Biology I Ch.17 (2)

7/24/2019 Biology I Ch.17 (2)

http://slidepdf.com/reader/full/biology-i-ch17-2 1/50

Michael Ye (예병억)

Associate Professor

Division of Liberal Arts & Sciences

General Biology IWeek 14 (2015.06.02)

7/24/2019 Biology I Ch.17 (2)


Week Description Notes

1st Introduction (3.03 & 3.05)

2nd Chapters 1 & 2. Study of Life & Chemistry of Life (3.10 & 3.12)

3rd Chapters 3 & 4. Chemistry of Water and Carbon (3.17 & 3.19) Exam #1

4th Chapter 5. Biomolecules (3.24 & 3.26) Exam #2

5th Chapter 6. The Cell (3.31 & 4.02) Exam #3

6th Chapters 7 & 8. The Cell Membrane & Metabolism (4.07 & 4.09) Exam #4

7th Chapters 9. Cellular Respiration (4.14 & 4.16) Exam #5

8th Midterm Exam

9th Chapter 12. The Cell Cycle (4.28 & 4.30)

10th Chapter 13. Meiosis (05.05 어린이날 & 5.07)

11th Chapter 14. The Gene (5.12 & 5.14) Exam #6

12th Chapter 15. Chromosomal Basis of Inheritance (5.19 & 5.21) Exam #7

13

th

Chapter 16. Molecular Basis of Inheritance (5.26 & 5.28) Exam #8

14th Chapter 17. From Gene to Protein (6.02 & 6.04) Exam #9

15th Chapter 18. Regulation of Gene Expression (6.09 & 6.11) Exam #10

16th Final Exam

7/24/2019 Biology I Ch.17 (2)


What is a Gene?

7/24/2019 Biology I Ch.17 (2)


Gene Structure (ORF)

The generic structure of a eukaryotic mRNA, illustrating some post-transcriptionalregulatory elements that affect gene expression. Abbreviations (from 5' to 3'): UTR,

untranslated region; m7G, 7-methyl-guanosine cap; hairpin, hairpin-like secondary

structures; uORF , upstream open reading frame; IRES, internal ribosome entry site;

CPE , cytoplasmic polyadenylation element; AAUAAA, polyadenylation signal.

7/24/2019 Biology I Ch.17 (2)


The two functions of DNA comprise the Central Dogma of Molecular Biology :

1. DNA can reproduce itself (replication)

2. DNA can copy its information into RNA (transcription)

3. RNA can specify a sequence of amino acids in a polypeptide (translation)

The Central Dogma of Molecular Biology

Replication

7/24/2019 Biology I Ch.17 (2)


Basic Principles of Transcription and Translation

• RNA is the bridge between genes and the proteins for which they code

•Transcription is the synthesis of RNA (messenger RNA, mRNA) under the direction ofDNA

• Translation is the synthesis of a polypeptide, using information in the mRNA

• Ribosomes are the sites of translation

• In prokaryotes, translation of mRNA can begin before transcription has finished

• In a eukaryotic cell, the nuclear envelope separates transcription from translation; also,

RNA transcripts are modified through RNA processing to yield finished mRNA

• A primary transcript is the initial RNA transcript from any gene prior to processing

• The central dogma:

7/24/2019 Biology I Ch.17 (2)


Basic Principles of Transcription and Translation

Coupled Transcription & Translation Uncoupled Transcription & Translation

7/24/2019 Biology I Ch.17 (2)


The Genetic Code

Some Important Questions

1. How are the instructions for assembling amino acids into proteins encoded into DNA? (There are

20 amino acids, but there are only four nucleotide bases in DNA)

2. How many nucleotides correspond to an amino acid?

Mechanism

• The flow of information from gene to protein is based on a codon

• The gene is transcribed into complementary, non-overlapping codon of mRNA, which is then

translated into amino acids (to form a polypeptide)

• During transcription, one of the two DNA strands, called the template strand , provides a template

for ordering the sequence of complementary nucleotides in an RNA transcript

• The template strand is always the same strand for a given gene

• During translation, the mRNA base triplets or codons, are read in the 5 to 3 direction

• Each codon specifies the amino acid (one of 20) to be placed at the corresponding position along a

polypeptide

7/24/2019 Biology I Ch.17 (2)


The Genetic Code

7/24/2019 Biology I Ch.17 (2)


Cracking the Code

• All 64 codons were deciphered by the mid-1960s

• Of the 64 triplets, 61 code for amino acids; 3 triplets are “stop” signals to end translation

• The genetic code is redundant (more than one codon may specify a particular amino acid) but not

ambiguous; no codon specifies more than one amino acid

• Codons must be read in the correct reading frame (correct groupings) in order for the specified

polypeptide to be produced

7/24/2019 Biology I Ch.17 (2)


• Degenerate & Specific: 64 codons encode 61 amino acids & 3 “stop” signals

• Multiple codes for an amino acid tend to have two bases in common

• Codons are written in a 5' 3' sequence

The Genetic Code

7/24/2019 Biology I Ch.17 (2)


Marshall Warren Nirenberg

Nirenberg (1962)

• Nobel Prize in Medicine (1968)

• NIH (National Institutes of Health)

• With Har Gobind Khorana and Robert W. Holley

• For…… "breaking the genetic code" and describing how it

operates in protein synthesis

• In August 1961, at the International Congress of

Biochemistry in Moscow , Nirenberg presented a paper to a

small group of scientists

• Poly-URIDINE (UUU): phenylalanine

•Poly-ADENOSINE (AAA): lysine

• Poly-CYTOSTINE (CCC): proline

• Poly-GUANOSINE (GGG): glycine

Har Gobind Khorana

7/24/2019 Biology I Ch.17 (2)


Translation

7/24/2019 Biology I Ch.17 (2)


The sequence of a hypothetical gene and the RNA transcribed from it are shown.

By convention, the gene is said to be transcribed from the 5’ end to the 3’ end, but

the template strand of DNA is copied from the 3’ end to the 5’ end. Growth of the

ribonucleotide chain proceeds 5‘ 3’

Direction of Transcription

• RNA sequences are written 5’ 3’ (left to right)

•Translation occurs 5’ 3’ with ribosomes reading the message 5’ 3’

• Genes are written so that transcription proceeds in a left to right direction

7/24/2019 Biology I Ch.17 (2)


Evolution of the Genetic Code

• The genetic code is nearly universal, shared by the simplest bacteria to the most

complex animals

• Genes can be transcribed and translated after being transplanted from one species to

another

7/24/2019 Biology I Ch.17 (2)


Molecular Components of Transcription

• Transcription is the first stage of gene expression

•

RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart andhooks together the RNA nucleotides

• The RNA is complementary to the DNA template strand

• RNA synthesis follows the same base-pairing rules as DNA, except that uracil

substitutes for thymine

• The DNA sequence where RNA polymerase attaches is called the promoter ; in bacteria,

the sequence signaling the end of transcription is called the terminator• The stretch of DNA that is transcribed is called a transcription unit

7/24/2019 Biology I Ch.17 (2)


The three stages of transcription

1. Initiation2. Elongation

3. Termination

Synthesis of an RNA Transcript

7/24/2019 Biology I Ch.17 (2)


• Promoters signal the transcriptional start point and usually extend several dozen

nucleotide pairs upstream of the start point

• Transcription factors mediate the binding of RNA polymerase and the initiation of

transcription

• The completed assembly of transcription factors and RNA polymerase II bound to a

promoter is called a transcription initiation complex

• A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes

Initiation of Transcription

A eukaryotic promoter1

7/24/2019 Biology I Ch.17 (2)


Transcription initiation

complex forms

3

DNA

PromoterNontemplate strand

5

3

5

3

5

3

Transcription

factors

RNA polymerase II

Transcription factors

5

3

5

3

5

3

RNA transcript

Transcription initiation complex

5

3

TATA box

T

T T T T T

A A A A A

A A

T

Several transcription

factors bind to DNA

2

A eukaryotic promoter1

Start point Template strand

7/24/2019 Biology I Ch.17 (2)


Elongation of the RNA Strand

• As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time

• Transcription progresses at a rate of 40 nucleotides per second in eukaryotes (E.coli DNA

polymerase III incorporates about 1000 nucleotides per second)

• A gene can be transcribed simultaneously by several RNA polymerases

• Nucleotides are added to the 3 end of the growing RNA molecule

7/24/2019 Biology I Ch.17 (2)


Termination of Transcription

• The mechanisms of termination are different in bacteria and eukaryotes

•

In bacteria, the polymerase stops transcription at the end of the terminator and themRNA can be translated without further modification

• In eukaryotes, RNA polymerase II transcribes the polyadenylation signal sequence; the

RNA transcript is released 10 –35 nucleotides past this polyadenylation sequence

• Eukaryotic cells modify RNA after transcription

• Enzymes in the eukaryotic nucleus modify pre-mRNA (RNA processing) before the

genetic messages are dispatched to the cytoplasm• During RNA processing, both ends of the primary transcript are usually altered

• Also, usually some interior parts of the molecule are cut out, and the other parts

spliced together

7/24/2019 Biology I Ch.17 (2)


Post-transcriptional Modification of mRNA

• Each end of a pre-mRNA molecule is modified in a particular way

1. The 5

end receives a modified nucleotide 5 cap

2. The 3 end gets a poly-A tail

• These modifications share several functions

1. They seem to facilitate the export of mRNA

2. They protect mRNA from hydrolytic enzymes

3. They help ribosomes attach to the 5 end

7/24/2019 Biology I Ch.17 (2)


Split Genes and RNA Splicing

• Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides

that lie between coding regions

• These noncoding regions are called intervening sequences, or introns

• The other regions are called exons because they are eventually expressed, usually translated into

amino acid sequences

• RNA splicing removes introns and joins exons, creating an mRNA molecule with a continuous

coding sequence

• In some cases, RNA splicing is carried out by spliceosomes

• Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins(snRNPs) that recognize the splice sites

d l

7/24/2019 Biology I Ch.17 (2)


snRNPs and Spliceosomes

h l d l f

7/24/2019 Biology I Ch.17 (2)


The Functional and Evolutionary Importance of Introns

• Alternative splicing: some genes can encode more than one kind of polypeptide,

depending on which segments are treated as exons during splicing

• Consequently, the number of different proteins an organism can produce is much

greater than its number of genes

• Proteins often have a modular architecture consisting of discrete regions called

domains…..different exons code for the different domains in a protein

M l l C t f T l ti

7/24/2019 Biology I Ch.17 (2)


Molecular Components of Translation

• A cell translates an mRNA message into protein with the help of transfer RNA (tRNA)

• tRNA transfer amino acids to the growing polypeptide in a ribosome

• Translation is a complex process in terms of its biochemistry and mechanics

Th St t d F ti f T f RNA

7/24/2019 Biology I Ch.17 (2)


The Structure and Function of Transfer RNA

• A tRNA molecule consists of a single RNA strand (80 nucleotides); tRNAs are not identical

1. Each carries a specific amino acid on one end

2. Each has an anticodon on the other end; the anticodon base-pairs with a complementary

codon on mRNA

• tRNA twists and folds into a 3-D molecule (due to hydrogen bonds) into “L-shaped ” structure; an

unfolded tRNA molecule looks like a “cloverleaf ”

• Accurate translation requires two steps

1. Correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA

synthetase

2. Correct match between the tRNA anticodon and an mRNA codon

• Flexible pairing at the third base of a codon is called wobble and allows some tRNAs to bind to

more than one codon

7/24/2019 Biology I Ch.17 (2)


Amino acid

attachment

site

3

5

Hydrogen

bonds

Anticodon

(a) Two-dimensional structure (b) Three-dimensional structure

Anticodon Anticodon

3 5

Hydrogen

bonds

Amino acid

attachment

site5

3

A A G

Aminoacyl-tRNA

7/24/2019 Biology I Ch.17 (2)


Aminoacyl-tRNA

synthetase (enzyme)

Amino acid

P P P Adenosine

ATP

P

P

P

PPi

i

i

Adenosine

tRNA

AdenosineP

tRNA

AMP

Computer model

Aminoacid

Aminoacyl-tRNA

synthetase

Aminoacyl tRNA

(“charged tRNA”)

Ribosomes

7/24/2019 Biology I Ch.17 (2)


Ribosomes

• Ribosomes facilitate joining of tRNA anticodons with mRNA codons in protein synthesis

• The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA

(rRNA)

• A ribosome has three binding sites for tRNA

1. The P site holds the tRNA that carries the growing polypeptide chain

2. The A site holds the tRNA that carries the next amino acid to be added to the chain

3. The E site is the exit site, where discharged tRNAs leave the ribosome

tRNA

Growing

polypeptide Exit tunnel

7/24/2019 Biology I Ch.17 (2)


tRNA

molecules

polypeptide

E P

A

Large

subunit

Small

subunit

mRNA5

3

(a) Computer model of functioning ribosome

Exit tunnel Amino end

A site (Aminoacyl-

tRNA binding site)

Small

subunit

Largesubunit

E P A mRNA

E

P site (Peptidyl-tRNA

binding site)

mRNA

binding site

(b) Schematic model showing binding sites

E site

(Exit site)

(c) Schematic model with mRNA and tRNA

5

Codons

3

tRNA

Growing polypeptide

Next amino

acid to be

added to

polypeptide

chain

Ribosome Association and Initiation of Translation

7/24/2019 Biology I Ch.17 (2)


Ribosome Association and Initiation of Translation

The three stages of translation (require proteins that aid in the translation process)

1. Initiation

2. Elongation

3. Termination

Initiation

• The initiation stage of translation brings together mRNA, a tRNA with the first amino

acid, and the two ribosomal subunits• First, a small ribosomal subunit binds with mRNA and a special initiator tRNA

• Then the small subunit moves along the mRNA until it reaches the start codon (AUG)

• Proteins called initiation factors bring in the large subunit that completes the

translation initiation complex

Initiation of Translation

7/24/2019 Biology I Ch.17 (2)


Initiation of Translation

Elongation of the Polypeptide Chain

7/24/2019 Biology I Ch.17 (2)


Elongation of the Polypeptide Chain

• Elongation: amino acids are added to the preceding amino acid at the C-terminus of

the growing chain; translation proceeds along the mRNA in a 5′ to 3′ direction

• Addition of each amino acid involves proteins called elongation factors and occurs in

three steps: codon recognition, peptide bond formation, and translocation

Termination of Translation

7/24/2019 Biology I Ch.17 (2)


Termination of Translation

• Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome

• The A site accepts a protein called a release factor which causes the addition of a water

molecule instead of an amino acid

• This reaction releases the polypeptide, and the translation assembly then comes apart

Polyribosomes

7/24/2019 Biology I Ch.17 (2)


Polyribosomes

Ribosomes can translate a single mRNA simultaneously, forming a polyribosome (or

polysome), which allows a cell to make many copies of a polypeptide very quickly

Targeting Polypeptides to Specific Locations

7/24/2019 Biology I Ch.17 (2)


Targeting Polypeptides to Specific Locations

• Two populations of ribosomes in cells

1. Free ribosomes mostly synthesize proteins that function in the cytosol

2. Bound ribosomes (attached to the ER) make proteins of the endomembrane system andproteins that are secreted from the cell

• Polypeptide synthesis always begins in the cytosol and finishes in the cytosol unless the

polypeptide signals the ribosome to attach to the ER

• Polypeptides destined for the ER or for secretion are marked by a signal peptide

• A signal-recognition particle (SRP) binds to the signal peptide and brings the signal peptide and its

ribosome to the ER

DNA Mutations

7/24/2019 Biology I Ch.17 (2)


• Mutations (changes in the genetic material) of one or a few nucleotides can affect protein

structure and function

• Point mutations are chemical changes in just one base pair of a gene; the change of a singlenucleotide in a DNA template strand can lead to the production of an abnormal protein; two types

of point mutations within a gene

1. Nucleotide-pair substitutions

2. One or more nucleotide-pair insertions or deletions

DNA Mutations

Nucleotide Substitutions

7/24/2019 Biology I Ch.17 (2)


Nucleotide Substitutions

Nucleotide-pair substitution: replace one nucleotide pair with another pair of nucleotides

1. Silent mutations have no effect on the amino acid produced by a codon because of

redundancy in the genetic code

2. Missense mutations still code for an amino acid, but not the correct amino acid

3. Non-sense mutations change an amino acid codon into a stop codon, nearly always

leading to a non-functional protein

Wild type

DNA template strand 5

T T T T TAAAACCA GC C3

7/24/2019 Biology I Ch.17 (2)


te p ate st a d

mRNA5

5

3

Protein

Amino end

A instead of G

(a) Nucleotide-pair substitution

3

3

Met Lys Phe Gly Stop

Carboxyl end

TTTTTA A A A A

C

C

A A A A A

G G G G

G GGU U U U UG

(b) Nucleotide-pair insertion or deletion

Extra A

3

5

5

3

Extra U

5 3

T T T T

T T T T

A

A A A

A

AT G G G G

GAAA

AC

CCCC A

T 3 5

5 3

5

T T T T TAAAACCA A C C

TTTTTA A A A AT G G G G

U instead of C

Stop

UA A A A AG GGU U U U UG

MetLys Phe Gly

Silent (no effect on amino acid sequence)

T instead of C

T T T T TAAAACCA GT C

T A T T TAAAACCA GC C

A instead of G

C A A A A AG A GU U U U UG U A A A AG GGU U U G AC

A A U U A AU UGU G G C UA

G A U A U AA UGU G U U CG

Met Lys Phe Ser

Stop

Stop Met Lys

missing

missing

Frameshift causing immediate nonsense

(1 nucleotide-pair insertion)

Frameshift causing extensive missense

(1 nucleotide-pair deletion)

missing

T T T T TTCAACCA AC G

AGTTTA A A A ATG G G C

Leu Ala

Missense

A instead of T

TTTTTA A A A ACG G A G

A

C A U A A AG GGU U U U UG

TTTTTA T A A ACG G G G

Met

Nonsense

Stop

U instead of A

3

5

3 5

5

3

3

5

5

3

3

5 3

Met Phe Gly

No frameshift, but one amino acid missing

(3 nucleotide-pair deletion)

missing

3

5

5

3

5 3

U

T CA AA CA TTAC GTA G T T T G G A ATC

T T C

A A G

Met

3

T

A

Stop

3

5

5

3

5

3

Insertions and Deletions

7/24/2019 Biology I Ch.17 (2)


Insertions and Deletions

• Insertions (additions) and deletions (losses) of nucleotide pairs in a gene have a

disastrous effect on the resulting protein more often than substitutions do

• Insertion or deletion of nucleotides may alter the reading frame, producing a

frameshift mutation

Wild type

7/24/2019 Biology I Ch.17 (2)


yp

DNA template strand

mRNA

5

Protein

Amino end

Stop

Carboxyl end

3

3

3

5

Met Lys Phe Gly

A

A

A A

A A A A

A AT

T T T T T

T T TT

C C C C

C

C

G G G G

G

G

A

A A A AG GGU U U U U

(b) Nucleotide-pair insertion or deletion: frameshift causing immediate nonsense

Extra A

Extra U

5

3

5

3

3

5

Met

1 nucleotide-pair insertion

Stop

A C A A GT T A TC T A C G

T A T AT G T CT GG A T GA

A G U A U AU GAU G U U C

A T

A

AG

5

Wild type

7/24/2019 Biology I Ch.17 (2)


DNA template strand

mRNA

5

Protein

Amino end

Stop

Carboxyl end

3

3

3

5

Met Lys Phe Gly

A

A

A A

A A A A

A AT

T T T T T

T T TT

C C C C

C

C

G G G G

G

G

A


(b) Nucleotide-pair insertion or deletion: frameshift causing extensive missense

yp

missing

missing

A

U

A A AT T TC C A T TC C G

A AT T TG GA A ATCG G

A G A A GU U U C A AG G U 3

5

3

3

5

Met Lys Leu Ala

1 nucleotide-pair deletion

5

5

Wild type

7/24/2019 Biology I Ch.17 (2)


DNA template strand

mRNA

5

Protein

Amino end

Stop

Carboxyl end

3

3

3

5

Met Lys Phe Gly

A

A

A A

A A A A

A AT

T T T T T

T T TT

C C C C

C

C

G G G G

G

G

A


(b) Nucleotide-pair insertion or deletion: no frameshift, but one amino acid missing

AT C A A A A T TC C G

T T C missing

missing

Stop

5

3

3

5

3

5

Met Phe Gly

3 nucleotide-pair deletion

A GU C A AG GU U U U

T GA A AT T TT CG G

A A G

5

Universality of the Gene

7/24/2019 Biology I Ch.17 (2)


Gene is Universal

• When comparing gene expression in bacteria, archaea, and eukarya gene expression

differs among the domains of life but the concept of a gene is universal• Archaea are prokaryotes, but share many features of gene expression with eukaryotes

• Bacteria and eukarya differ in their RNA polymerases, termination of transcription, and

ribosomes; archaea tend to resemble eukarya in these respects

Transcription and Translation

• Bacteria can simultaneously transcribe and translate the same gene

• In eukarya, transcription and translation are separated by the nuclear envelope

• In archaea, transcription and translation are likely coupled

y

Coupled Transcription and Translation

7/24/2019 Biology I Ch.17 (2)


p p

7/24/2019 Biology I Ch.17 (2)


7/24/2019 Biology I Ch.17 (2)


Sample Problems

In-Class Problem #1

7/24/2019 Biology I Ch.17 (2)


CDNA Double Helix

T G A

C A U mRNA Codon

G C A tRNA Anticodon

Tryptophan Amino Acid

In-Class Problem #2

7/24/2019 Biology I Ch.17 (2)


A double-stranded DNA molecule with the sequence shown here produces, in

vivo, a polypeptide that is five amino acids long.

TAC ATG ATC ATT TCA CGG AAT TTC TAG CAT GTA

ATG TAC TAG TAA AGT GCC TTA AAG ATC GTA CAT

a. Which strand of DNA is transcribed and in which direction?

b. Label the 5’ and the 3’ ends of each strand.

Biology I Ch.17 (2)

Documents

Transcript of Biology I Ch.17 (2)