PHA6112 LEC: Nucleic Acids and the Central Dogma

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181 Terms

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genome

total cellular DNA

molecular file for all the activities of a single organism

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Deoxyribonucleic acid

nucleic acid found inside the nucleus

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Histones

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

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60S + 40S = 80S

eukaryote ribosome svedberg

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A site

holds an aminoacyl tRNA

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3' end of tRNA

attachment point for amino acid residue

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Kozak Sequence

Translation initiating sequence in euKaryotes

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Nucleotides

three subunit: nitrogenous base, sugar, phosphate group

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Nucleoside

two subunit: nitrogenous base, sugar

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Storage and transfer of genetic information from one cell to another

Template for RNA biosynthesis

DNA functions

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Ribonucleic acid

nucleic acid occurring in all parts of the cell

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template for protein biosynthesis

RNA function

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Cytosine

Uracil

Thymine

Pyrimidine bases

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Adenine

Guanine

Purine bases

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B-N-glycosidic linkage

nucleoside linkage

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-osine

Nucleoside formed by purines ends in:

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-idine

Nucleoside formed by pyrimidine ends in:

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Phosphate-ester linkage

Phosphate + sugar linkage type

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nucleoside + 5-monophosphate

nucleotide nomenclature

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3',5'-phosphodiester linkage

DNA/RNA primary structure backbone linkage type

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free phosphate group

5' end has free what

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free hydroxyl group

3' end has free what

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Base sequence

determined by the 1º structure of the nucleic acid

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Primary structure

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

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Secondary structure

interaction of bases through hydrogen bonds

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Secondary strucutre

refers to the 3d conformation of the polynucleotide backbone

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Tertiary structure

involves supercoiling of the DNA strand

common for DNA

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Quaternary structure

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

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DNA double helix

secondary structure

presents the 3D arrangement of nucleic acid strands

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Antiparallel

the strands run on opposite directions

5' to 3' and 3' to 5'

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Antiparallel

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

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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

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Semi-conservative

two strands are always composed of one old and one new

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antiparallel

complementary

semi-conservative

description of DNA helix

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Chargaff's Rule

base pairing should have 1:1 ratio

amount of paired purine and pyrimidine bases should be equal

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Base pair stacking

positions the rings of bases parallel to each other

achieved via LDF

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2 H bonds

# of H bonds between Adenine and Thymine

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3 H bonds

# H bonds between guanidine and cytosine

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B-DNA

physiologic DNA

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

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A-DNA

dehydrated DNA form

11 bases per turn

thicker than B-DNA

bases are not perpendicular to the helix axis

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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

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Major and minor groove

sites at which drug or polypeptides bind to DNA

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DNA supercoiling

tertiary structure of DNA

aids in cellular packing of DNA

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Positive supercoils

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

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Negative supercoils

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

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DNA gyrase

Facilitates supercoiling

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Topoisomerase

facilitates relaxation of supercoiled DNA

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Nucleosomes

DNA bound to histones

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Nucleosome

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

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Chromatin

complex of DNA and protein found in eukaryotic nuclei

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ribose sugar

T is replaced with U and pairs with A

does not follow Chargaff's Rule

smaller than DNA

RNA differences with DNA

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Stem loop (hairpin loop) structures

RNA can form double helix by folding back on itself

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Pseudoknots

2 stem loop intercalated with each other

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Heterogenous nuclear RNA (hnRNA)

RNA directly formed from DNA transcription

precursor of mRNA

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Messenger RNA (mRNA)

RNA that carries the genetic information for protein synthesis

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Small nuclear RNA (snRNA)

facilitates the conversion of hnRNA to mRNA

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Ribosomal RNA (rRNA)

combines with specific proteins to form ribosomes

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Transfer RNA (tRNA)

RNA that delivers amino acid into ribosomes for protein synthesis

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Replication

process of producing new DNA from old DNA

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Transcription

process of producing RNA strands from DNA stand

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Translation

process of producing protein strands from RNA strands

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high fidelity

bidirectional

semi-conservative

Replication features

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Meselson-Stahl Experiment

supported the theory that replication is semi-conservative

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Semi-conservative

one old one new

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Conservative model

both strands are new

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Dispersive model

portions of the parent DNA are found on the daughter strands

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Replication origin

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

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Replication fork

Y-shaped regions of replicating DNA

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unidirectional

replication at replication fork is:

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Replication bubble

unwound regions of DNA open for replication

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bidirectional

replication at replication bubble is:

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Helicase

enzyme responsible for breaking H bonds and unwinding the parent DNA

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DNA topoisomerase/DNA gyrase

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

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Single-strand binding proteins (ssBP)

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

protects the ssDNA from nuclease cleavage

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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

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Primase

enzyme used to synthesize RNA primers

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DNA Polymerase

enzyme responsible for the elongation of the DNA daughter strand

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DNA Pol I and III

has proofreading capacity for mismatch addition in the bases

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DNA Pol I

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

fills the gap with deoxynucleotide triphosphate (dNTP)

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DNA Pol II

repair function

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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

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Leading strand

synthesized continuously in 5' to 3' direction

needs only 1 RNA primer

moves toward the replication fork

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Lagging strand

synthesized discontinuously

uses multiple RNA primers

moves away from replication fork

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Okazaki Fragments

short sequence of DNA fragments on the lagging strand

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DNA ligase

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

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Replication termination

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

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Ter-Tus complex

aids in stopping the DNA helicase activity

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Ter

DNA replication terminus site binding protein

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Tus

termination utilization substance

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lower fidelity than replication

unidirectional (5' to 3')

carried out by RNA polymerase

transcription features

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RNA polymerase

enzyme used to link free ribonucleotides as the template strand grows

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Sigma

removal will signal the start of elongation

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Core

performs the process of elongation

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Omega

associated with stability of RNA polymerase

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Promoter Regions

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

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-35 region

Pribnow-Schaller Box

Promoter regions in prokaryotes

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CAAT box

Goldberg-Hogness (TATA) Box

Promoter regions in eukaryotes

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Transcription factors

RNA Polymerase works with :

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Template/Antisense Strand

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

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Informational/Sense

strand that does not participate in transcription