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MindMap Gallery Structure and function of nucleic acids

Structure and function of nucleic acids

Mind map of the structure and function of nucleic acids. The functions of nucleic acids are: (DNA) the main genetic material of biological questions, (RNA) acting as the genetic material of RNA viruses, acting as a biological catalyst (ribozyme), and participating in the biosynthesis of proteins. .

Edited at 2023-10-31 09:39:34

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Structure and function of nucleic acids

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Outline

Structure and function of nucleic acids

Nucleotide

structure

Phosphate group

nucleoside

structure

base

structure

pyrimidine base

purine base

Base properties

conjugated double bond

UV——260nm

Poor water solubility

hydrophobic heterocyclic structure

dissociate

The basis of double helix formation

Contains multiple hydrogen bond donors or acceptors

Make the bases interact with each other

Form specific hydrogen bonds with hydrogen bond acceptors or donors on the side chains of hydrophilic amino acids in proteins

Enable some proteins to recognize and bind to specific base sequences on DNA molecules

tautomerism

Keto-enol

Amino-imino form

common bases

pyrimidine base

Cytosine (C)

Uracil (U)

Thymine (T)

purine base

Adenine (A)

Guanine (G)

modified base

There are hundreds of modified bases in the body

Most are modifications or metabolites of five common bases

Pentose

D-ribose

D-deoxyribose

nature

base

water soluble

Much larger than the free base

Highly hydrophilic nature of ribosyl groups

Alkaline hydrolysis

Stablize

acid hydrolysis

pyrimidine nucleoside

resistance

purine nucleoside

Easy to hydrolyze

nature

base determination

tautomerism

Ribose/deoxyribose decision

Optical activity

Phosphate group and base jointly determine

sexual dissociation

Isoelectric point

Phosphate group Ribose/deoxyribose jointly determine

hydrophilicity

N-glycosidic bond related

Acidic debasing reaction of purine nucleotides

Function

As a precursor for nucleic acid synthesis

Acts as energy currency

Participate in cell signal transduction

As a precursor or coenzyme/prosthetic group component of other substances

Participates in the regulation of metabolism as an allosteric effect of certain enzymes

Regulate gene expression

English abbreviations

r (can be omitted)

NMP

ribonucleoside monophosphate

NDP

ribonucleoside diphosphate

NTP

ribonucleoside triphosphate

d (deoxygenation)

dNMP

deoxyribonucleoside monophosphate

dNDP

deoxyribonucleoside diphosphate

dNTP

deoxyribonucleoside triphosphate

cyclic nucleotides

specific conditions

cyclase

second messenger

structure of nucleic acids

Comparing the structures of RNA and DNA

Four common characteristics

Adjacent nucleotides are linked by 3',5'-phosphodiester bonds

A 3',5'-phosphodiester bond consists of a 3' monoester bond and a 5' monoester bond

Has two asymmetric ends

5' end and 3' end

polarity

Nucleic acid is a polyanion

The nucleotide residues in each chain have a certain order

Three major differences

Pentose

The pentose sugar in RNA molecules is ribose

The pentose sugar in the DNA molecule is deoxyribose

base

The fourth base of RNA is usually U

The fourth base of DNA is T

chain

RNA is usually single-stranded

DNA is usually double-stranded

primary structure of nucleic acids

definition

The sequence of all nucleotides or bases in a polynucleotide chain that makes up a nucleic acid

write

5'-3'

What it means for DNA

The genetic information of organisms is stored in specific sequences encoded by four nucleotides

Has nothing to do with high-level structures

secondary structure of nucleic acids

DNA secondary structure

Type B double helix

Two antiparallel polydeoxynucleotide strands

right hand spiral

The two strands are complementary in base sequence

A-T(2)

C-G(3)

The base pairs are located inside the double helix and perpendicular to the axis of the helix

The base pairs are stacked together through hydrophobic bonds and van der Waals forces.

The surface of the double helix is irregular

Dagou

2.2nm

Xiaogou

1.2nm

Other parameters

The distance between adjacent bases is about 0.33nm

The difference is about 36°

The spiral diameter is about 2nm

The pitch is about 3.32nm

Each complete helix contains 10 base pairs (bp)

However, each turn of the DNA double helix contains 10.4~10.6bp

A-type double helix

Generally related to RNA double helix and DNA-RNA hybrid double helix

Main factors promoting the formation of A-DNA

Relative humidity

Type and concentration of salt

Base composition and sequence

Amount and direction of supercoils

Z-shaped double helix

Structural features

The deoxyribose phosphate backbone on the helix stretches in a zigzag or Z-shape

left-handed spiral

The sugar ring C2' of deoxycytidylic acid is in the internal form and the base is in the trans form, causing the sugar ring to move away from the minor groove.

The parameters of the spiral have changed

Evidence supporting the double helix structure of DNA

X-ray diffraction

Chargaff's Law

Factors that stabilize the double helix structure

hydrogen bond

Inside the spiral

between base pairs

spiral outside

Between the hydrophilic groups on the pentose-phosphate backbone and the water environment

base stacking force

vertically

hydrophobicity

Van der Waals forces

ionic bond

The meaning of DNA double helix

It provides important clues for biologists to reveal the inheritance, replication, repair, diversity of genetic material and the evolution of species.

wider meaning

complementary structure

Nonstandard secondary structure of DNA

bending

When a strand of DNA contains strings of A sequences (4 to 6) in a certain segment and adjacent strings are separated by 10 bases, it is easier to bend.

Sometimes DNA can bend due to the action of certain proteins

DNA bending helps compress larger genomic DNA

cross shape

If some regions within DNA contain inverted repeat sequences, after unzipping, a cross-shaped secondary structure can be formed through complementary base pairing within the chain.

mismatch slipping DNA

DNA containing direct repeats

During dissolution and reassociation, the nucleotide sequence of one repeat unit slips and mismatches with the complementary sequence in another repeat unit.

triple helix

The third strand follows the major groove of the double helix and forms Hoosgteen base pairs with one strand of the double helix, thereby forming a stable triple helix.

H-DNA

base flipping

Sometimes, a base in the DNA double helix moves away from its mate and protrudes outside the double helix.

Four chain structure

RNA secondary structure

Overview

Some secondary structures that single-stranded RNA can form

Simple single chain structure

continuous double helix

single nucleotide bulge

hairpin structure

Most common

Symmetric inner ring

asymmetric inner ring

trinucleotide protuberance

Double stem connection

three-stem connection

four-stem connection

The basic principle

What kind of secondary structure is formed mainly depends on the base composition, that is, its primary structure

As much as possible, the complementary sequences within the chain must be paired to form a local double helix.

Then let the non-complementary sequences escape from the double helix in various forms

GU base pair

Create more opportunities for the intra-chain double helix

Secondary structure of tRNA

73-94 nucleotides

elements

loop

stem

arm

rRNA secondary structure

Ribosomal RNA

It is divided into several types according to its settlement coefficient

Its intra-chain complementary sequence makes it highly folded

secondary structure of mRNA

The secondary structures at both ends have a certain impact on translation

The most common secondary components are stem-loop structures

Tertiary structure of nucleic acids

It is a three-dimensional structure including all atoms formed on the basis of secondary structure.

Tertiary structure of DNA

supercoil

Insufficient winding

Easy to unchain

Conducive to DNA replication, recombination, and transcription

Classification

negative supercoil

positive supercoil

Relaxed

Type B double helix

10bp per circle has the lowest energy

Less or more than 10bp will result in over- or under-winding

form superhelical structure

Tertiary structure of RNA

It is further folded and packaged based on the secondary structure.

RNA chaperone

main structural motif

pseudosection structure

"Kiss" hairpin

Complex formed by nucleic acid and protein

Complex of DNA and protein

eukaryotic nucleosome

primary structural unit of nuclear chromatin

Archaeal nucleosomes

bacterial nucleoid

Mitochondria and chloroplast nucleoids

complex of RNA and protein

Ribosome

Signal Recognition Particle (SRP)

small nuclear RNA protein complex (snRNP)

small nucleolar RNA protein complex (snoRNP)

spliceosome

RNase P

telomerase

RNA virus

Function of nucleic acids

DNA

The main genetic material of biology questions

RNA

Acts as genetic material for RNA viruses

As a biological catalyst (ribozyme)

Participate in protein biosynthesis

As a primer, participates in DNA replication

Participate in post-processing of RNA precursors

Involved in the regulation of gene expression

Involved in protein co-translational orientation and sorting

Involved in the inactivation of the X chromosome

Nucleic acid research methods

Isolation, purification and quantification of nucleic acids

Extraction of nucleic acids

Separation of two nuclear proteins

protein removal

Precipitation of nucleic acids

electrophoresis

centrifuge

Chromatography

Detection and quantification of nucleic acid purity

Determination of primary structure of nucleic acids

Determination of DNA primary structure

Dideoxy method

base-specific chemical cleavage method

G-specific reaction

C specific reaction

Purine base specific reaction

Pyrimidine base specific reaction

Automation of DNA sequence analysis

Sequencing of RNA primary structure

properties of nucleic acids

base

acid-base dissociation

viscosity

precipitation

transsexual

The double helix region unwinds due to the destruction of hydrogen bonds and base stacking forces.

Physical and chemical properties will change

Color enhancement effect

UV absorption increases during deformation

Base leakage

Increase the buoyant density of DNA

Reduce the viscosity of DNA solution

Optical rotation change

conformational changes

Thermal denaturation

The temperature corresponding to when half of the DNA double helix undergoes thermal deformation or when half of the hydrogen bonds are destroyed due to heat

Usually at 82-95℃

Make A260-T drawing

S type

Influencing factors

DNA homogeneity

GC content

ionic strength

length of double helix

Restoration

Influencing factors

temperature

DNA concentration

ionic strength

DNA sequence complexity

hybridization

hydrolysis

acid hydrolysis

Alkaline hydrolysis

enzymatic hydrolysis