Molecular genetics Flashcards by Jumana A

What does DNA consist of?

DNA is a polynucleotide

Each nucleotide consists of:
-a nitrogen base (adenine, guanine, cytosine, or thymine)
-a pentose sugar (deoxyribose)
-a phosphate

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What does 5 prime and 3 prime mean

5 prime: the 5th carbon of each sugar has a phosphate group attached

3 prime: the 3rd carbon of each sugar has a hydroxyl group attached

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What are the difference between DNA and RNA

-DNA-
sugar: deoxyribose
bases: GCAT
length and shape: double-stranded, long
location: nucleus

-RNA-
sugar: ribose
bases: GCAU (uracil)
length and shape: single-stranded, short
location: nucleus, cytoplasm

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What are genes?

coding regions on DNA
–> determines phenotypical characteristics of an organism

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What is a mutation? How is it caused?

an alteration in the DNA sequence
–> may be caused by chemical agents, ultraviolet radiation, or natural causes, can also occur during the process of DNA replication

e.g. dyes, tobacco smoke, UV rays, X rays, benzene, viruses (ex. HPV)

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What are telomeres?

-are repetitive sequences of DNA at the ends of chromosomes
-prevent the loss of genetic information during DNA replication

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What are the three steps of DNA replication?

Initiation, elongation, termination

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What is Initiation? And what enzymes are involved with it?

a step in DNA replication
-separating the two strands
-creates a replication bubble with two replication forks

Enzymes Involved: DNA Gyrase, DNA helicase, ssB’s

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What is DNA gyrase? and what step is it in?

In step 1, Initiation
-helps unwind the DNA by relieving the tension in the double helix

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What is DNA helicase? and what step is it in?

In step 1, Initiation
-unwinds DNA by breaking the H-bonds between the strands

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What are ssB’s, and what step are they in?

In step 1, Initiation
-single-stranded binding proteins keep strands from re-annealing (re-binding)

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What is RNA primase? and what step is it in?

In step 2, Elongation
-anneals the RNA-primer to the exposed 3’ end of the replication fork

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what is RNA primer? and what step is it in?

In step 2, Elongation
-10-60 base strand of RNA that serves as a starting point for DNA synthesis

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What is DNA polymerase III? and what step is it in?

In step 2, Elongation
-Adds complementary bases in the 5’ to 3’ direction
-the energy released by removing 2 phosphate groups allows the bonding
-the strand that is copied continuously (5’ to 3’) towards the replication fork is called the leading strand

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What is elongation?

the second step of DNA replication
-building complementary strands

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What are the differences between the leading and lagging strand?

-Leading strand is being replicated towards the fork, and the lagging strand is being replicated away from the fork

-Leading strand is being replicated continuously, while lagging strand is being replicated in discontinuous fragments

What are Okazaki fragments? and what step are they in?

In step 2, Elongation
-DNA polymerase III only moves 5’ to 3’ so the lagging strand is built discontinuously (in short segments) –> that is what okazaki fragments are!

What is DNA polymerase I? and what step is it in?

In step 2, elongation
-removes the RNA primers and replaces the primers with appropriate DNA bases

What is DNA ligase? and what step is it in?

In step 2, elongation
-attaches Okazaki fragments by creating phosphodiester bonds between sugars and phosphates

What is Termination? And what is involved in it?

the third and last step of DNA replication
-completion of process

DNA polymerase II

What is DNA polymerase II, and what step is it in?

In step 3, Termination
-proofreads the newly synthesized DNA and fixes incorrect nucleotides
-after proofreading, termination occurs when the two new DNA molecules separate from each other

What are the steps in making mRNA?

Initiation, Elongation, Termination, Post-transcriptional modifications

What is involved in Initiation (mRNA)?

-RNA polymerase binds to a specific region of the DNA, upstream of the gene to be transcribed (called the promoter)
-The DNA is unwound and the two strands are separated

What is involved in Elongation (mRNA)?

-only 3’ to 5’ strand is copied (called the template strand)
-the unused strand (5’ to 3’) is called the coding strand
-free floating nucleotides are H-bonded to their complementary bases by RNA polymerase (2 phosphates are removed to create a bond)
-RNA polymerase moves along the DNA (in the 5’ to 3’ direction), unwinding and separating as it goes while the DNA winds back up behind it
-the mRNA hands free of the side of the DNA strand attached only at a few base pairs

What is involved in termination (mRNA)?

-RNA polymerase encounters a sequence of bases at the end of the gene called a terminator sequence -RNA polymerase and primary transcript are released from the DNA

What is involved in the post transcriptional modifications of mRNA?

-a 5' cap is added to the mRNA to protect it from cytoplasmic enzymes -a poly-A tail of ~200 adenines is added by poly-A-Polymerase to the 3' end -capping and tailing results in the mRNA transcript being ready for release from the nucleus -spliceosomes remove all the non-coding regions (introns) and join the coding regions (exons) to form the mature mRNA transcript

What are the different steps of translation?

Step 1. The mRNA code, Step 2. the ribosomes, step 3. The tRNA, Step 4. Elongation of the Polypeptide Chain

Describe the first step of translation, the mRNA code

-the message on mRNA is written in 3-letter triplets called codons -all proteins must start with AUG (methionine) as the start codon; this may be removed later -there is no amino acid that is coded by UAA, UAG, or UGA, and so the protein breaks here

Describe the second step of translation, the ribosomes

-ribosomes are composed of ribosomal RNA (rRNA) and protein -the 5' (cap region) of mRNA adheres to the active ribosome -the ribosomes will move the mRNA through it starting at the 5' end and going towards the 3' end

Describe the third step of translation, the tRNA

-each tRNA has a cross like structure -at the base there is an anticodon which is the complement of the codon on the mRNA -at the 3' end of the tRNA is the acceptor site that holds the amino acid -1 ATP is required to attach each amino acid to correct tRNA to make aminoacyl-tRNA -enzymes join amino acids to tRNA

Describe the fourth and last step of translation, the elongation of the polypeptide chain

-the ribosomes moves the mRNA until the AUG codon fits into the P site (peptide site) -any bases before the AUG codon are simply ignored -amino-acyl tRNA brings methionine to the P site -a peptide bond forms between the methionine and the second amino acid -the process is repeated until the ribosome reaches a stop codon for which no tRNA exists -a protein (release factor) allows the polypeptide chain to be released from the ribosome

Name each type of point mutation

Substitution, deletion, addition/insertion

What are the different types of mutation

silent mutation: nothing is affected as amino acid stays the same missense mutation: amino acid is changed, thereby changing the purpose of the protein/coding of it Nonsense mutation: When a stop codon is created, causing the protein to change/stop being created framseshift mutation: substitution of many different amino acids or can create or remove a stop codon (basically big change)

What are the different types of chromosomal mutations?

translocation, inversion, duplication, deletion

Why is the top of the gel in electrophoresis negatively charged, and the bottom positively charged?

-DNA is negatively charged, thereby the DNA would be repelled by the negative charge at the top and travel to the bottom

Why do DNA fragments get shorter as the move along the gel

The smallest DNA fragments can continue through the gel, while the largest ones are too big to continue further