DNA Transcription & Translation

Question 1

Ribosome

Answer 1

A ribosome is an organelle composed of ribosomal RNA and ribosomal proteins (known as a Ribonucleoprotein or RNP)‏

• RNA protein
• Free ribosomes
• Attached ribosomes

Question 2

Peptide Bond

Answer 2

Question 3

Polypeptides

Answer 3

Question 4

AA Structure

Answer 4

Question 5

Proteins

Answer 5

• Shape is essential to function – Denatured protein no longer functional
• One or more polypeptides
• Composed of amino acids
  
  • 20 amino acids
  • Directed by sequence of bases (codons)‏

Question 6

Protein Synthesis:

Who decides what proteins must be made?
Who determines the sequence of Amino Acids?

Answer 6

Ribosome
T-RNA
M-RNA

Question 7

DNA backbone & bonds

Answer 7

OH end: 3’ end
P end: 5’ end
Number is d/t sugar molecule

Question 8

DNA makeup

Answer 8

• Pentose sugar (deoxyribose)‏
• Phosphate molecule
• Four nitrogenous bases
  
  • Pyrimidines: cytosine and thymine
  • Purines: adenine and guanine

each sugar attaches to a nucleic acid

Question 9

Pairing of nitrogenous bases

Answer 9

• T and A always bind to one another – through 2 bonds
• C & G bind, through 3 bonds = harder to break
• It is these bonds that hold the structure together

Question 10

Pyrimidines

Answer 10

cytosine, thymine

(uracil in RNA)

Question 11

purines

Answer 11

adenine, guanine

Question 12

Image: DNA molecule w/ sugars, bases, phosphate groups

Answer 12

Question 13

Which end of the DNA strand can you elongate?

Answer 13

The 3’ end

OH + PPP –> release 2P & H20 –> phospate bond

Question 14

structure: 3’ vs 5’ end

Answer 14

5’ end has the 5th carbon

3’ end has the 3rd carbon

Question 15

antiparallel

Answer 15

Question 16

Basic goal of translation

Answer 16

DNA is a double helix where genes/codons are.

To express the genes as Protein A/B/C… they must be translated

Question 17

Transcription vs translation

Answer 17

Transcription = DNA → RNA
Translation = RNA → protein

Question 18

What happens after transcription?

Answer 18

In transcription, everything is copied, but not all is necessary

Thus, must next undergo splicing (posttranscriptional)

Introns are filler, they’re spliced out.

Exons are the desired code - they remain and are later translated to protein

Could happen anywhere between transcription & protein synthesis

Chromosomal DNA –> Primary RNA transcript/nuclear RNA –> mRNA

Question 19

Intronic Character of DNA

Answer 19

Since less than 2% of the human genome encodes proteins and most genes primarily consist of introns, it is difficult to “find” the genes in the DNA sequence

Real genome is buried.

Question 20

True or False: RNA polymerasemakes an exact mirror image of the strand

Answer 20

False.

takes bases & makes mirror image of strand, in every way reflects original pairing EXCEPT uses uracil instead of thymine.

Question 21

Transcription Factors

Answer 21

Read and interpret the genetic blueprint thereby controlling transcription or the flow of genetic information from DNA to mRNA

• Regulate timing of transcription
• Regulate tissues in which genes are actively prescribed (e.g., clotting factor VIII primarily in hepatocytes)
• can activate or repress expression of genes
  
  • e.g., protens that function as receptors, enzymes, biomarkers
  • Environmental stimuli: hormones involve signaling cascades that can involve transcription factors
  • can alter gene expression to promote pathophysiology

Question 22

Transcription factors image

Answer 22

Question 23

What opens the DNA helix for transcription?

Answer 23

1. RNA polymerase
2. Some 50 different protein transcription factors

Question 24

What is a promoter site?

Answer 24

a sequence of DNA that specifies the beginning of a gene

Question 25

Transcription Story

Answer 25

1. some 50 different protein transcription factors, bound to DNA sequences called transcription factor binding sites/promoter site (usually on 5' side) 2. RNA polymerase binds to the promoter site where TFs are 3. Together, RNA polymerase & transcription factors open the DNA double helix - and the TFs position the RNA polymerase between the strands 4. RNA polymerase leaves the TFs behind, proceeds in the 3' to 5' direction (can be initiated by *enhancers* - nearby DNA sequences) 5. In eukaryotes, 3' to 5' movement requires that nucleosomes in front of the advancing RNA polymerase be removed (= *unzipped?)* 6. As RNA polymerase travels along the DNA strand, it is reading ONE strand and assembles corresponding ribonucleotides into a strand of RNA 7. Each ribonucleotide is inserted into the growing RNA strand following the rules of base parings (A-U, C-G) - *the pyrimidine **U replaces T (U from uridine triphosphate)* 8. Synthesis of the RNA proceeds in the 5' to 3' direction 9. As each nucleoside triphosphate is brought in to add to the 3' end of the growing strand, the two terminal phosphates are removed. 10. When transcription is complete, the transcript is released from the polymerase and shortly thereafter, the polymerase is released from the DNA ## Footnote *then to posttranscriptional splicing*

Question 26

Start Code

Answer 26

AUG: tells to read upstream to 3' end

Question 27

Template strand, coding strand, and transcription bubble

Answer 27

Template strand: 3' to 5' (being read) Coding Strand: 5' to 3' (what mRNA will match, except U) Transcription bubble: whole unzipped area

Question 28

Translation

Answer 28

Process by which RNA directs the synthesis of a polypeptide

Question 29

Site of protein synthesis

Answer 29

Ribosome (on rER) ribosome moves along the mRNA sequence to translate the AA sequence

Question 30

Role of tRNA in protein synthesis

Answer 30

tRNA contains a sequence of nucleotides (anti-codon) complementary to the triad of nucleotides on the mRNA strand (codon)

Question 31

Translation story

Answer 31

*just before: mRNA leaves nucleus and travels to ribosome, undergoing postranscriptional modification along the way* 1. Ribosome binds to mRNA at a specific area 2. Ribosome reads mRNA codons and "calls" matching tRNA anticodon sequences 3. Each time a new tRNA comes into the ribosome, the AA that it was carrying gets added to the elongating polypeptide chain and the tRNA leaves, mRNA moves long sequence and "calls" a new one 4. The ribosome continues until it hits a stop sequence, then it releases the polypeptide and the mRNA 5. The polypeptide heads where it needs to go, forms into its native shape and starts acting as a functional protein in the cell (*tertiary or quaternary structure essential to correct functioning)*

Question 32

tRNA structure

Answer 32

Site for amino acid attachment on 3' end anticodon on loop (3 loops, only one anticodon) Loop is like a hairpin, has anticodon

Question 33

How many nucleotides for one amino acid

Answer 33

3 - a codon

Question 34

How many possible codons

Answer 34

64 16 possible couplets (4x4); codon is series of 3 (4x4x4 = 64)

Question 35

Codons & amino acids

Answer 35

Can have a number of codes for one amino acid. This is protective - if there's a mistake, more likely to end up with the correct protein Problem: some are very polarized, others not. e.g., Valine has no polarity, Thr does - so if you substitute one for another, a structure is polarized that was not meant to be --\> shape is changed --\> pathophysiologic basis of disease

Question 36

Start & Stop Codons

Answer 36

Start: AUG Stop: UAA, UAG, UGA

Question 37

Protein composition

Answer 37

one or more polypeptides polypeptides composed of sequences of amino acids

Question 38

How many termination/nonsense codons?

Answer 38

3

Question 39

How many codons specify AAs?

Answer 39

61 there are only 20 AAs, thus the genetic code is redundant

Question 40

universality of genetic code

Answer 40

w/exception of ciliated protozoa and some plants, all organisms use same DNA codes to specify proteins EXCEPT: in mitochondria - own DNA w/different codes