Genome：the Genome is the entirety of an organism's hereditary information

The genome includes both the genes and the non-coding sequences of the DNA/RNA.

Genomics is the study of the genomes of organisms.The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts.

Genome Structure

Genome Structure：The distribution and arrangement of different gene functional region on chromosome

1.DNA function advantage over RNA：

the most immediate being when one strand breaks the entire molecule does not fall apart;if an error is made in one strand on one base the other strand is still there in its original order to help maintain the original sequence on the opposite strand when a correction enzyme comes along to clip out the mismatch

2.DNA denaturation, also called DNA melting, is the process by which double-stranded DNA unwinds and separates into single-stranded strands through the breaking of hydrogen bonding between the bases

3. Renaturation is the reassociation of denatured complementary single strands of a DNA double helix

4.The prokaryotes are a group of organisms that lack a cell nucleus, or any other membrane-bound organelles.

5.The organisms that have a cell nucleus are called Eukaryotes

6.operon is a functioning unit of genomic DNA containing a cluster of genes under the control of a single regulatory signal or promoter

7. Plasmid is a DNA molecule that is separate from, and can replicate independently of , the chromosomal DNA, They are double-stranded and, in many cases, circular

•Plasmid sizes vary from 1 to over 1,000 kilobase pairs (kbp).

•Plasmids are considered “replicons", capable of autonomous replication within a suitable host.

8.Operon is a unit of bacterial gene expression and regulation, including structural genes and control elements in DNA recognized by regulating gene product

9.乳糖操纵子最早在Ecoli中发现，它由三个相邻的结构基因lacZ、lacY和lacA组成。

LacY编码β-半乳糖苷渗透酶(LacY)，一种膜结合运输蛋白泵乳糖进入细胞。

LacZ编码β-半乳糖苷酶(LacZ)，一种细胞内酶，将双糖乳糖分解成葡萄糖和半乳糖。

LacA编码β-半乳糖苷转乙酰酶(LacA)，一种将乙酰基从乙酰辅酶a转移到β-半乳糖苷的酶。

The lac operon consists of three structural genes, and a promoter, a terminator, regulator, and an operator. The three structural genes are: lacZ, lacY, and lacA.

10.A gene cluster is a set of two or more genes that serve to encode for the same or similar products. Gene clusters are created by the process of gene duplication and divergence.基因复制和分化

11.Gene redundancy is the existence of several genes in the genome of an organism that perform the same role to some extent.When an individual gene in such a set is disrupted by mutation or targeted knockout,there can be little effect on phenotype as a result of gene redundancy.

12.Overlapping genes are defined as a pair of adjacent genes whose coding regions are partially overlapping. In other words, a single stretch of DNA codes for portions of two separate proteins

Monocistron(单顺反子)  ：An mRNA encoding a single polypeptide

Gene family : Genes are categorized into families based on shared nucleotide or protein sequences

The total amount of DNA in the haploid genome is a characteristic of each living species known as its C-value.

An intron is a sequence present in the gene but absent from the mRNA (here shown in terms of the cDNA sequence).

Gene family ： a set of several similar genes, formed by duplication of a single original gene,and generally with similar structure and similar biochemical functions

Gene cluster ：a set of two or more genes that serve to encode for the same or similar products

Tandem repeats occur in DNA when a pattern of two or more nucleotides is repeated and the repetitions are directly adjacent to each other

13. Tandem repetitive gene Features：

Sequences of the repeating units are highly consistent

High copy number

Non-transcribed spacer is very short and consistent

Tandem repetitive genes are evolutional conservative

Satellite DNA consists of many tandem repeats (identical or related) of a short basic repeating unit

Centromere: is a region of DNA typically found near the middle of a chromosome where two identical sister chromatids come closest in contact. It is involved in cell division as the point of mitotic spindle attachment.有丝分裂纺锤体附着点

它通常由大量重复的DNA(如卫星DNA)组成，其中单个重复元素的序列相似但不完全相同

Telomere: is a region of repetitive DNA sequences at the end of a chromosome,  which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes不变质或与邻近的染色体融合

DNA Replication

DNA replication is a biological process that occurs in all living organisms and copies their DNA.The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule. Each strand of the original double-stranded DNA molecule serves as template for the production of the complementary strand.

Process of replication

Initiation ：involves recognition of an origin by a complex of proteins

Elongation ：related to the occurrence of a replication fork, series of processes, including parental polynucleotide is replicated

Termination ：DNA replication stops at the termination region, following termination, the duplicate chromosomes must be separated from one another

Topoisomerase helps relax the supercoils by nicking  one or both strands of the DNA

Topoisomerases include type I and type II

复制的起始、终止、方向

A replicon is a DNA molecule or RNA molecule, or a region of DNA or RNA, that replicates from a single origin. For most prokaryotic chromosomes, the replicon is the entire chromosome

Leading strand of DNA is synthesized continuously in the 5’-3’  direction.

Lagging strand of DNA must grow overall in the 3’-5’ direction and is synthesized discontinuously in the form of short fragments (5’-3’) that are later connected covalently

Okazaki fragments are the short fragments of  1000-2000 bases produced during discontinuous replication; they are later joined into a covalently intact strand.

Semi-discontinuous replication is mode in which one new strand is synthesized continuously while the other is synthesized discontinuously

The replication fork is a structure that forms within the nucleus during DNA replication. It is created by helicases, which break the hydrogen bonds holding the two DNA strands together

Primer is a short sequence (often of RNA) that is paired with one strand of DNA (A-T, G-C) and provides a free 3’-OH end at which a DNA polymerase starts synthesis of a DNA chain

A replicon is a replication unit. Each replicon consists of a origin of replication, and a termini

Telomere: a region of repetitive DNA sequences at the end of a chromosome

DNA复制前，GATC位点完全甲基化，复制后，GATC位点变为半甲基化。复制的半甲基化起点是不活跃的，这一机制限制了DNA每细胞周期复制一次

Mutations and DNA Repair

A mutation is a small-scale change in the nucleotide sequence of a DNA molecule

Results of DNA mutations

Point mutation ： 

is a type of mutation that causes the replacement of a single base nucleotide with another nucleotide of the genetic material, DNA or RNA

           transitions: replacement of a purine base (A and G) with another purine or replacement of a pyrimidine (T and C) with another pyrimidine

           transversions: replacement of a purine with a pyrimidine or vice versa.

Deletion:

remove one or more nucleotides from the DNA. These mutations can alter the reading frame of the gene

Insertion: 

Insertions add one or more extra nucleotides into the DNA, insertions in the coding region of a gene may alter splicing of the mRNA(splice site mutation), or cause a shift in the reading frame (frame shift), both of which can significantly alter the gene product

Transposition: 

a mutation in which a chromosomal segment is transferred to a new position on the same or another chromosome

Double-strand break

DNA repairing refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules. It is essential that cells possess efficient repair systems, without these repair systems a genome would not be able to maintain its essential cellular functions for more than a few hours before key genes became inactivated by DNA damage

Genome Expression

Coding strand is the DNA strand which has the same base sequence as the RNA transcript produced (with thymine (T) replaced by uracil (U))

Template strand is complementary to coding strand, is used as a template for RNA synthesis

Messenger RNA (mRNA) : A molecule of RNA that serves as a template for protein synthesis. mRNA is transcribed from a gene and then translated by ribosomes in order to manufacture a protein. The sequence of a strand of mRNA is based on the sequence of a complementary strand of DNA.

Transfer RNA (tRNA): It is an adaptor molecule composed of RNA, typically 73 to 93 nucleotides in length.It is involved in protein synthesis in that it brings the correct amino acid to the ribosomes.

Ribosomal RNA (rRNA): A molecular component of a ribosome, the cell's essential protein factory. rRNA fabricates polypeptides (assemblies of amino acids that make up proteins)