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FOOD 521 > Molecular Biology: DNA, RNA, and Protein > Flashcards

Molecular Biology: DNA, RNA, and Protein Flashcards

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1
Q

What is a genome?

A
  • Every organism has a genome that contains the information needed to make and maintain itself
  • Most genomes are made of DNA but some viruses have an RNA genome
  • The human genome has 3,235,000,000 base pairs of DNA
  • We also have a mitochondrial genome that is 16,569 base pairs of DNA
  • Can be over 1000 mitochondria per human cell and each mitochondria can have 5 to 10 copies of mitochondrial DNA
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2
Q

What is a chromosome?

A
  • The human genome has 3,235,000,000 base pairs of DNA
  • In eukaryotic organisms, the DNA is not a single long chain
  • Instead the DNA is split up into different sizes of linear molecules that condense to form a chromosome
A chromosome is a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.
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3
Q

This is a karyotype of which organism?

A

Diploid organism (in this case a bull)
29 autosomal chromosomes x 2 copies
2 sex chromosomes (X and Y)
Total = 60 chromosomes

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4
Q

How many chromosomes does each organism have?

A

39 (1n); 78 (2n) = chicken
23 (1n); 46 (2n) = human
52 (1n); 104 (2n) = catfish
1n = 1 set (copy) of chromosomes (haploid)
2n = 2 sets (copies) of chromosomes (diploid)

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5
Q

All organisms have DNA made from the same molecules.
True or False?

A

True.

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6
Q

DNA =

A

Deoxyribonucleic acid

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7
Q

Genetic material is a long double stranded DNA polymer.
The sequence of units in DNA are called […].

A

deoxyribonucleotides

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8
Q

The chemical composition of deoxyribonucleotides is the same in all organisms.
True or False?

A

True.

This is one reason why molecular biologists can transfer genes
amongst organisms

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9
Q

Describe the structure of nucleotide.

A
This is a deoxyribonucleotide triphosphate - a nucleotide only has one phosphate group.
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10
Q

Pyrimidines [2].

A
  • Cytosine
  • Thymine (uracil in RNA)
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11
Q

Purines [2].

A
  • Adenine
  • Guanine
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12
Q
  • Cytosine
  • Thymine (Uracil in RNA)
A

Pyrimidines [2].

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13
Q
  • Adenine
  • Guanine
A

Purines [2].

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14
Q

How are nucleotides abbreviated?

A
  • Abbreviations of the four nucleotides are dATP, dCTP, dGTP, dTTP
  • For example, dATP = 2ʹ-deoxyadenosine 5ʹ-triphosphate
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15
Q

Nucleotide subunits are joined by […].

A
  • Nucleotide subunits are joined by phosphodiester bonds.
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16
Q

Describe the chemical structure of a single strand of DNA.

A
  • The phosphate group of the 5’-carbon of one nucleotide is linked to the 3’-OH group of the deoxyribose of the adjacent nucleotide.
  • The polynucleotide strand has a 3’-OH group at one end and a 5’-phosphate group at the other end.
  • The nucleotide subunits are joined by phosphodiester bonds.
The directionality of DNA (5' to 3') is important to know since the two ends of the polynucleotide are chemically distinct.
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17
Q

How do nucleotides join together to make DNA?

A
  • DNA synthesis occurs in the 5’ to 3’ direction.
  • An enzyme called DNA polymerase adds nucleotides to the DNA strand.
  • The alpha-phosphate of the nucleotide gets incorporated into the DNA strand and the beta-gamma phosphates (called pyrophosphates) are removed.
Synthesis occurs in the 5' to 3' direction with the new nucleotide being added to the 3'-carbon at the end of the existing polynucleotide. The beta- and gamma-phosphates are removed as a pyrophosphate molecule.
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18
Q

Describe the structure of a double strand of DNA.

A
  • Antiparallel
  • C pairs with G (3 h-bonds)
  • T pairs with A (2 h-bonds)
Left: The structure is shown with the sugar-phosphate backbone of each polynucleotide drawn as a gray ribbon with the base pairs in green. Right: A base-pairs with T, and G base-pairs with C. The bases are drawn in outline, with the hydrogen bonding indicated by dotted lines. Note that a G-C base pair has three hydrogen bonds and a T-A base pair has just two.
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19
Q

Adenine and thymine bond via 2 hydrogen bonds.
True or False?

A

True.

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20
Q

Adenine and thymine bond via 3 hydrogen bonds.
True or False?

A

False.
They bond by only 2.

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21
Q

Cytosine and guanine bond via 2 hydrogen bonds.
True or False?

A

False.
They bond via 3.

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22
Q

Cytosine and guanine bond via 3 hydrogen bonds.
True or False?

A

True.

Think C3PO. (3 bonds goes with cytosine)

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23
Q

How much DNA do organisms have?

A
  • A thousand base pairs = kilobase pairs or Kb
  • A million base pairs = megabase pairs or Mb
  • A billion base pairs = gigabase pairs or Gb
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24
Q

What are the major functions of DNA? [4]

A
  • Encodes the information for the production of proteins
  • It is reproduced (replicated) with a high degree of accuracy to pass the encoded information onto new cells.
  • DNA single-strand can act as a template for the production of a new complementary strand.
  • Sequence of nucleotides in a gene provides the code for the production of a protein.

Watson-Crick-Franklin model of DNA fully meets these requirements.

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25
Q

What is the complementary DNA strand?
5’-TAGGCAT-3’

A

3’-ATCCGTA-5’

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26
Q

How do RNA molecules differ from DNA? [3]

A
  • Sugar is ribose instead of deoxyribose
  • Instead of thymine (T), the base is uracil in RNA
  • Most RNA is single stranded
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27
Q

List the different types of RNA in the cell.

A
  • sncRNA
  • lncRNA
  • hnRNA
  • mRNA
  • rRNA
  • tRNA
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28
Q

What is sncRNA?

A

short non-coding RNA < 200 nucleotides

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29
Q

What is lncRNA?

A

long noncoding RNA

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30
Q

What is hnRNA?

A

heterogenous nuclear RNA (term for unprocessed mRNA)

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31
Q

What is mRNA?

A

messenger RNA - codes for a protein, goes to the ribosome for translation

32
Q

What is rRNA?

A

ribosomal RNA - becomes part of the ribosome (large complex that translates proteins)

33
Q

What is tRNA?

A

transfer RNA - attaches to an amino acid and carries the amino acid to incorporation into a protein (translation)

34
Q

Which types of RNA are only found in eukaryotes? [2]

A

hnRNA (pre-mRNA)
lncRNA

35
Q

Of total RNA, how much is coding and how much is non-coding?

A
  • Coding RNA = 4% of total
  • Non-coding RNA = 96% of total
36
Q

Which RNA is coding?

A
  • mRNA
37
Q

Which RNA is non-coding?

A
  • rRNA
  • tRNA
  • sncRNA
  • lncRNA
38
Q

Is RNA inherited like DNA?

A

No.

39
Q

How is RNA synthesized?

A
  • One strand of DNA is the template for RNA synthesis
  • The template strand (a.k.a. anti-sense strand), is in the 3’ to 5’ direction
  • mRNA transcription proceeds in the 5’ to 3’ direction
  • An enzyme called RNA polymerase joins the ribonucleotides together via phosphodiester linkages to make the RNA strand.
  • No primer necessary in RNA synthesis
40
Q

The anti-sense strand in RNA synthesis is in the […] direction.

A
  • 3’ to 5’ direction
  • mRNA transcription proceeds in the 5’ to 3’ direction
41
Q

What defines a gene?

A
  • Only specific regions of the genomic DNA are transcribed
  • mRNA, tRNA, and rRNA all need to be transcribed from the genomic DNA
  • Sequences that control the initiation of transcription occur before the gene coding sequence
42
Q

Describe the lay-out of a gene.

A
  • Promoter - sequence of this region is where RNA polymerase binds DNA
  • Terminator - sequence where RNA polymerase falls off the DNA
  • Initiation (start) and termination (stop) codons for protein translation
AUG is always the initiation codon.
43
Q

DNA synthesis occurs in the 5’ to 3’ direction.
True or False?

A

True.

44
Q

DNA synthesis occurs in the 3’ to 5’ direction.
True or False?

A

False.
DNA synthesis occurs in the 5’ to 3’ direction.

45
Q

mRNA transcription proceeds in the 5’ to 3’ direction.
True or False?

A

True.

46
Q

mRNA transcription proceeds in the 3’ to 5’ direction.
True or False?

A

False.
mRNA transcription proceeds in the 5’ to 3’ direction.

47
Q

Describe the prokaryotic gene structure.

A
  • Shine-Dalgarno sequence - ribosome binding site in prokaryotic mRNA
  • No separation between DNA and cytoplasm
48
Q

RNAs are synthesized as precursor RNAs that need to be processed to their final form.
True or False?

A

True.

Eukaryotic mRNA molecules often require extensive processing and transport, while prokaryotic mRNA molecules do not.

However, the primary transcripts of both rRNAs and tRNAs must undergo a series of processing steps in prokaryotic as well as eukaryotic cells.

49
Q

Where does the splicing occur?

A
  • Splicing occurs in the nucleus
  • Introns are cut out of the pre-mRNA and the exons are rejoined to give the functional mRNA.
  • mRNA exits the nucleus and goes into the cytoplasm for translation
  • Introns can also be present in rRNA and tRNA genes
50
Q

Describe modifications to the 5’ end of mRNA in eukaryotes.

A
  • 5’ cap added to the 5’ end of the mRNA (modified guanine nucleotid: 7-methyl guanine)
The cap structure is needed to help initiate translation of the mRNA into a protein by the ribosome.

In prokaryotic cells, the triphosphate is present at the 5’ end of the mRNA but no modified guanine nucleotide.

51
Q

Why is the cap structure (the modified guanine nucleotide) added to the 5’ end of mRNA in eukaryotes?

A
  • Required to help initiate translation of the mRNA into a protein by the ribosome in the cytosol
52
Q

Describe modifications to the 3’ end of mRNA in eukaryotes.

A
  • The poly(A) tail is a series of up to 250 adenine nucleotides that is added to the 3ʹ-end of the mRNA – only occurs in eukaryotic cells.
  • Long poly(A) tail needed to protect against mRNA degradation
53
Q

The 5’-cap and the poly(A) tail added to the ends of mRNA in eukaryotes help to [3]:

A
  • Increase the stability of the mRNA - protects mRNA from ribonucleases and degradation
  • Transport the mature mRNA out of the nucleus and into the cytoplasm
  • Help the ribosome to bind to the mRNA to begin translation.
54
Q

What is the main purpose of the poly(A) tail?

A

Long poly(A) tail needed to protect against mRNA degradation

mRNA is cleaved downstream of the polyA cleavage signal (AAUAAA in human cells), then PolyA polymerase
adds the adenine nucleotides

55
Q

Discuss the total RNA in a cell.

A
  • The thousands of mRNAs in a cell represent only about 3 to 5% of the cellular RNA
  • Greater than 90% of the RNA in a metabolically active cell is rRNA which is found in ribosomes
  • tRNA represents ~4% of the cellular RNA
  • rRNA combines with ribosomal proteins to form ribonucleoprotein complexes that make up the large and small subunit of the ribosome
  • During protein synthesis, one large ribosomal subunit and one small ribosomal subunit combine to form a ribosome
  • The ribosome translates mRNA into proteins
56
Q

What are ribosomes?

A
  • Proteins are synthesized by the large RNA–protein complexes called ribosomes
  • An E. coli cell contains approximately 20,000 ribosomes in the cytoplasm
  • Human cells contains more than a million ribosomes, some free in the cytoplasm and some attached to the outer surface of the rough endoplasmic reticulum
Endoplasmic reticulum (ER) - the membranous network of tubes and vesicles that permeates the cell.
57
Q

Compare the composition of eukaryotic and bacterial ribosomes.

A
  • Eukaryotic ribosomes are 80S - composed of a 40S small subunit and a 60S large subunit.
  • Bacterial ribosomes are 70S, composed of a 50S large subunit and a 30S small subunit.
The 'S' stands for svedbergs, a unit used to measure how fast molecules move in a centrifuge. 'S' is an indirect measure to determine the density and size of ribosomal subunits and their RNA.
58
Q

What is the function of tRNAs and how many types are there?

A
  • Transfer RNAs carry amino acids to the ribosome for incorporation into proteins
59
Q

Describe the detailed structure of a bacterial ribosome.

A
60
Q

Which strand codes for the protein: sense or anti-sense?

A
  • The sense strand codes for the protein
  • The anti-sense strand acts as the template for mRNA synthesis
61
Q

What occurs at the E site of a bacterial ribosome?

A

tRNA departs to go and pick up another amino acid

62
Q

What happens at the P site of a bacterial ribosome?

A

tRNA with amino acid that is being attached to the protein

63
Q

What happens at the A site of a bacterial ribosome?

A
  • tRNA carrying the next amino acid to be attached to the protein
64
Q

Describe translation initiation in prokaryotes.

A
  • Translation is initiated by the binding of a small ribosomal subunit to an mRNA by base pairing between a sequence of ~7 nucleotides called the Shine-Dalgarno (SD) sequence
  • SD sequence is near the 5’ end of the mRNA and is complementary to the 3’end of the rRNA of the small ribosomal subunit
  • The anticodon (UAC) of the initiator tRNA- Methionine base pairs with the start codon (AUG) of the mRNA
  • The large subunit then comes in to form the initiation complex
The initiator Methionine is Formylated at the amino group (fMet)
65
Q

What is the start codon and what does it code for?

A

AUG - methionine

66
Q

Describe translation initiation in eukaryotes.

A
  • Translation is initiated by the binding of an initiator Methionine-tRNA and translation initiation factors (not shown here) to a small ribosomal subunit
  • Next the 5’capped end of the mRNA, which is combined with specific proteins, associates with the initiator Met-tRNA- small ribosomal complex
  • The complex moves along the mRNA until a start codon (AUG) is found
  • Once the UAC anticodon sequence of the initiator Met-tRNA base pairs with the AUG sequence of the mRNA, the large ribosomal subunit joins the complex to form the initiation complex
67
Q

Describe translation elongation in prokaryotes and eukarotes.

A
  • Elongation and termination of translation are similar in prokaryotes and eukaryotes
  • Elongation is the formation of peptide bonds between adjacent amino acids
  • After the initiation complex is formed, the second set of three nucleotides (triplet or codon) in the mRNA that follows the start codon will be bound by a tRNA carrying the complementary anticodon
  • In this example the second codon in the mRNA is “CUG” which is recognized by a tRNA carrying Leucine and the ‘GAC’ anticodon
  • A peptidyl bond is formed in the ‘P’ position by a peptidyl transferase (RNA enzyme that is part of the large ribosomal subunit)
  • Once the amino acid from a tRNA has been incorporated into the peptide chain, the tRNA exits the ribosome (E site)
68
Q

Describe translation termination in prokaryotes and eukaryotes.

A
  • The elongation process continues until a UAA, UAG or UGA stop codon (or termination codon) is encountered
  • There are no naturally occurring tRNAs with anticodons that are complementary to these codons (this is mostly true…)
  • A protein called a termination factor or release factor recognizes the stop codon and binds to the ribosome
  • The uncharged tRNA, completed protein, and the mRNA dissociate from the ribosome
  • A ribosome releasing factor separates the ribosomal subunits
69
Q

What is the stop codon?

A

There are 3: UAA; UAG; UGA

70
Q

Describe the genetic code.

A
  • The codons are read in the 5’ to 3’ direction in an mRNA.
  • Amino acids are designated by the standard three-letter abbreviations.
71
Q

The genetic code is universal.
True or False?

A

False.

72
Q

What is the Shine-Dalgarno sequence?

A
  • Shine-Dalgarno a ~7 nucleotide sequence is near the 5’ end of prokaryotic mRNA and is complementary to the 3’ end of the rRNA of the small ribosomal subunit.
  • It is located ~8 nucleotides upstream of the AUG start codon and does not get translated into the protein.

In prokaryotes

73
Q

How does the initiator transfer RNA differ in prokaryotes and eukaryotes?

A
  • In prokaryotes, the initiator Methionine is Formylated at the amino group (fMet)
  • In eukaryotes, the initiator Methionine is NOT formylated.
74
Q

What happens to the DNA products during the second and third cycles of PCR?

A
  • From the first-cycle products shown at the top of the diagram, the next cycle leads to four products, two of which are identical to the first-cycle products, and two of which are made entirely of new DNA.
  • During the third cycle, the latter give rise to short products that, in subsequent cycles, accumulate in an exponential fashion.

Typically PCR reactions are 25 to 30 cycles.

After n cycles there are 2^n copies of the target sequence.
75
Q

There is more than one restriction site for each
enzyme in the pUC8 plasmid.
True or False?

A

False.
There is only one restriction site for each enzyme in the plasmid

76
Q

There is only one restriction site for each enzyme in the pUC8 plasmid
True or False?

A

True.

FOOD 521 (8 decks)

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