nucleic acids

nucleic acids

biomolecules involved in the transfer of genetic information from existing cells to new cells, composed of nucleotides

• polymeric

• chiral

• water soluble due to ribose sugar

2 nucleic acid classifications

1. ribonucleic acid (RNA)

2. deoxyribonucleic acid (DNA)

ribonucleic acid RNA

found mainly in the cytoplasm of cells

• dynamic: roles in translation, transcription, regulation

• single strand

• AGCU

• less stable

deoxyribonucleic acid DNA

found primarily in the nuclei or mitochondrial of cells

• static: long term genetic info storage

• double stranded

• AGCT

• stable

• right handed double helix

DNA discovery

James Watson and Francis Crick based on Rosalind Franklin and Maurice Wilkins

chargaff’s rules

[A]=[T]; [G]=[C]

base pairing

A+G=C+T

base-stacking interactions

bases stack perpendicular to the helix axis, enhanced by hydrophobic shielding

nucleotide

repeating structural unit or monomer of polymeric nucleic acids

• sugar (ribose) + base + phosphate

• formation results in 2 moles H2O liberated

3 nucleotides composition

1. pyrimidines and purines

2. ribose or 2-deoxyribose

3. phosphate

nucleoside

sugar + base

heterocyclic compounds pyrimidine and purine

based found in nucleic acids are derived from…

pyrimidine

single 6-membered ring containing 2 nitrogen atoms

purine

fused ring system containing both a 6-membered ring with 2 nitrogen atoms and a 5-membered ring with 2 nitrogen atoms

3 major bases of pyrimidines

1. uracil (RNA only)

2. thymine (DNA only)

3. cytosine

2 major bases of purines

1. adenine

2. guanine

D-ribose

sugar component of RNA, present hydroxy (-OH) group on 2’ position in the furanose ring

D-deoxyribose

sugar component of DNA, absent hydroxy (-OH) group on 2’ position in the furanose ring

phosphate

derived from phosphoric acid

phosphoric acid

exists in ionic form in cellular pH conditions and has a 2- charge

nucleotide formation

base is always attached to 1’ position of the sugar, and phosphate is located at the 5’ position

DNA structure

nucleotides are joined together in nucleic acids by phosphate groups that connect the 5’ carbon of one nucleotide to the 3’ carbon of the next

linkages

are phosphodiester bonds

nucleic acid backbone

sugar phosphate chain that is common to all nucleic acids

secondary structure of DNA

proposed by watson and crick (1953)

• 2 intertwined polynucleotide chains of the DNA double helix run in opposite directions

• bases point inward

complementary DNA strands

in the double helix are held together by hydrogen bonds

2 complementary base pairs

1. adenine and thymine (2H bonds)

2. guanine and cytosine (3H bonds)

ex. original strand: 5’ CCATTG 3’

complementary strand: 3’ GGTAAC 5’

46 chromosomes

the human cell contains how many chromosomes

23 pairs

the human cell contains how many pairs

chromosome

tightly packed bundle of DNA and protein that is involved in cell division

histones

small basic proteins coiling each DNA molecule in each chromosome tightly

genes

DNA segments which are the fundamental units of heredity

• each gene directs the synthesis of a specific protein

• number of genes in an organism structural unit varies with the type of organism

DNA replication

process by which an exact copy of a DNA molecule is produced

• occurs simultaneously ay many points along the original DNA molecule

2 DNA strands

1. A and T

2. C and G

semiconservative replication

process by which a new DNA molecule that has one strand from the parent and a new complementary strand us produced

DNA replication step 1

unwinding of the double helix

• catalyzed by the enzyme helicasd

• replication forms are exposed

replication fork

point where the double helix unwinds during replication

DNA replication step 2

synthesis of DNA

• daughter strands form as nucleotides are linked together under the influence of DNA polymerase

• the second daughter strand is synthesized as a series of fragments

nicks

gaps between segments in the daughter strand

okazaki fragments

DNA fragments produced during replication as a result of strand growth in a direction away from the replication fork

DNA replication step 3

closing the nicks

• catalyzed by DNA ligase

polymerase chain reaction (PCR)

developed by Kary Mulis in 1983

• mimics the natural process of replication

• small quantity of the target DNA, buffered solution containing DNA polymerase, cofactor MgCl2, 4 nucleotides, 4 building blocks, and primers are added to a test tube

• genetic disease and degradation

PCR 30 3-step replication cycles

for a theoretical amplification factor of 1 billion

1. heat

2. tube is cooled

3. tube is heated

heat (94*C-96*C)

used to unravel DNA to single strands

tube is cooled (50*C-65*C)

to allow primers to hydrogen bond to the separated strands of target DNA

tube is heated (72*C)

for DNA polymerase to synthesize new strands

PCR as a standard research technique:

1. detects all manner of mutations with genetic disease

2. detects the presence of unwanted DNA in case of infection

3. used on degraded DNA samples

4. allows DNA from extinct mammals, mummies, ancient insects trapped in amber to be amplified

ribonucleic acid RNA

long unbranched polymer consisting of nucleotides joined by 3’ to 5’ phosphodiester bonds (A with U, G with C)

• ranges from 73 to many thousands of nucleotides

• found in nucleus, cytoplasm, mitochondria

• base: uracil and thymine

• single stranded (doesn’t have a 1:1 complementary base)

• has regions with double helical structure and loops

3 types of RNA

1. messenger RNA (mRNA)

2. ribosomal RNA (rRNA)

3. transfer RNA (tRNA)

messenger RNA (mRNA)

carries genetic information from the DNA in the cell nucleus to the site of protein synthesis in the cytoplasm

• lifetime is less than an hour

• synthesized as needed and the rapidly degraded to the constituent nucleotides

• carrying or encoding genetic information

• adenosine 5’-triphosphate (ATP)

ribosomal RNA (rRNA)

constitutes 80-86% of the total RNA of the cell

• accounts for about 65% of the material in ribosomes

• UTP, GTP, CTO

ribosomes

site of protein synthesis

transfer RNA (tRNA)

delivers individual amino acids to the site of protein synthesis

• cells contain at least one specific type of tRNA for each of the 20 common amino acids

• smallest of the nucleic acids (73-93 nucleotides per chain)

• translate information (anticodon)

• carrier of chemical energy

2 regions id a tRNA molecule

1. anticodon

2. 3’ end of the molecule

anticodon

enables tRNA to bind to the mRNA during protein synthesis

3’ end of the molecule

binds an amino acid with an ester bond and transports it to the site of protein synthesis

central dogma of molecular biology

well established process by which genetic information stored in DNA molecules is expressed in the structure of synthesizer proteins

• genes directs the synthesis of certain proteins

• each protein corresponds to a DNA gene

2 central dogma steps

1. transcription

2. translation

transcription

transfer of genetic material from a DNA molecule to messenger RNA

transcription in prokaryotic cells

genes exist as a continuous segment of a DNA molecule

• produces mRNA that undergoes translation immediately due to the absence of a nuclear membrane

transcription in eukaryotic cells

segments of DNA are interrupted by introns

introns

do not carry codes for amino acids

exons

carry codes for amino acids

heterogeneous nuclear RNA (hnRNA)

transcription occurs in both introns and exons which leads to the production of…

• undergoes a series of enzyme-catalyzed reactions to produce mRNA

translation

conversion of the code carried by mRNA into an amino acid sequence of a protein

writing RNA sequences

G with C, A with U, T with A

ex. 5’ GCAACTTG 3’

3’ CGUUGAAC 5’

genetic code

translation is called this, mRNA serves as a template in which amino acids ate assembled in the proper sequence to produce the specified protein

• exact word to word translation is made from mRNA to tRNA

codon

sequence of 3 nucleotide bases that represents a code word on mRNA molecules

stop codons

1. UAG

2. UAA

3. UGA

chain termination is coded

methionine AUG

chain initiation is coded

3 stages of protein synthesis

1. chain initiation

2. chain elongation

3. chain termination

N-formylnethionine

initiated the growing polypeptide chain as the N-terminal amino acids ate assembled

• cleaved from the finished protein when protein synthesis is complete

elongation of the chain

incoming tRNA carrying the next amino acid bonds at the A(aminoacyl) site on the mRNA

• after the peptide bond forms, tRNA is empty and the growing peptide chain is attached to the tRNA bound to the A site

• during translocation, the ribosome moves and the empty tRNA is released (A site still available)

• process is repeated until entire polypeptide chain is synthesized

peptidyl transferase

second amino acid is linked to N-formylmethionine by a peptide bond whose formation is catalyzed by

termination factor

a specific protein, binds to the stop codon, catalyzes the hydrolysis of the completed polypeptide chain from the final tRNA

polyribosome or polysome

complex of mRNA and several ribosomes

growing peptide chains

extend from the ribosomes into the cellular cytoplasm and fold to assume 3D secondary and tertiary configurations

mutation

any change resulting in an incorrect base sequence on DNA

• can occur naturally during DNA replication or environmental factors (repeated exposure to ionizing radiations)

• some may be beneficial and some may be lethal or may produce genetic diseases

mutagen

chemical that induces mutations by reacting with DNA

recombinant DNA

DNA of an organism that contains genetic material from another organism

3 enzymes used in genetic engineering

1. restriction enzyme

2. palindrome

3. DNA ligase

restriction enzyme

protective enzyme found in some bacteria that catalyzes the cleaving of all but a few specific types of DNA, acts as palindromes

palindrome

section in which 2 strands have the same sequence but run in opposite directions

DNA ligase

used to connect DNA fragments during replication and to put together pieces of DNA produced by restriction enzymes

6 substances produced by genetic engineering

1. human insulin

2. human growth hormone

3. interferon

4. hepatitis B vaccine

5. malaria vaccine

6. tissue plasminogen activator

human insulin

treatment for diabetes mellitus

human growth hormone

treatment for dwarfism

interferon

fights viral infections

hepatitis B vaccine

protection against hepatitis

malaria vaccine

protection against malaria

tissue plasminogen activator

promotes the dissolving of blood clots

plasmids

circular, double stranded DNA found in cytoplasm of bacterial cells

• used as vectors to insert DNA into new hosts to produce recombinants

vector

carrier of foreign DNA into a new cell, holds the ability to replicate independently of chromosomal DNA

grooves in DNA helix

major and minor grooves, binding sites for replication, transcription and regulation

CoA, NAD+, FAD with adenosine

aids in binding and energy transfer

cAMP (cyclic AMP)

produced from ATO by adenyl cyclase, common second messenger

acetyl CoA

thioester molecule, carbs, lipids, AA metabolism, delivers acetyle group to TCA cycle

5 mutation classifications

1. silent mutation

2. missense mutation

3. nonsense mutation

4. insertion

5. deletion