MOLBIO LEC 3: NUCLEIC ACIDS AND PROTEIN

DNA Replication Phase of Cell Cycle

S phase

Interphase DNA Error-Checking Phase

G2 phase

Cell Growth Phase Before DNA Synthesis

G1 phase

Cell Cycle Phase Targeted by Methotrexate and Hydroxyurea

S phase

Phase Arrested by Vincristine and Vinblastine

M phase (mitosis)

Nucleoside Components

Nitrogenous base and pentose sugar

Nucleotide vs Nucleoside Difference

Presence of a phosphate group

Purine Bases

Adenine and Guanine

Number of Rings in Pyrimidines

One ring

Pyrimidine Found in Both DNA and RNA

Cytosine

RNA Base Replacing Thymine

Uracil

Bond Linking Nucleotides

Phosphodiester bond

Direction of Nucleic Acid Sequence Writing

5′ → 3′

Right-Handed DNA Helix Name

B-DNA (Watson-Crick DNA)

Base Pairs per DNA Helix Turn

Approximately 10 base pairs

Opposite Direction DNA Strands Arrangement

Antiparallel

Chargaff's Rule

Purines equal pyrimidines

Hydrogen Bonds in G-C Pair

Three

Stable pH Range of Double-Stranded DNA

pH 4-9

DNA vs RNA 3D Structure

DNA is uniform double helix; RNA is irregular and folded

Human Homologous Chromosome Pairs

23 pairs

Basic Chromatin Packaging Unit

Nucleosome

Base Pairs in Nucleosome Core

146 base pairs

Histone Octamer Composition

Two each of H2A, H2B, H3, and H4

Histone Associated with Linker DNA

Histone H1

Linker DNA Length

20-80 base pairs

Reason Histones Are Positively Charged

Rich in lysine and arginine residues

Gene-Rich Less Condensed Chromatin

Euchromatin

Chromosome Movement Regions During Division

Centromeres

Telomere Sequence Type

Repetitive nucleotide sequences

Chromatin in Lymphoblast vs Mature Lymphocyte

Lymphoblast chromatin is less condensed

Premalignant vs Normal Chromatin (Pap Smear)

Premalignant cells show fine dispersed chromatin

Unit of DNA Encoding Protein or RNA

Gene

DNA Replication Type

Semi-conservative

Enzyme Relieving DNA Supercoiling

Topoisomerase

Enzyme Unwinding DNA Strands

Helicase

Enzyme Synthesizing DNA 5′→3′

DNA polymerase III

Primer Required for DNA Synthesis

RNA primer

Discontinuous Daughter Strand

Lagging strand

Short DNA Segments on Lagging Strand

Okazaki fragments

Enzyme Replacing RNA Primers with DNA

DNA polymerase I

Enzyme Joining Okazaki Fragments

DNA ligase

Polymerase Error-Correction Feature

Proofreading exonuclease activity

Proteins Preventing DNA Reannealing

Single-strand binding proteins

Transcription Product

mRNA strand

RNA Polymerase Binding Region

Promoter

Site of Translation

Ribosomes

Three-Nucleotide mRNA Unit

Codon

Total Codons and Stop Codons

64 codons; 3 stop codons

Stop Codons

UAA, UAG, UGA

Start Codon Amino Acid

Methionine

tRNA Function in Translation

Delivers amino acids by anticodon-codon pairing

Bond Between Amino Acids

Peptide bond

5′ mRNA Modification

5′ methylated cap

3′ mRNA Modification

Poly(A) tail

Single Base-Pair Replacement Mutation

Point mutation

Amino Acid Substitution in Sickle Cell Disease

Valine replaces glutamic acid

Frameshift Mutation Effect

Alters reading frame and downstream amino acids

Antibiotics Inhibiting DNA Gyrase

Quinolones (fluoroquinolones)

Retroviral DNA-from-RNA Enzyme

Reverse transcriptase

Scientist Who Discovered Nucleic Acids

Johann Friedrich Miescher

Scientists Proving Semi-Conservative Replication

Meselson and Stahl

Developer of First DNA Sequencing

Frederick Sanger

Human Genome Project Completion

Declared complete in 2003; gapless assembly in 2022

Constant Amino Acid Chemical Groups

Amino group and carboxyl group

Variable Amino Acid Group

R group (side chain)

Proteins with Non-Protein Components

Conjugated proteins

Linear Amino Acid Sequence Level

Primary structure

Alpha Helices and Beta Sheets Level

Secondary structure

Single Polypeptide 3D Folding Level

Tertiary structure

Multiple Subunit Protein Level

Quaternary structure

Protein Changes After Translation

Post-translational modifications

Procollagen to Collagen Process

Post-translational modification

Single-Ring Pyrimidines

Cytosine, Thymine, Uracil

Case Study Diagnosis

Sickle cell anemia

Hemoglobin Electrophoresis HbS Result

92% HbS

Common Quinolone Drug Suffix

-floxacin

Purine Metabolites Not in Nucleic Acids

Xanthine, hypoxanthine, uric acid

10-nm Chromatin Fiber Nickname

Beads on a string

Two-Subunit Protein

Dimer

Four-Subunit Protein

Tetramer

Acidic Amino Acids (Negative Charge)

Aspartate and Glutamate

Basic Amino Acids (Positive Charge)

Lysine, Arginine, Histidine

DNA from RNA Synthesis Process

Reverse transcription

DNA Nucleotide Components

Nitrogenous base, five-carbon pentose sugar, phosphate group

Purine Bases

Adenine and Guanine

RNA-Unique Pyrimidine

Uracil

DNA-Only Nitrogenous Base

Thymine

Bond Joining Adjacent Nucleotides

Phosphodiester bond

Direction of Nucleic Acid Sequence

5′ → 3′ direction

DNA vs RNA Sugar

DNA has deoxyribose; RNA has ribose

Native DNA Secondary Structure

Right-handed double helix (B-DNA)

Force Holding DNA Strands Together

Hydrogen bonds between complementary bases

A=T and G=C Rule

Chargaff's rules

Hydrogen Bonds in A-T Pair

Two

Hydrogen Bonds in G-C Pair

Three

Opposite DNA Strand Orientation

Antiparallel

Base Pairs per B-DNA Turn

~10 base pairs

Significance of Base Stacking

Shields H-bonds from water and stabilizes helix

Stable pH Range of dsDNA

pH 4-9