Lecture 6- Protein Structure and Introduction to Gene Expression

Question 1

What are the 4 hierarchical structure of proteins and describe them?

Answer 1

1. ) Primary Structure: Single polypeptide strand.
2. ) Secondary Structure: Local structure along a polypeptide backbone (alpha/beta sheets).
3. ) Tertiary Structure: 3-D configuration of all atoms of the polypeptide chain, including R-Groups.
4. ) Quaternary Structure: Combination of 2 or more polypeptide chains that assemble into a protein complex.

Question 2

What is the primary protein structure?

Answer 2

• Primary protein structure is linear and with the N-terminal to the left and C-terminal to the right.
• Has polar side chains on one side and nonpolar side chains on the other.
• Peptide bonds between amino acids.

Question 3

What are the structures of secondary proteins?

Answer 3

1. ) Alpha helix- Hydrogens bonds form between amino acids after every four residues apart.
   - R- groups stick outside
   - N-H groups stick upwards, COOH groups stick downwards and hydrogen bonds form between the two.
2. ) Beta helix- Hydrogen bonds form between the N-H and COOH groups.
   - Polypeptide chains can run parallel or anti-parallel to one another.
   - R-groups also stick out.

Question 4

What are the structures of tertiary structure?

Answer 4

• Folding of secondary proteins results in tertiary proteins.
• Folded conformation in an aqueous environment: hydrophobic nonpolar side chains found on the inside.
• Polar side chains on the outside can hydrogen bond with water.

Question 5

What are the bonds necessary for proteins compared to covalent bonds?

Answer 5

• Noncovalent weak bonds specify the exact shape of macromolecules.

Question 6

What is a quaternary/multimeric protein?

Answer 6

• Multimeric proteins consist of many protein subunits.

- Quaternary proteins based on organization and number of protein subunits.

Question 7

What is differential Gene Expression? In which organisms is it found?

Answer 7

• Only a certain number of genes in multicellular eukaryotes are expressed.
• The different expression of genes determines the proteins created.
• Generation of different cell types is determined by the right genes activated in the right cell during the right time of development.

Question 8

What is gene equivalence theory?

Answer 8

• The theory that cells have an equivalent amount of complementary genetic information.

Question 9

Why do cells differ in structure and function?

Answer 9

• Not because they have different genetic information but rather because different genes are expressed in these cells common genome.

Question 10

What study was the evidence for genomic equivalence in mammals?

Answer 10

• Sheep experiment
• Oocyte donors egg was removed, spindle fiber removed
• Uder cell from nuclear donor sheep injected into endonucleated egg then egg and cell are fused with electric current.
• Embryo injected into surrogate mother and genetically identical sheep to nuclear donor was born.
• Baby sheep born from different species of sheep.

Question 11

What are the three ways in which identical cells instruct one another to express distinct sets of genes?

Answer 11

1. ) Fertilization of an egg
   - Before the mRNA or protein of the unfertilized egg is spread evenly throughout the egg.
   - After the mRNA or protein of the fertilized egg is asymmetrically localized.
   - Localization of mRNA or protein can affect gene regulation.
2. ) Single cell to cell signaling with protein receptors.
3. ) Cell releasing signaling molecules to many cells
   - All three regulate gene regulatory protein activity.

Question 12

What is asymmetrical cell division and how does it impact cells? What does it result in?

Answer 12

• Asymmetrical cell division is when the two daughter cells have two different life passages.
• Regulator proteins are what cause the differences between these two daughter cells.
• This results in different cell types.

Question 13

Does RNA polymerase II requires Gene regulatory sequences and proteins for in vitro?

Answer 13

Yes

Question 14

What are most eukaryotic genes regulated by?

Answer 14

-Multiple transcription contol elements.

Question 15

What is an enhancer and what is its role?

Answer 15

• The enhancer is short DNA sequences that are bound by transcription factors which may help increase the chance a gene is transcribed or not.

Question 16

How do transcription factors regulate gene expression? How do they perform this?

Answer 16

• They regulate the genes (turn them off or on) at the right times depending on the needs of the cell.
• They do this by binding directly or by recruiting co-factors (co-activators or co-repressors) which dictate gene-specific regulation.

Question 17

What determines an active core promotor? (Effect of the nucleosome).

Answer 17

• Areas where there is an active core promoter, there are nucleosome-depleted regions.

Question 18

How can activators promote transcription? Name an example.

Answer 18

• Activators can displace the nucleosome which allows transcription factors to bind to newly active promoter regions.
• The chromatin remodeling factor is an example of an activator.

Question 19

What do activators do to chromatin? Results? Name two ways?

Answer 19

• Activators make alterations to chromatin structure which open promoter regions.
  1. ) Histone modifying enzyme- makes specific histone modification pattern.
  2. ) Chromatin remodeling complex- displaces nucleosomes.
• Both allow for transcription to occur which results in gene expression.

Question 20

What are the steps in initiation transcription?

Answer 20

1. ) Preinitiation complex and RNA polymerase II recruitment
2. ) Promoter clearance
3. ) Promotor proximal pausing sequence (pause and release) - About +20-+50
4. ) Productive elongation begins

Question 21

How do repressors inhibit transcription?

Answer 21

• They either interact with the activator or alter the chromatin structure.

Question 22

Can individual regulatory proteins participate in different regulatory complexes?

Answer 22

yes.

Question 23

What does the combinatorial control of gene expression require?

Answer 23

• Requires a presence or absence of a certain combination of regulatory proteins.
• Certain combinations of these regulatory proteins can induce high or low-level gene expression.
• Active regulators tip the scale.

Question 24

If there is the same DNA in all cells, what specifically helps with gene expression and cell specificity?

Answer 24

• Expression occurs due to the right regulatory protein combinations present to active transcription.

Question 25

What sequences activate specific gene transcription?

Answer 25

• Enhancer sequences.