dna structure and function chapter 10. dna structure

DNA STRUCTURE AND FUNCTION

CHAPTER 10

1. DNA: a. Nucleic acid which is a polymer of monomers

called nucleotides. b. Nucleotide made of: Phosphate group,

sugar (deoxyribose: 5 carbon atom molecule) and nitrogenous base.

DNA STRUCTURE

c. Nitrogenous bases: A (Adenine), T(thymine), G (Guanine), and C(cytosine). Specific DNA information is stored according to the nitrogenous bases arrangement.

1. Cont. DNA:

i. Cont. Nitrogenous bases: ii. Two kinds :

1. Pyrimidines: C and T 2. Purines: A and G 3. In a DNA molecule, a pyrimidine binds by

hydrogen bond to a purine.

1. Cont. DNA:

d. DNA is a double stranded helix, and has a backbone of sugar-phosphate and the N bases are arranged as appendages along this back bone.

e. The two DNA strands are antiparallel to each other (oriented in opposite directions).

1. Cont. DNA:

2. RNA a. Nucleic acid which is a polymer of monomers

called nucleotides. b. Nitrogenous bases: Same as DNA except

T(Thymine) is changed for Uracyl (U) c. Sugar: Ribose instead of deoxyribose d. One strand.

3. DNA replication: a. Starts at “origin of replication”, where DNA is

uncoiled by a gyrase.

DNA FUNCTION

3. DNA replication: a. Initiation proteins bind to origin and both DNA strands

open like a zipper, and two new daughter strands are synthesized by the enzyme DNA polymerase.

b. Both parental strands are used as templates (leading and lagging strands).

e. Replication is bidirectional, and two replication forks are formed moving in different directions.

3. Cont. DNA replication:

f. DNA polymerases catalyze the insertion of free nucleotides complementary to the parental DNA strand: semiconservative replication.

g. Lagging strand: Okazaki fragments. h. ATTAGGACCATTAGGACC Parental strand

TAATCCTGGTAATCCTGG Daughter strand

3. Cont. DNA replication:

DNA REPLICATION

THE SEQUENCE

DNA POLYMERASE

4. Transcription: DNA → RNA

4. Transcription: DNA > RNA a. Types of RNA:

i. mRNA( Messenger RNA):Carries the message of DNA (has the message for a specific protein)

ii. r RNA (Ribosomal RNA): Form part of ribosomes.

iii. tRNA: (Transfer RNA):Amino acid carrier

b. Process of transcription: i. DNA serves as template for RNA

synthesis. ii. Unzipping of DNA; RNA polymerase

recognizes promoter, binds to it and bring new nucleotides for new RNA strand complementary to the parental DNA template.

ATTAGGACCATT Parental DNA strand UAAUCCUGGUAA Daughter RNA strand

U instead of T

b. Process of transcription:

TRANSCRIPTION

THE PROCESS

SENSE STRAND

ANTI-SENSE STRAND

Notes: 1. mRNA: Messenger RNA

a. Carries the message from DNA b. Has CODONS (Triplets of nucleotides)

Ie AUG, AGC, GAA c. Each codon specifies an amino acid

2. tRNA: Transfer RNA a. Clover leaf form b. Carries the anticodon c. On the opposite side, tRNA carries a

Specific aminoacid d. Each Anticodon binds to the codon of

mRNA bringing the corresponding amino acid

e. Redundancy of the genetic code: f. Starting codon: AUG g. Stop codons: UGA, UAG, UAA

Notes: 1. mRNA: Messenger RNA

a. Carries the message from DNA b. Has CODONS (Triplets of nucleotides)

Ie AUG, AGC, GAA c. Each codon specifies an amino acid

2. tRNA: Transfer RNA a. Clover leaf form b. Carries the anticodon c. On the opposite side, tRNA carries a

Specific aminoacid d. Each Anticodon binds to the codon of

mRNA bringing the corresponding amino acid

e. Redundancy of the genetic code: f. Starting codon: AUG g. Stop codons: UGA, UAG, UAA

iii. Eukaryotic RNA is processed before leaving the nucleus. It is cut by some proteins and RNA. Sometimes the RNA transcript itself catalyses the process. It cuts genes that do not encode for proteins (introns).

4. Translation: mRNA → Proteins a. Flow of genetic information: CENTRAL DOGMA

DNA → mRNA → Proteins

REVERSE TRANSCRIPTASE ( HIV)

b. Translation occurs in three stages: i. Chain initiation: Ribosomes recognize

initiation codon: AUG. tRNA with UAC anticodon brings amino acid (Met) and bind.

ii. Chain elongation: Next codon of mRNA is read by ribosome UUA and tRNA brings Leu. Met and Leu are attached by an enzyme, and first tRNA breaks free. Ribosome moves and reads next codon; t RNA brings respective amino acid. This process is repeated, and protein chain grows.

Cont. Translation

iii. Chain termination: Terminator codon is reached. (UGA,UAA,UAG)

TRANSLATION

THE PROCESS

U

Met

A C

U

Met

A C A

Leu

A U

U

A C A

Leu

A U

Met

U

A C A

Leu

A U

Met

GG

U

A

Leu

A UC

Gly

AC

Met

A

A UC

Gly

AC

Leu

Met

AG

A

U C U

Arg

C

AC

Met

Leu

Gly

U C U

Arg

Met

Gly

Leu

5. Mutations: Change in DNA that will imply a change in mRNA and proteins. A change in a nucleotide can mean a big change in a protein molecule that no longer can serve its purpose.

Mutations can be:

i. Spontaneous: Occur naturally, every 106 to 1010 divisions.

ii. Induced: Physical and chemical agents are involved called mutagens.

ii. Cont. Induced mutations:

1. Physical agents that produce mutations: a. Ultraviolet light (UV): Causes thymine

dimmers: ATTCGGG → UAAGCCC (NORMAL)

ATTCGGG → UV light → AT=TCGGG Cannot be rea

ii. Cont. Induced mutations:

1. Physical agents: a. Ultraviolet light (UV): Causes thymine

dimmers: ATTCGGG → UAAGCCC (NORMAL)

ATTCGGG → UV light → AT=TCGGG → Cannot be read

b. X Rays and Gamma rays: Bombard electrons in DNA, causing changes.

1. Cont. Physical agents that produce mutations:

a. Base analogs: Mimic nitrogenous bases, and take their place. DNA malfunctions.

ATTCGGG → Add T* → AT*T* CGGG → can’t

be read

2. Chemical Agents that produce mutations:

Binds GBinds A

AAAGGGCCCTG

T*T*T*CCCGGGAC

GGGGGGCCCTG

c. Kinds of mutations: i. Affect one nitrogenous base in DNA. Can be

substitution, addition, and deletion 1. Base substitution:

TTAACC → substitution by G → TTAGCC

↓ ↓

AAUUGG AAUCGG

↓ ↓ ↓ ↓

Asn Trp Asn Arg

DNA

RNA

PROTEIN

2. Base deletion and addition: Causes frameshift mutations. THE FAT CAT EAT THE RAT

↓ deletion of F

THE ATC ATE ATT HER AT: Frameshift

A piece of chr A broken pi                                         

MUTATIONS MAY INVOLVE LARGER SEGMENTS OF DNA

6. Repair mechanism: To correct mistakes in DNA.

a. Mismatch repair: Proofreading by DNA polymerase. b. Excision repair: Nucleases excise thymine dimmers.

7. Transposable genetic elements: i. Insertion sequences: Carry no genetic

information. Only insert and make copies of them.

ii. Transposons: Jumping genes. Carry R genes.

Insertion sequence

8. Microbial genetics: i. Viruses :

1. Are made of a protein coat and nucleic acid. Either DNA or RNA.

2. Viruses infect animal cells, plant cells and bacteria ( Bacteriophages)

Cell Size and Scale Resource at the University of Utah.

i. Cont.Viruses :

3. When bacteriophages infect a bacterium, they can go two ways:

a. Lytic cycle: Lyses or break the cell by entering and taking up the cell synthetic machinery to reproduce itself.

Cont. Microbial genetics: b. Lysogenic cycle: Instead of lysing the

cell, the DNA of the virus inserts in the cell DNA and can be passed on from parent cells to daughter cells. Sometimes those genes confer toxic genes.

ii. Bacteria and Genetic Engineering What are PLASMIDS?

Extra chromosomal circular pieces of DNA in bacteria that normally carry genes such as:R genes : Resistance to antibiotic genes, TOX genes: Toxic genes (poisons)F Factors : Fertility factors (Sex factors) Plasmids are the vehicles of Genetic Engineering

1. Genetic recombination: Transfer of DNA (plasmid DNA or chromosomal DNA fragments) from donor to recipient cell forming a new combination of genes

a. Forms of genetic recombination: i. Transformation: A metabolic active

bacteria acquires a piece of “naked” DNA (from a dead bacteria) from the environment.

ii. Conjugation: Transfer of DNA form one bacteria (male) to another (female) by means of a sex pilus.

1. Needs cell to cell contact 2. Mediated by plasmids.

iii.Transduction: DNA is transferred from one bacterium to another by means of a virus or bacteriophage.

2. Recombinant DNA technology: a. Techniques to combine genes from

different sources into a single DNA molecule that is used for practical purposes

b. Bacteria are used, especially E. coli.

c. Genetic engineering: 1. The use of microbial DNA to manipulate or control gene expression. 2. Biotechnology: Industrial and commercial applications of genetic engineering

3. Construction of a recombinant DNA molecule: