a gene? No, really, what specifically is a gene? (Did you think about the definition - if you did you begin to see the functional relationship of polynucleotides and proteins.)

Answer 34

A gene is a 3´ ➟ 5´ sequence of DNA nucleotides that serves as directions on how to polymerize amino acids into a 1° sequence to make a specific protein.

Question 35

What is gene expression?

Answer 35

The process by which a gene gets turned on in a cell to make RNA and proteins.
A gene is expressed as a protein.

Question 36

If DNA serves as directions on how to polymerize amino acids into specific proteins, what does RNA do?

Answer 36

RNA facilitates gene expression/protein synthesis.