Chapter 3 - Nucleotides, Nucleic Acids and Genetic Information

Nucleotides

Composed of a nitrogenous base linked to a pentose sugar to which at least one phosphate group

Nucleoside

Composed of a nitrogenous base linked to a sugar without the phosphate group

Purine (NH group)

Adenine and Guanine. Binds to sugar at N9. Two ring structures

Pyrimidine (N group)

Thymine, Cytosine, Uracil. Binds to sugar at N1. One ring structure

Adenine

Guanine

Cytosine

Thymine

Ribose

Pentose sugar with oxygen on the 2 carbon

Deoxyribose

Pentose sugar with no oxygen on the 2 carbon

Phosphate bridges

the 3’ and 5’ positions of neighboring ribose units

phosphodiester bond

the linkage between individual nucleotides

phosphodiester bond formation

condensation reaction catalyzed by DNA

Sequence of nucleotide residues

written from 5’ to 3’ with a free phosphate group at 5’ end

Observations lead to double helix model

(1) Nucleotide bases are mainly present in their keto form

(2) X-ray diffraction photograph of a DNA fiber predicting its a helical molecule

(3) Chargaff’s rule C=G and A=T

Watson and Crick model of DNA

(1) two polynucleotide chains wind around a common axis to form a double helix.

(2) the two strands of DNA are antiparallel and form a right-handed helix.

(3) the bases occupy the core of the helix and sugar-phosphate chains run along the periphery

(4) The suface of the double helix contains two grooves: major and minor

(5) Each base to hydrogen bonded to a base in the opposite strand to form a planar base pair

bases per turn

10.4

Histones

small, positively charged proteins that are crucial for DNA packaging. They bind tightly to the negatively charged DNA, helping condense and organize it within the cell’s nucleus

Nucleosomes

The fundamental unit of chromatin. It consists of a segment of DNA wrapped around a core of eight histone proteins

Chromatin

The complex of DNA and proteins (primarily histones) that makes up chromosomesC

Chromosomes

Highly condensed structures of chromatin

Human DNA

23 pairs of chromosomes (46 total)

5’GAGA3’

3’CTCT5’

RNA

Single-stranded DNA, which usually forms compact structures rather than loose extended chains

When a cell divides

each DNA strand acts as a template to form its complementary strand

Each DNA molecule consists of

one parental strand and one daughter strand

Replication

Daughter strands are synthesized by the stepwise polymerization of nucleotides using parental strand as template

DNA replication catalysis

DNA polymerase

DNA helicase

Catalyzes unwinding of DNA helix

DNA ligase

Seals gaps between fragments

Topoisomerase

Relieves strain ahead of replication, prevents tangling

DNA polymerase

Adds nucleotides dNTPs to growing DNA strand

Polymerase Chain Reaction

An exponential amplification of a piece of DNA without a live cell

the four ingredients of PCR

DNA template, primers, nucleotides, Taq polyermase

Primers

Short stretches of DNA fragments complementary to sequences of flanking the target gene. Primer binds to unwound single stranded DNA template.

Taq polymerase role

incorporates nucleotides and extends the chain

strand separation temp

94 celsius

primer annealing temp

55

primer extension temp

70

after pcr cycles

2ⁿ copies after each cycle

Central dogma of molecular biology

DNA replicates, DNA is transcribed into RNA, RNA is translated into amino acids for protein formation

RNA strands synthesis

From free ribonucleoside triphosphates using DNA strand of a gene as a template

messenger RNA (mRNA)

the RNA corresponding to a protein coding gene

transfer RNA (tRNA)

mRNA is transported to ribosomes, where each set of three nucleotides in the mRNA pairs (codon) with three complementary nucleotides

Mutations

Alterations to the genetic material of an organism may result in proteins with altered structures and functions

single-nucleotide polymorphisms (SNPs)

DNA sequence differs among individuals at one nucleotide

Genome

Genetic material of an organism

Genomics

The study of the genome’s side, organization, and gene content

Transcriptomics

the study of gene expression

Proteomics

The study of the proteins (proteome)

Although an organism’s genome remains unchanged through its lifetime,

, it’s transcriptome and proteome vary significantly among different types of tissues, developmental stages, and environmental conditions