Lecture 3 - Making Proteins

Question 1

Structures of proteins

Answer 1

• Primary structure: amino acid sequence
• Secondary structure: hydrogen bonds between amino acids form alpha helices or beta sheets
• Tertiary structure: 3D structure of the protein, a single polypeptide chain
• Quaternary structure: two or more polypeptides aka protein-complex

Question 2

The Central Dogma

Answer 2

DNA => RNA => Protein

transcription: RNA polymerase uses DNA as a template to produce pre-mRNA
translation: a ribosome builds the protein molecule (polypeptide) from a mature mRNA

protein is encoded in a gene

Question 3

Where is ribosomal RNA encoded?

Answer 3

in a nucleolus

Question 4

What does RNA polymerase do?

Answer 4

it catalyzes the chemical reactions that synthesize RNA from a DNA template

Question 5

What are the 3 types of RNA polymerases?

Answer 5

• RNA polymerase I: rRNA genes
• RNA polymerase II (**): mRNA, snRNA, and snoRNA genes
• RNA polymerase III: tRNA and 5S rRNA genes

Question 6

What’s at the active site of RNA polymerase? What does RNA polymerase do?

Answer 6

• active site has 2 DNA strands and an RNA strand
• two DNA strands form a double helix at the top
• RNA polymerase separates the 2 DNA strands in the middle and builds an RNA strand
• the 2 DNA strands come back together

Question 7

What are the 4 types of RNAs mentioned in class?

Answer 7

• mRNAs: messenger RNAs, code for proteins
• rRNAs: ribosomal RNAs, form basic structure of ribosome; catalyze protein synthesis
• tRNAs: transfer RNAs, adaptors between mRNA and amino acids
• snRNAs: small nuclear RNAs, function in nuclear processes

Question 8

What is the TATA box?

Answer 8

• a DNA sequence primarily composed of T and A nucleotides
• typically located about 30 nucleotides upstream from transcription start site
• TATA binding proteins (TBPs) recognize the TATA box

Question 9

What are general transcription factors?

Answer 9

a set of proteins that RNA Polymerase II requires
- their point is to start transcription

Question 10

Where does the RNA Polymerase II and the rest of the general transcription factors assemble?

Answer 10

at the promoter

Question 11

Nuclear pore complex

Answer 11

• where mRNA leaves the nucleus from
• particle movement by NPC is controlled
• mRNA, ribosomes, and proteins leave the nucleus through the NPC
• protein import also happens through the NPC

Question 12

How does a ribosome translate information from the mRNA into a polypeptide?

Answer 12

• 2 subunits lock together with the mRNA strand locked inside
• ribosome then walks down the mRNA and translates the nucleotides into amino acid chains
• 3 nucleotides (codon) = one amino acid

Question 13

What is the catalytic site of the ribosome?

Answer 13

in the large subunit

contains the active site of the ribosome: the site that creates the new peptide bonds when proteins are synthesized

where amino acids are added => where proteins are made

Question 14

What does the small subunit of the ribosome do?

Answer 14

finds a mRNA strand and ensures that each codon pairs with the anticodon

Question 15

What does tRNA do?

Answer 15

translates the mRNA into amino acids
- tRNAs are a link between the mRNA molecule and the growing chain of amino acids
- anticodons and codons

Question 16

What stops translation?

Answer 16

Translation termination factor

Question 17

Why do cells have a nucleus?

Answer 17

RNA must be spliced to remove untranslated regions from mRNA
- exons = part of RNA that code for proteins
- introns = regions residing within a gene but does not remain in the final mature mRNA
if mRNA was not spliced in nucleus, it would be translated before being spliced

Question 18

What is the protein responsible for splicing mRNA

Answer 18

spliceosomes cut up the exons and reconnect them to produce the mRNA molecules that are used to make proteins
- if this doesn’t happen, proteins will be faulty
- splicing allows multiple proteins to be encoded in a single gene