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WBiology > Molecular Genetics > Flashcards

Molecular Genetics Flashcards

1
Q

What are the types of nucleic acids?

A 
Ribonucleic acid (RNA)
Deoxyribonucleic acid (DNA)
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2
Q

What are the nitrogenous bases of DNA/RNA?

A

DNA:
Purines: AG
Pyrimidines: TC

RNA:
Purines: AG
Pyrimidines: CU

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3
Q

What is the shape of DNA/RNA?

A

DNA:
Double stranded alpha helix

RNA:
mitoRNA: single stranded alpha helix

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4
Q

What are the types of DNA/RNA?

A

DNA: 1

RNA:

  1. mRNA
  2. tRNA
  3. rRNA
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5
Q

What is the function of DNA/RNA?

A

DNA: Contains hereditary info for your proteins

RNA:

  1. Copy of DNA
  2. Carry (transfer) amino acids
  3. Part of ribosomes
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6
Q

How many copies are there of DNA/RNA?

A

DNA: One

RNA: Many

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7
Q

What are the ‘ ends?

A

5’ is end with the carbon with the phosphate, 3’ is carbon with hydroxyl

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8
Q

What is DNA/RNA composed of?

A

Polymers made up of many monomers called nucleotides

5 carbon sugar
- Deoxyribose or ribose

Phosphate joined to 5’ carbon

Nitrogenous base which stick out from 5 carbon sugar
- Cytosine, thymine, uraciil, adenine, guanine

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9
Q

How is DNA strands held together?

A
  • Alternating sugar and phosphate group backbone
  • Joined by dehydration synthesis reactions
  • As the linkages are formed the molecule twists into alpha helix
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10
Q

What is the DNA/RNA backbone? What significance does this hold regarding nitrogenous bases?

A

Hydrogen bonds due to highly EN N of bases and OH

This holds the two strands of DNA together between complementary nitrogenous bases

A always pairs with T (2 H bonds); G always pairs with C (3 H bonds)

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11
Q

What is the difference between molecule and strand?

A

Molecules (identical) vs strand (complementary)

Each DNA molecule is identical to parent molecule.

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12
Q

What does semi-conservative mean and how was it proven?

A

New DNA molecule contains one parental strand and one newly synthesized strand

Demonstrated by Meselson and Stahl who replicated heavy DNA in presence of light nucleotide triphosphate molecules and found that after the first division the density of the DNA molecules was between that of heavy and light

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13
Q

How is the new strand synthesized using what material? What are the characteristics of the new strand? How is the energy supplied?

A
  • Synthesized using deoxyribonucleotides (dNT) floating in nucleus (eukaryote) or cytosol (prokaryote)
  • Newly synthesized strand is complementary and anti-parallel (opposite polarity) of template strand
  • Energy for process is supplied using hydrolysis of nucleotide triphosphate molecules
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14
Q

What is the role of each strand of the DNA molecule in DNA replication?

A
  • Each strand of DNA molecule acts as template for synthesis of new strand
  • Contains necessary information to replicate molecule due to complementary base pairing
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15
Q

What is the process of DNA replication?

A
  1. Replication fork is generated: helicase breaks the H bonds to separate the strands
  2. Single-stranded binding proteins bind to hold DNA strands apart because otherwise they would rejoin (anneal)
  3. A short RNA sequence (primer) is added to each strand using primase
  4. DNA polymerase III adds complementary nucleotides to 3’ hydroxyl of adjacent nucelotide
  5. RNA primers are removed and gaps are filled with DNA using DNA polyermase I
  6. Enzyme DNA ligase attaches Okazaki fragments together fixing nicks (no phosphodiester linkage)
  7. DNA polermase I and III proof-read the newly synthesized strand of DNA to ensure complementary base pairing is correct
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16
Q

What is the role and mechanisms behind helicase?

A
  • Recognition, separation
  • Recognizes specific sequence of nucleotides called “origin of replication” and binds to DNA molecule
  • Unwinds double helix, separating DNA strands
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17
Q

What is the role and mechanisms behind single stranded binding proteins?

A
  • Stabilize single strand

- Molecules line up on single DNA strands after separation and hold them apart so they can serve as templates

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18
Q

What is the role and mechanisms behind DNA polymerase?

A

III:

  • Elongation
  • Adds complementary NT to template to 3’ hydroxy terminus

I:

  • Primer removal
  • Replaces RNA NT of primer with appropriate DNA NT

BOTH:

  • Mismatch repair
  • Proofreads each nucleotide inserted against the template and removes incorrectly paired NT and replaces with correct NT
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19
Q

What is the role and mechanisms behind ligase?

A
  • Nick repair

- Creates phosphodiester linkage between phosphate and 3’ hydroxyl within DNA strand

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20
Q

What is the role and mechanisms behind nucleases?

A
  • Excision repair
  • Removes damaged NT in strand

Either act as exonuclease to change incorrect nucleotide
Either act as endonuclease which corrects mismatch after replication

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21
Q

What is the role and mechanisms behind telomerase?

A
  • Lengthens telomere

- Contains an RNA sequence that serves as template for new telomere on 3’ end of DNA strand

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22
Q

Where is the primer added for DNA replication?

A

For one parent strand it’s added to the end of the molecule and for other it’s at the top of the fork (new DNA always 5’ to 3’

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23
Q

How can you tell which is the leading and which is the lagging strand?

A
  • Leading strand elongates in 5’ to 3’ direction, synthesized continuously, growing towards the fork
  • Lagging strand grows away from fork, synthesized in Okazaki fragments (short pieces 100-200 NT in length separated by RNA segments) as more DNA must be unwound before the next fragment can be made
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24
Q

What are replication bubbles and how are they formed in eukaryotes and prokaryotes?

A

Replication bubbles are formed with each bubble having 2 replication forks and DNA synthesis proceeds in both directions simultaneously

Prokaryotes: replication begins at specific sequence called ori (origin of replication)

Eukaryotes: multiple bubles are generated simultaneously as DNA is big

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25
Q

Why does DNA get shorter after each replication?

A

At 5’ ends of newly synthesized strands the primer can’t be filled as there is no 3’ hydroxyl group: each division the DNA gets shorter

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26
Q

What is gyrase as well as its function?

A
  • Found only in prokaryotes

- Relieves tension due to unwinding DNA

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27
Q

What are telomeres and what do they do? What is the enzyme associated with them?

A
  • Long sequence (100-1000s of copies of short sequences) of non-coding nucleotides found at ends of DNA molecule
  • Prevents loss of important DNA
  • Enzyme called telomerase replaces telomere after each replication
    Found in high concentrations of stem cells and cancer cells
28
Q

Why is protein synthesis called gene expression?

A

Uses information in genes on DNA to make proteins

29
Q

What is the central dogma of protein synthesis?

A

Each gene contains info for 1 polypeptide chain/subunit

eg. Haemoglobin has 2 alpha chains and 2 beta chains so there are 2 genes

30
Q

What is a brief summary of the stages of protein synthesis?

A
  • Transcription: makes an RNA copy that is complementary + antiparallel to one DNA strand for 1 gene
  • Post-Transcriptional Modification: mRNA is given protection to become final RNA which goes out to the cytoplasm
  • Translation: nucleotide sequence converts to polypeptide chain (amino acid sequence)
31
Q 
Describe the following for mRNA.
Function
Location
Size
Source
Structural Features
A 
Provide copy of DNA info for 1 gene
Made in nucleus
Move to cytosol
Depends on gene (largest of 3)
DNA
Single stranded alpha helix
32
Q 
Describe the following for tRNA.
Function
Location
Size
Source
Structural Features
A 
Carry amino acids
Made in nucleus
Move to cytosol
70-90 bases
DNA
Clover leaf
33
Q 
Describe the following for rRNA.
Function
Location
Size
Source
Structural Features
A 
Structural part of ribosome 
Made in nucleus 
Move to cytosol 
100 bases 
DNA 
Bound to proteins
34
Q

What are the 3 stages of transcription? How about translation?

A

Initation, elongation, and termination

35
Q

What happens during the initation phase of transcription? Describe the promoter.

A
  • Enzyme RNA polymerase recognizes and binds to DNA at specific site called promoter
  • Located at 5’ end of DNA
  • String of A and T bases which form only 2 H bonds (less energy to break)
  • RNA polyermase unwinds DNA
36
Q

What happens during the elongation phase of transcription? What are the strands called?

A
  • RNA polymerase builds single-stranded RNA copy of DNA (5’-3’) without the help of a primer
  • NOTE: promoter is not transcribed
  • Strand used: template strand, RNA copy is complementary
  • Strand not used: coding strand; RNA copy is identical
37
Q

What happens during the termination phase of transcription?

A
  • Terminator sequence is specific sequence of nucleotides on DNA at end of gene that tells RNA polyermase to stop transcribing
  • mRNA dissociates from DNA and enzyme detaches and repeats
38
Q

What is an intron? An exon?

A

Introns: intervening sequences in eukaryotic DNA that do not code for proteins
Exons: expressed (coding) regions of DNA

39
Q

What is the primary transcript and the mRNA transcript?

A

Primary Transcript: when mRNA detaches from DNA

mRNA Transcript: after modifications

40
Q

In which cells do you need post-transcriptional modifications and what do they do?

A
  • Only eukaryotic cells

- Protect mRNA from degradation, help ribosome binding, removes unnecessary segments of mRNA

41
Q

Answer the following for the 3 types of post-transcriptional modifications;

Description
Enzyme
Function

A

Capping (Gm)

  • Modified guanine added to 5’ end
  • Protects 5’ end of mRNA
  • Ribosome binding site

Tailing (AAA)

  • Poly a tail (string of adenines) is added to 3’ end
  • PolyApolymerase
  • Protects 3’ end of mRNA
  • Helps mRNA out of nucleus

Splicing

  • Introns are cut out, exons are spliced together
  • Spliceosome (snRP or small nuclear riboproteins)
  • Make a functional mRNA
42
Q

What is a codon?

A

Base triplet on mRNA that determines a specific amino acid

43
Q

What is the genetic code? How many codons for each function? How is it read?

A
  • Comprises of 64 triplet mRNA nucleotides (codons) which are translated into 20 different amino acids (61 codons) or signals for stopping translation (3 codons)
  • mRNA is always read in 5’ to 3’ direction
44
Q

What is the reading frame? How is it established?

A

Correct set of codons to read; established by ribosomes

45
Q

What is the organelle responsible for translation? Where do they bind?

A

Ribosomes; Bind to mRNA at 5’ cap but don’t start translation until read AUG codon (start codon) and stops at stop codon

46
Q

What is tRNA’s role in translation? Talk about nucleotides, amino acids, and enzymes.

A

Each tRNA molecule has sequence of 3 nucleotides called anticodon that is complementary to codon on mRNA

Forms amino acytl tRNA (amino acid bound to 3’ end of tRNA; eg. met-tRNA)

Attached by amino acyl tRNA synthetase (20 enzymes for 20 amino acids) which recognize anticodon sequence

47
Q

What is a polyribosome?

A

many ribosomes simultaneously transcribing an mRNA

48
Q

What happens during the initiation phase during translation?

A
  • Ribosome binds to mRNA at 5’ cap and moves along mRNA in 5’ to 3’ direction until it reaches AUG
  • tRNA molecule carrying amino acid “met” binds to ribosome
  • Ribosomes have two binding sites; acceptor (A) which received incoming aminoacyl-tRNAs and peptidyl (P) which holds tRNA carrying growing polypeptide chain
  • Met-tRNA binds to P site and A site is vacant
49
Q

What happens during the elongation phase during translation?

A
  • Codon comes to A site
  • Aminoacyl-tRNA with anticodon complementary to codon at A site binds to mRNA
  • Ribosome catalyzes dehydration synthesis reaction between the 2 amino acids, forming peptide linkage
  • tRNA is P site detaches and recycles, leaving tRNA with polypeptide chain in A site
  • Ribosome moves along 1 codon in 3’ direction, so tRNA with growing chain is in P site
  • New tRNA binds to A site, etc.
50
Q

What happens during the termination phase during translation?

A
  • Stop codon reaches A site of ribosome
  • No tRNA to bind to mRNA so ribosome stalls
  • Protein called release factor binds to stop codon in A site causing release of polypeptide chain from tRNA and from ribosome
  • Ribosome detaches from mRNA by separating subunits
51
Q

Why is regulation of gene expression important?

A

Only a bit of the genome is expressed (transcribed and translated) at one time
mRNA is only produced when protein is needed

52
Q

What gene expression mechanisms are studied? Where can they be found and why?

A

The control mechanisms were studied in bacteria which have operons (to make things more efficient as they are simple and the genes are involved in only 1 parthway)

53
Q

What is an operon? What are its components?

A

Operon: 2+ genes that code for proteins in same metabolic pathway with one promoter

Regulatory Sequence: part of operon with promoter and operator

Transcription Unit: genes that are transcribed

54
Q

What is the promoter and operator in terms of gene regulation?

A

Promoter: RNA polyermase binding site; if not blocked then gene is on and transcriptional unit will be transcribed

Operator: repressor protein binding site; turns gene on and off

55
Q

What is an inducible operon and an example? What is a repressible operon and an example?

A

Inducible Operon: off unless induced to turn on (Lac)

Repressible Operon: on unless repressed (Trp)

56
Q

What is an inducer? In which type of operon does it occur?

A

substance that binds to repressor causing conformational change to turn operon on

Inducible

57
Q

What is a corepressor? In which type of operon does it occur?

A

binds to repressor causing conformational change so it is functional

Repressible

58
Q

How does the Lac Operon work?

A
  • Transcription unit consists of 3 genes (LacZ, lacY, lacA) that make proteins (enzymes) allowing bacteria to use lactose as energy souce
  • Repressor protein is called LacI protein and is made by its own operon which is always on
  • When no lactose, LacI binds to operator, preventing RNA polymerase from binding to the adjacent promoter, turning gene off
  • When lactose is present, lactose (the inducer) binds to LacI causing conformational change so it can’t bind to operator and leaves so RNA polymerase can bind
59
Q

How does the Trp Operon work?

A
  • Trp is important amino acid needed and is often not available for bacteria so they must make it themselves using enzymes coded for in trp operon
  • Repressor is unable to bind to operator until bound to corepressor (for this case is trp)
  • If lots of trp, don’t need to make own so trp binds to repressor protein causing a conformational change, allowing it to bind to operator
  • Operon turns off, preventing the transcription of mRNA
60
Q

What are mutations? How do they affect phenotypes?

A
  • Change in DNA nucleotide sequence (NOT RNA)

- Alters phenotype as alters RNA and amino acid sequence

61
Q

What is a point mutation?

A

Change in 1 or a few base pairs in a gene

62
Q

What is a base-pair substitution? What is a deletion/insertion?

A

Nucleotide pair is replaced with another

1 or a few base pairs is deleted/added

63
Q

What are the types of base-pair substitutions?

A

Silent Mutations: change DNA without changing amino acid sequence due to redundancy of genetic code

Missense Mutations: changes codon to code for different amino acid

Nonsense Mutations: causes premature termination of polypeptide chain

64
Q

What are the types of deletion/insertions? When would it not occur?

A

Frameshift Mutation: alter reading frame

All the base pair substitution mutations also apply

If 3 NT codon are added/deleted between codons then will not cause frameshift mutations

65
Q

What are the causes of mutations? Give definitions and examples/

A

Spontaneous Mutations: errors in DNA replication

Mutagens: chemical/physical agents that cause mutations

  • X rays/high energy radiation cause DNA strand to break
  • UV radiation cause thymine dimers (2 thymines to attach together)
  • Chemical agents cause base pair analogues (mimics)

WBiology (8 decks)

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