L14: Gene Expression: Protein Synthesis

Question 1

What is a gene?

Answer 1

A gene is a linear (3ʹ to 5ʹ) sequence of DNA nucleotides found in a strand of DNA whose Nitrogenous bases are
read as directions on how to make RNA and, then, a protein.

Question 2

Where do you find genes in a cell?

Answer 2

Our genes are found in our chromatin (chromosomes).

Chromatin: dsDNA wrapped around histone proteins.

Question 3

What happens when a cell expresses a gene?

Answer 3

Genes are expressed as traits when your cells read genes to make RNA and, then, proteins.

Proteins, with their myriad of functions, make up your traits

Question 4

Which cellular organelle makes proteins?

Answer 4

ribosomes

Gene expression involves: amino acids, DNA, RNA, and ribosomes.

Question 5

What is the overall flow of information during gene expression/protein synthesis? State the orientation of each sequence.

Answer 5

1. Eukaryotic gene expression begins in the nucleus and concludes in the cytoplasm at a ribosome.
2. DNA sequence of the gene is used as a template to polymerize RNA into a single strand called mRNA during transcription.
3. mRNA is processed and exits nucleus
4. mRNA docks at a ribosome.
5. Ribosome (made up of proteins and
   rRNA) acts as an enzyme complex that polymerizes amino acids into a polypeptide during translation.
6. Translation requires tRNA to transfer amino acids from cytoplasm to ribosomes for polymerization.

Question 6

How do the following relate to each other: primary protein structure, DNA sequence, protein function, tertiary protein structure, RNA sequence?

Answer 6

Genes are recipes written in sentences of 3-lettered words (DNA triplets).

Each is transcribed into a complementary 3-lettered RNA word (RNA codon).

Each RNA codon is translated into a particular amino acid to be placed in a specific position in the primary structure (1°) of a polypeptide (right)

Question 7

If you change a gene sequence, what do you expect to happen to its protein product?

Answer 7

A polypeptide’s 1° structure causes it to fold into its 3° structure (right) impacting its function.

Question 8

Which three forms of RNA are required for protein synthesis? What role does each serve?

Answer 8

messenger RNA (mRNA) - DNA sequence of gene polymerized into RNA during transcription

ribosomal RNA (rRNA) - one component of ribosomes. polymerized amino acids into polypeptide

transfer RNA (tRNA) - translation requires tRNA to
transfer amino acids from cytoplasm to ribosomes for polymerization.

Question 9

Which are involved in transcription? Which are involved in translation?

Answer 9

all

Question 10

What is a codon and in which form of RNA do you find a codon?

Answer 10

transcribed DNA triplets into complimentary 3-lettered RNA word carried by the mRNA

Question 11

What is an anticodon and in which form of RNA do you find an anticodon?

Answer 11

transfer RNA (tRNA) anticodons complement (H bond) mRNA codons

Question 12

What is transcription?

Answer 12

Cells transcribe DNA nucleotide sequence of genes into transcripts of RNA in the nucleus.

Question 13

Where does transcription occur?

Answer 13

in the nucleus

Question 14

What happens during the three sequential processes of transcription?

Answer 14

Transcription is catalyzed by RNA polymerases (RNA pols) during:
1) initiation: RNA pol and transcription factors attach to upstream promoter; unzips DNA helix
2) elongation: RNA pol reads DNA template strand 3´➟5´; polymerizes RNA nucleotides 5´➟3´ (1° transcript)
3) termination: RNA pol detaches releasing 1° RNA transcript

Question 15

What is a promoter?

Answer 15

start point of a gene found at the beginning that RNA polymerase (RNA pols) i’ll attach to

Question 16

Which enzyme is responsible for carrying out the processes of transcription?

Answer 16

RNA pols

Question 17

What must happen to mRNA after it is transcribed by eukaryotic cells?

Answer 17

it has to be processed

Question 18

If given a DNA sequence, can you transcribe a gene sequence into a mRNA sequence using Chargaff’s rules?

Answer 18

si

Question 19

What happens during RNA processing?

Answer 19

mRNA is edited to remove unnecessary information (intons)

Question 20

Where does RNA processing occur?

Answer 20

nucleolus in the nucleus

Question 21

Which cellular components carry out RNA processing?

Answer 21

spliceosomes

Question 22

What are exons and introns?

Answer 22

Eukaryotic genes have intervening DNA nucleotide sequences called introns not used to make proteins.

Exons are segments of the mRNA that obtains information for coding a protein

Question 23

Which is excised (i.e., removed) and which is spliced (i.e., joined together)?

Answer 23

Spliceosomes excise introns and splice together exons
to be used to make a protein.

Question 24

Beyond editing, how else is mRNA modified during RNA processing?

Answer 24

receives a ‘cap’ and a ‘tail’

Question 25

Where does the mature mRNA that has been fully processed go next?

Answer 25

nuclear envelope

Question 26

What is translation?

Answer 26

Cells translate mature mRNA from start to stop codon into an amino acid sequence of a polypeptide

Question 27

Where does translation occur?

Answer 27

cytoplasm at ribosomes

Question 28

What happens during the three sequential processes of translation?

Answer 28

1. initiation
   a) mRNA bonds with small ribosomal rRNA subunit
   b) initiator tRNA (with methionine and UAC anticodon) joins mRNA at start codon (AUG) at ribosome’s P site
   c) large rRNA subunit joins to form complete ribosome
2. elongation
   a) Next tRNA-amino acid moves into A site (tRNA anticodon Hydrogen bonds with mRNA codon)
   b) amino acids bonded via peptide bond
   c) mRNA moved through ribosome; tRNA without a.a., now in E site, exits; A site opens for next tRNA
3. termination
   a) release factor attaches to stop codon (UAA, UAG, or UGA)
   b) ribosome subunits disassemble releasing polypeptide (protein)

Question 29

Which tRNA initiates translation? Which amino acid does it deliver?

Answer 29

methionine amino acid on tRNA with anticodon UAC

Question 30

What happens during elongation?

Answer 30

2. elongation
   a) Next tRNA-amino acid moves into A site (tRNA anticodon Hydrogen bonds with mRNA codon)
   b) amino acids bonded via peptide bond
   c) mRNA moved through ribosome; tRNA without a.a., now in E site, exits; A site opens for next tRNA

Question 31

What is the APE cycle?

Answer 31

Elongation involves repetition of the APE cycle: A = arrival site; P = polymerization site; and E = exit

Question 32

What happens during termination?

Answer 32

3. termination
   a) release factor (a protein with anticodon because there are no tRNA with anticodon) attaches to stop codon (UAA, UAG, or UGA)
   b) ribosome subunits disassemble releasing polypeptide (protein)

Question 33

Which three stop codons signal termination?

Answer 33

UAA, UAG, or UGA

Question 34

Can you translate mRNA into an amino acid sequence if given a translation table similar to the one included in your textbook?

Answer 34

maybe

Question 35

Beyond folding, which three ways are proteins routinely modified during post-translational modification?

Answer 35

proteolysis, glycosylation, & phosphorylation

Question 36

What overall role does such modification serve?

Answer 36

Modification activated proteins so they function properly

1. proteolysis - cut protein into pieces
2. glycosylation - addition of different carbohydrates or sugar to protein
3. phosphorylation - has phosphate groups added to protein

Question 37

Which organelles/cell components carry out post-translational modification?

Answer 37

endoplasmic reticulum (ER), Golgi, and vesicles

Question 38

What might happen if a secretory protein is activated prematurely?

Answer 38

harm cell

Question 39

What is a protein domain?

Answer 39

Exon are directions on how to build domains.
Domains comprise different regions of a protein.

Question 40

Do different proteins possess the same kinds of domains?

Answer 40

Different proteins are made up of different combinations of the same kinds of domains

Question 41

What is exon shuffling and how does it contribute to the answer to the previous question?

Answer 41

Exon shuffling copies/moves exons among new genes resulting to new ways to assemble domains.

Question 42

What happens during alternative splicing?

Answer 42

Alternative splicing: spliceosomes splice exons of a given gene in different sequences

Question 43

How does the process of alternative splicing impact our view that a single gene codes for a single kind of protein?

Answer 43

one gene can make multiple kinds of proteins whenever the cons of that gene are spliced alternatively during RNA processing

Question 44

How much larger is the transcriptome than the genome?

Answer 44

transcriptome refers to all of the RNA transcripts that can be made

Transcriptome may be 10x larger than genome

Question 45

What happens during RNAi?

Answer 45

Some RNA is cut into fragments called micro RNA (miRNA).
miRNA may block translation of mRNA. This processes is known as interference RNA (RNAi).

Question 46

Why did RNAi likely evolve in our cells?

Answer 46

help regulate gene expression

likely evolved in cells to protect a cell from viruses

Question 47

How might we exploit RNAi in a medical application?

Answer 47

it may be used to used to devise treatment for virus’s for which we have limited options

ex: herpes simplex virus 2 (HSV-2) clinicians are looking at ways to help treat viral infections tat in the past have ben difficult to treat