PHA6112 LEC: Nucleic Acids and the Central Dogma

genome

total cellular DNA

molecular file for all the activities of a single organism

Deoxyribonucleic acid

nucleic acid found inside the nucleus

Histones

highly alkaline protein found in the nucleus which winds DNA into spools

60S + 40S = 80S

eukaryote ribosome svedberg

A site

holds an aminoacyl tRNA

3' end of tRNA

attachment point for amino acid residue

Kozak Sequence

Translation initiating sequence in euKaryotes

Nucleotides

three subunit: nitrogenous base, sugar, phosphate group

Nucleoside

two subunit: nitrogenous base, sugar

Storage and transfer of genetic information from one cell to another

Template for RNA biosynthesis

DNA functions

Ribonucleic acid

nucleic acid occurring in all parts of the cell

template for protein biosynthesis

RNA function

Cytosine

Uracil

Thymine

Pyrimidine bases

Adenine

Guanine

Purine bases

B-N-glycosidic linkage

nucleoside linkage

-osine

Nucleoside formed by purines ends in:

-idine

Nucleoside formed by pyrimidine ends in:

Phosphate-ester linkage

Phosphate + sugar linkage type

nucleoside + 5-monophosphate

nucleotide nomenclature

3',5'-phosphodiester linkage

DNA/RNA primary structure backbone linkage type

free phosphate group

5' end has free what

free hydroxyl group

3' end has free what

Base sequence

determined by the 1º structure of the nucleic acid

Primary structure

refers to the sequence by which the nucleotides are linked together in a nucleic acid

Secondary structure

interaction of bases through hydrogen bonds

Secondary strucutre

refers to the 3d conformation of the polynucleotide backbone

Tertiary structure

involves supercoiling of the DNA strand

common for DNA

Quaternary structure

interaction of nucleic acids with other biomolecules such as proteins specifically histones.

DNA double helix

secondary structure

presents the 3D arrangement of nucleic acid strands

Antiparallel

the strands run on opposite directions

5' to 3' and 3' to 5'

Antiparallel

it is only in this orientation that the H bonding is possible to stabilize the double helix

Complementary

two strand follow base pairing

base on one strand will match the base of the other and will be stabilized by their corresponding H bonds

Semi-conservative

two strands are always composed of one old and one new

antiparallel

complementary

semi-conservative

description of DNA helix

Chargaff's Rule

base pairing should have 1:1 ratio

amount of paired purine and pyrimidine bases should be equal

Base pair stacking

positions the rings of bases parallel to each other

achieved via LDF

2 H bonds

# of H bonds between Adenine and Thymine

3 H bonds

# H bonds between guanidine and cytosine

B-DNA

physiologic DNA

a right-handed helix with an 11Å diameter composed of 10 base pairs per turn

A-DNA

dehydrated DNA form

11 bases per turn

thicker than B-DNA

bases are not perpendicular to the helix axis

Z-DNA

zigzag DNA, derivative of B-DNA

occur naturally in sequences having an alternating purine and pyrimidine bases

highly experimented for its potential role in gene expression

Major and minor groove

sites at which drug or polypeptides bind to DNA

DNA supercoiling

tertiary structure of DNA

aids in cellular packing of DNA

Positive supercoils

circular DNA with more than the normal number of turns of the helix

Negative supercoils

circular DNA with fewer than normal number of turns of the helix

DNA gyrase

Facilitates supercoiling

Topoisomerase

facilitates relaxation of supercoiled DNA

Nucleosomes

DNA bound to histones

Nucleosome

globular structure of chromatin in which DNA is wrapped around an aggregate of histone molecule found in chromatin

Chromatin

complex of DNA and protein found in eukaryotic nuclei

ribose sugar

T is replaced with U and pairs with A

does not follow Chargaff's Rule

smaller than DNA

RNA differences with DNA

Stem loop (hairpin loop) structures

RNA can form double helix by folding back on itself

Pseudoknots

2 stem loop intercalated with each other

Heterogenous nuclear RNA (hnRNA)

RNA directly formed from DNA transcription

precursor of mRNA

Messenger RNA (mRNA)

RNA that carries the genetic information for protein synthesis

Small nuclear RNA (snRNA)

facilitates the conversion of hnRNA to mRNA

Ribosomal RNA (rRNA)

combines with specific proteins to form ribosomes

Transfer RNA (tRNA)

RNA that delivers amino acid into ribosomes for protein synthesis

Replication

process of producing new DNA from old DNA

Transcription

process of producing RNA strands from DNA stand

Translation

process of producing protein strands from RNA strands

high fidelity

bidirectional

semi-conservative

Replication features

Meselson-Stahl Experiment

supported the theory that replication is semi-conservative

Semi-conservative

one old one new

Conservative model

both strands are new

Dispersive model

portions of the parent DNA are found on the daughter strands

Replication origin

where replication is initiated; usually areas with high A-T base pairing

Replication fork

Y-shaped regions of replicating DNA

unidirectional

replication at replication fork is:

Replication bubble

unwound regions of DNA open for replication

bidirectional

replication at replication bubble is:

Helicase

enzyme responsible for breaking H bonds and unwinding the parent DNA

DNA topoisomerase/DNA gyrase

relieves stress ahead of the DNA double helix replication fork by introducing negative supercoils

Single-strand binding proteins (ssBP)

proteins which attaches to the ssDNA and keeps the two strands apart;

protects the ssDNA from nuclease cleavage

RNA primers

short segment RNA required to be present to start the addition of nucleotides by DNA polymerase

found in the lagging strand during the replicaiton stage

Primase

enzyme used to synthesize RNA primers

DNA Polymerase

enzyme responsible for the elongation of the DNA daughter strand

DNA Pol I and III

has proofreading capacity for mismatch addition in the bases

DNA Pol I

removes the RNA primers by exonuclease activity (5' to 3')

fills the gap with deoxynucleotide triphosphate (dNTP)

DNA Pol II

repair function

DNA Pol III

responsible for elongation using a 3'-OH of an RNA primer to add dNTP

uses Mg as cofactor as it helps in binding of 3'-OH

Leading strand

synthesized continuously in 5' to 3' direction

needs only 1 RNA primer

moves toward the replication fork

Lagging strand

synthesized discontinuously

uses multiple RNA primers

moves away from replication fork

Okazaki Fragments

short sequence of DNA fragments on the lagging strand

DNA ligase

enzyme responsible for sealing the nicks or spaces between the fragments on the lagging strand by creating phosphodiester bonds

Replication termination

Brought by the collision of two replication forks resulting in catenation and decatenation of the strands

Ter-Tus complex

aids in stopping the DNA helicase activity

Ter

DNA replication terminus site binding protein

Tus

termination utilization substance

lower fidelity than replication

unidirectional (5' to 3')

carried out by RNA polymerase

transcription features

RNA polymerase

enzyme used to link free ribonucleotides as the template strand grows

Sigma

removal will signal the start of elongation

Core

performs the process of elongation

Omega

associated with stability of RNA polymerase

Promoter Regions

regions which signal the RNA polymerase where the direction of movement and unwinding of DNA strand

-35 region

Pribnow-Schaller Box

Promoter regions in prokaryotes

CAAT box

Goldberg-Hogness (TATA) Box

Promoter regions in eukaryotes

Transcription factors

RNA Polymerase works with :

Template/Antisense Strand

strand is the one used and where the copy is made to get hnRNA

Informational/Sense

strand that does not participate in transcription