DNA Test

Question 1

Transcription takes place where in a Eukaryote? In prokaryote?

Answer 1

• The Nucleus in eukaryotic
• Cytoplasm in prokaryotic

Question 2

What are the 3 main steps to transcription?

Answer 2

• Initiation: RNA polymerase binds to the promoter sequence at the start of a gene
  
  • Promoter sequence frequently includes a sequence of TATAAAA – Not all promoter sequences are identical.
• Elongation: RNA polymerase moves along the template strand, connecting the RNA nucleotides by bonding the sugar-phosphate backbone
  
  • RNA is synthesized from its 5’ to its 3’ end
• Termination: RNA polymerase lets go of the DNA and releases the mRNA when it gets to the terminator sequence at the end of the gene

Question 3

New RNA strand only grows 5’ –> 3’ (what enzyme does this?)

Answer 3

• RNA polymerase

Question 4

How is sequence of mRNA molecule determined?

Answer 4

• It is determined by the DNA strand which it is being transcribed from (because the DNA and mRNA are complementary)

Question 5

Role of Promoter sequence in translation? Role of Terminator sequence? Are these sequences found in DNA or RNA?

Answer 5

• Promoter is a sequence of DNA that encourages helicase to land there and start splitting the RNA polymerase to replicate it from that point
• The terminator sequence tells the enzymes to stop making the RNA strand (terminator sequence is in the DNA)

Question 6

Purpose of mRNA processing?

Answer 6

• Prepares the RNA to leave the nucleus
• Introns are removed since they are not necessary for making the certain proteins the cell wants
• 5’ cap:
  
  • helps the mRNA move through the nuclear pore and attach to a ribosome
  • helps protect mRNA from hydrolytic enzymes and functions as an “attach here” signal for ribosomes
• PolyA tail stalls the destruction of the important parts of the RNA

Question 7

Purpose of 5’ methyl cap? Purpose of 3’ polyA tail?

• Why might a cell add a longer polyA tail to an mRNA molecule?
• What might happen if the 5’ cap was not added?

Answer 7

• Longer tail: proteins that are needed over long periods of time
• No cap: the mRNA might not be able to leave the nucleus or attach to a ribosome

Question 8

What is splicing? Purpose? What happens to introns & exons in RNA splicing?

Answer 8

• Before RNA leaves the nucleus, introns are removed and the exons are joined to produce an mRNA molecule with a continuous coding sequence
• Catalyzed by a complex of proteins and small RNA molecules
• Purpose:
  
  • At least some introns contain sequences that control gene activity in some way
  • Regulate the passage of mRNA from the nucleus to the cytoplasm
  • Enable a one gene to encode for more than one polypeptide

Question 9

Translation takes place where in a Eukaryote? In prokaryote?

Answer 9

Takes place in cytoplasm for both.

Question 10

How does the Genetic Code work? What is a codon? Why are there three nucleotides in a codon? In what direction is mRNA read?

Answer 10

A codon is a series of three nucleotide bases that make up the code for one amino acid. mRNA is translated from the 5’->3

Question 11

What is the start codon? Stop codons?

Answer 11

• Start codon is a pattern of 3 bases which tells the ribosomes to start producing the amino acid
• A stop codon is the same thing except it tells the ribosome to stop producing the amino acids

Question 12

How many codons are there total? How many codons code for amino acids?

Answer 12

• 4 x 4 x 4 = 64 codons total
  
  • ​4 possibilities for 1st, 2nd, and 3rd base
• 64 - 3 = 61 amino acids
  
  • ​3 stop codons

Question 13

What is an advantage to having a redundant Genetic Code? (having more than one codon for a given amino acid)

Answer 13

• If there is a mutation, there is a chance that the amino acid will stay the same, so the protein function might not change

Question 14

Structure and role of mRNA, tRNA and the ribosome? What is the ribosome made of?

Answer 14

• mRNA – contains codons complementary to the sequence of nucleotides on template DNA and directs the formation of amino acids through the action of ribosomes and tRNA
  
  • Cap, tail, coding region
• tRNA – picks up appropriate amino acids and recognizes the appropriate codons in the mRNA
  
  • Top: amino acid attachment site
  • Bottom: Anticodon
• Ribosomes – coordinate the functioning of the mRNA and the tRNA and make polypeptides
  
  • 2 subunits each made up of proteins and rRNA

Question 15

What is an Anticodon? What type of RNA is the anticodon found on? How do anticodons work? (what do they pair with?)

Answer 15

• The opposite of the codon during translation that hydrogen bonds, attaching the AA to the polypeptide chain
• It’s found on ribosomal RNA (rRNA)

Question 16

How is translation terminated? Where might a protein go after translation?

Answer 16

• Stop codon – signal to stop
• The completed polypeptide is released from the last tRNA and exits the ribosome
• Then to the Golgi bodies for further processing, to be used in the cell, or excreted by exocytosis to be used by other cells.

Question 17

Point mutation by substitution

Answer 17

• DNA/RNA mutation
• A simple substitution in one base of the gene sequence

Question 18

Frame-shift mutation by insertion or deletion

• Why do some insertions and deletions not result in a frameshift?

Answer 18

• DNA/RNA mutation
• All the nucleotides downstream of the deletion or insertion will be improperly grouped into codons
• The result will be extensive missense, ending sooner or later in nonsense - premature termination.

Question 19

Silent mutations

Answer 19

• Polypeptide mutation
• One that does not alter the amino acid that is incorporated, due to the redundancy of the genetic code

Question 20

Nonsense mutation

Answer 20

• Polypeptide mutation
• Change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein

Question 21

Missense mutation

Answer 21

• Polypeptide mutation
• Those that still code for an amino acid but change the indicated amino acid

Question 22

Effect of mutations on polypeptide a.a. sequence? Effect on protein folding?

Answer 22

*

Question 23

What is cell differentiation?

Answer 23

• Cells must become specialized in structure and function
• Results from selective gene expression

Question 24

How do different specialized cells (from a particular multicellular organism) compare in their patterns of gene expression?

Answer 24

*

Question 25

Gene expression

Answer 25

• -The turning on and off of specific genes
• the process by which the instructions in DNA are converted to a functional protein

Question 26

Genome

Answer 26

• A complete set of an organism’s genes
• An organism’s genetic material

Question 27

Genes

• “housekeeping” genes

Answer 27

• A segment of DNA that codes for a certain characteristic or
  trait. Ex) Blue eyes, Black hair, Dark skin, etc.
• Housekeeping gene involved in the basic functions necessary for the sustenance or maintenance of the cell

Question 28

Chromosome packing: histones, nucleosomes, coils, supercoils

Answer 28

• DNA (2 nm)
• Histones attached to DNA
• Nucleosome – DNA wound around a protein core of 8 histones (10 nm diameter)
• Beaded string wrapped into a tight helical fiber (30 nm diameter)
• Fiber coils into a thick supercoil (300 nm diameter)
• Chromosome – more looping and folding

Question 29

Chromatin (loose packing) v. chromosome (tight packing) structure

Answer 29

-

Question 30

Histone modification

Answer 30

Allows for looser coiling around histones and tends to increase gene expression of affected regions

Question 31

X chromosome inactivation in female mammals

Answer 31

• In female mammals, one of the two X chromosomes is highly compacted and transcriptionally inactive
• Random inactivation of either the maternal or paternal chromosome
• Occurs early in embryonic development and all cellular descendants have the same inactivated chromosome
• Inactivated X chromosome is called a Barr body
• Tortoiseshell fur coloration is due to inactivation of X chromosomes in heterozygous female cats

Question 32

DNA methylation

Answer 32

• Add of a methyl (CH3) group to cytosines in a gene inactivates that gene
• Causes nucleosomes to pack tightly together
• Transcription factors cannot bind the DNA

Question 33

Transcription factors: Activator proteins, repressor proteins (silencers), & other transcription factor proteins

Answer 33

• A protein that functions in initiating or regulating transcription
• Bind to DNA or other proteins that bind to DNA
• The first step of initiating gene transcription is the binding of activator proteins to DNA sequences called enhancers
  
  • ​Usually far away from the gene they help regulate
  • Binding of activators –> bending of DNA
• Silencers bind to DNA sequences and inhibit the start of transcription

Question 34

Enhancer sequences in Euk. DNA: site of activator protein binding, remote/far away from gene (as seen in last transcription animation)

Answer 34

• Enhancers are far away from the gene they help regulate
• Binding of activators to enhancers lead to the bending of DNA
• Bound activators interact with other transcription factor proteins, which then bind as a complex at the gene’s promoter

Question 35

Alternative RNA splicing

Answer 35

• Production of different mRNAs from the same transcript
• Results in production of more than one polypeptide from the same gene
• Can involve removal of an exon with the introns on either side

Question 36

mRNA breakdown (long v. short-lived mRNA)

• How is mRNA built if it needs to be long-lived?
• What is the advantage to the cell/organism to having long-lived mRNA? Disadvantage?

Answer 36

• mRNA is eventually broken down by exonucleases in cytoplasm

Question 37

Protein activation

Answer 37

*

Question 38

Protein breakdown

Answer 38

-

Question 39

What is the epigenome? What types of modifications comprise the epigenome and how do they affect gene expression?

Answer 39

• The study of changes in organisms caused by the modification of gene expression rather than alteration of the genetic code itself

Question 40

5’ and 3’ at each step

Answer 40

• Synthesis:
  
  • Moves 5 to 3
  • Polymerase adds onto the 3 end
• Transcription:
  
  • RNA synthesized 5 to 3
  • RNA polymerase reads the template strand from 3 to 5
• Translation:
  
  • Ribosome moves 5 to 3

Question 41

Promotor vs start codon

Answer 41

• Promoters are regions of DNA where transcription starts and RNA polymerase attaches (transcription)
• Start codons are the first bases to be translated on an mRNA (AUG) (translation)