生化总复习版本1[1].2
1. What is life?
A、structures: living organisms are structurally complicated and highly organized. They possess intricate internal structures.
B、energy: living organisms extract, transform and use energy from their environment, usually in the form of either chemical nutrients or the radiant energy of sunlight.
C、bio-information: the most characteristic attribute of living organism is the capacity for precise self-replication and self-assembly, a property that can be regarded as the quintessence of the living state.
2. What is biochemistry?
Biochemistry or biological chemistry is the branch of science dealing with the chemical compounds, reactions, and other processes that occur in living organisms.
3. Macromolecules？
Deoxyribonucleic acids (DNA)；4 Deoxynucleotides；Ribonucleic acids (RNA)；4 Ribonucleotides；Proteins:；20 Amino acids；Polysaccharides；Monosaccharides
Configuration（构型）: The arrangement of the atoms of a molecule in space, without regard to arrangements that differ only as after rotation about one or more single bonds.
Conformation（构象）: The various arrangements of the atoms of a molecule in space, that differ only as after rotation about single bonds. 4对细胞内含物的分离方法？
Organelles Can Be Isolated by Centrifugation
1、Organelles can be isolated by centrifugation. In a typical cellular fraction, cell or tissues are disrupted by gentle homogenization in a medium containing sucrose (about 2.0m).This treatment ruptures the plasma membrane, but leaves most of the organelles intact；
2、Organelles differ in size and specific gravity；
3、Different centrifugation result in a rough fractionation of the cytoplasmic contents which may be further purified by isopycnic centrifugation；
5. Endosymbiosis theory（evolution）
6.
Five general types of chemical Transformations occur in cell.
Oxidation-reduction 氧化还原
Cleavage and formation of carbon-carbon bounds C-C
Internal rearrangements内部重排
Group transfers and Condensation reactions in which monomeric subunits are joined, with the elination of a molecule of water
7. Cells Have a Structural Hierarchy
Cells have four levels :the level 1 is monomeric units,level 2 is macromolecules ,level 3 is supramolecular complexes, the level 4 is the cell and its organelles. For example: the nucleus is an organelle containing several types of supramolecular complexes, including chromosomes. Chromosomes consist of macromolecules of DNA and many different proteins. Each type of macromolecule is made up of simple subunits—DNA of nucleotides (deoxyribonucleotides).
8. Five types of A.A全部记忆的
9. Working with Protein
Column Chromatography:
Ion-exchange chromatography:
exploits differences in the sign and
magnitude of the net electric charges of a
proteins at a given pH. The column matrix a
synthetic polymer containing bound charge
groups are called cation exchanger. The
separation can be optimized by gradually
changing the pH and or salt concentration.
Size-exclusion chromatography:this method separates proteins according to size. The column contain contains a cross-linked polymer with pores of selected size. Larger proteins migrate faster than smaller ones because they are too large to enter the pores in the beads and hence take a more direct route through the column. The smaller proteins enter the pores and are slowed by the more labyrinthian path they take through the column.
Affinity chromatography: separates proteins by their binding specificities. The proteins retained on the column are those that bind specifically to a ligand cross-linked to the beads. After nonspecific proteins are washes through the column, the bound protein of particular interest is eluted by a solution containing free ligand.
10. Electrophoresis
Important technique for the separation of proteins is based on the migration of changed of charged proteins in an electric field a process called electrophoresis.
a.SDS-page: separates proteins almost exclusively on the basis of mass.
b.Isoelectric focusing: when a protein mixture is applied, each protein migrates until it reaches the pH that matched its pI.
c.Two-dimensional electrophoresis: combining isoelectric focusing and SDS electrophoresis sequentially in a process called two
dimensional electrophoresis.
11.Determination of amino acid sequence of peptides and proteins
1.Isolation and purification of peptides
2.Analysis of the peptide mass (mass spectrometry and SDS-PAGE electrophoresis)
3.Breaking Disulfide bonds
4.Purification of the peptides with cleaved disulfide bonds
5.N-terminal amino acid sequence analysis of the peptides
6.Cleaving the peptides
7.Purifying the digests
8.Sequencing of each purified peptide fragments
9.Ordering the peptide fragments
10.Location disulfide bonds
12.Five Themes for Three-Dimensional Structure of Proteins
First, the three-dimensional structure of a protein is determined by its amino acid sequence.
Second, the function of a protein depends upon its three-dimensional structure.
Third, the three-dimensional structure of a protein is unique, or nearly so.
Fourth, the most important forces stabilizing the specific three-dimensional structure maintained by a given protein are noncovalent interactions.
Finally, even though the structure of proteins is complicated, several common patterns can be recognized.
13.α Helix Structure：conformation of a polypeptide chain in which successive turns of the helix are held together by hydrogen bonds between the amid (peptide) links.
Each helical turn includes 3.6 amino acids. The twisting of the helix has a right-handed sense in the most common form of a helix. The a helix is a common protein secondary structure.
The structure is stabilized by the hydrogen bond. At the same time, amino acid sequence affects a helix stability.
14.β-conformation
β-conformation; An extended, zigzag arrangement of a polypeptide chain in which the chain is almost fully extended but slightly puckered. ? sheet; The zigzag peptide chains can be arranged side by side to form a structure resembling a series of plates.
? turns; A type of secondary structure in polypeptides consisting of four amino acid residues arranged in a tight turn (180 o) so that the polypeptide turn back on itself.
Motif
Structrual domains
15.蛋白质变性复性。RNA也有类似的变性复性（作对比）
Denaturation;A loss of three-dimensional structure sufficient to cause loss of function is called protein denaturation (by heat, extremes of pH, organic solvents, urea, guanidine hydrochloride, or detergents).
Certain globular proteins denatured by heat, extremes of pH, or denaturing reagents will regain their native structure and their biological activity, if they are returned to conditions in which the native conformation is stable, this process called renaturation.
16.蛋白质的三四级构造。
Tertiary structure describes all aspects of the three-dimensional folding of a polypeptide. When a protein has two or more polypeptide subunits, their arrangement in space is referred to as quaternary structure.
17. 蛋白质的功能functions of protein？（自己扩充点）
1. Catalysis(酶)
2. Structure（头发）
3. Movement（鞭毛）
4. Defense（IgG）
5. Regulation(酶)
6. Transport(膜蛋白)
7. Storage
8. Stress Response
18. What is enzyme？
The enzymes，the most remarkable and highly specialized proteins. They have a high degree of specificity for their substance they
accelerate chemical reactions tremendously and they function in aqueous, solutions under very mild conditions of temperature and pH. Most enzymes are proteins with the exception of a small group of catalytic RNA molecules. 19. Enzymes Are Classified by the Reactions They Catalyze
1、oxidoreductases(氧化还原酶);
2、Transferases(转运酶)；
3、Hydrolases （水解酶）；
4、Lyases （裂解酶）；
5、Isomerases （异构酶）；
6、Ligases （连接酶）； 20. 酶的高效和专一性（图示）
21. 酶米氏方程相关的名词解释： [s]：concentration of substrate ：底物浓度
[ES]：concentration of enzyme-substrate complex ：酶-底物复合物浓度； K m ：Michaelis constant ：米氏方程常数 [Vo]：initial rate ：初始反应速度
[V max ]：maximum velocity ：最大反应速度 [E]：concentration of enzyme ：酶浓度
22. Feedback Inhibition;
The regulatory enzyme is specificity inhibited by the end product of the pathway whenever the concentration of the end product exceeds the cell’s requirements.
23. Protein kinases
Protein kinases: any of a number of enzymes that phosphorylate one or more hydroxyl or phenolic groups in proteins, ATP being the phosphoryl-group donor. 24.The biological functions of the lipids:
1. Energy storage (fats and oils)
2. Major structural elements of biological membrane (phospholipids and sterols).
3. Others (enzyme cofactors, light-absorbing pigments, hormone, electron carrier) 1. Phosphatidylinositols (Intracellular Signals) 2. Eicosanoids (Messages to nearby Cells) 3. Steroids (Messages between Tissues)
4. Vitamins A and D (Hormone Precursors)
5. Vitamins E and K (Cofactors)
6. Dolichols (Activate Sugar Precursors)
25. Biological membranes
Biological membranes are central to life. They define cellular boundaries, divide cells into discrete compartments, organize complex reaction sequences, and act in signal reception and energy transformations. Membranes are composed of lipids and proteins in varying combinations that are specific to each species, cell type, and organelle. 26.Membranes proteins
Integral proteins are very firmly bound to the membrane, removable only by agents that interfere with hydrophobic interaction such as detergents, organic solvents or denaturants.
peripheral proteins, which are bound more loosely, or reversibly, it can be released from membranes by relatively mild treatments 27.Major Functions of Integral Proteins
1) transporters and ion channels 2) receptors for hormones,
neurotransmitters, and growth factors
3) oxidative phosphorylation and
photosynthesis
4) cell-cell and antigen-cell
recognition in the immune system 5) membrane fusion that
accompanies exocytosis, endocytosis entry of many types of viruses into host cells.
28. Three Major Types of Membrane Transport Proteins
1. Channel Proteins
2. Transporters
3. ATP-powered pumps
29Four General Types of Signal Transducers(如右图) 30. The nucleic acids
d eoxyribo n ucleic a cid (DNA) and r ibo n ucleic a cid (RNA), ar
e the molecular repositories for genetic information. 31. DNA 测序（如下图）
32. 着丝粒和端粒
Centromere : the region of a eukaryotic chromosome that is attached to the spindle during nuclear division
Telomeres : the structure that seals the end of a chromosome that help stabilize the chromosome
33.
Genome and Proteome
Genome ; the whole of the genetic information of an organism. It is contained as DNA
in eukaryoties and prokaryotes, and as either DNA or RNA in viruses. A given organism has only one genome regardless of whether the organism is haploid, diploid, or polyploid.
Proteome; the complete expression profile of the proteins of an organism.
34.Replication Steps
1.Initiation
2.Elongation
3.Termination
35. Four DNA Repair Systems(四点展开)
36. functions of genetic recombination
a. operation of specialized DNA repair systems and specialized activities in DNA replication.
b. regulation of expression of certain genes.
c. facilitation of proper chromosome segregation cell division in eukaryotes.
d. maintenance of genetic diversity.
e. implementation of programmed genetic rearrangements during embryonic development.
37.Functions of Capping
1.Protect mRNAs from degradation
2. Enhance the translatability
3. Enhance the transport of mRNAs from the nucleus into cytoplasm
4. Enhance the efficiency of splicing of mRNAs
38.Three major RNA processing Steps
Three major RNA processing steps
1/capping: the process of forming or playing a cap on a RNA molecule.
2/po lyadenylation: Addition of poly (A) to the 3’end of mRNA
3/splicing: the enzymic process in eukaryotic cells by which introns are excised from heterogeneous nuclear RNA (hnRNA) following its transcription from DNA, and the ends are rejoined to form messenger RNA.
39.开放阅读框架\阅读框架( RF and ORF)。
Reading frame: a group of triplet of nucleotides condons which are successsive and nonoverlapping in DNA or RNA
Open reading frame: in general, a reading frame without a termination codon among 50 or more codons is called an open reading frame. 40Protein targeting and degradation
Targeting: one targeting mechanism involves a peptide signal sequence and the signal recognition particle (SRP).SRP binds the signal sequence as soon as it appears on the ribosome and transfers the entire ribosome and incomplete polypeptide to the endoplasmic reticulum. Then, polypeptide may be modified nf moved to the Grolgi complex, then sorted and sent to lysosomes, the plasma membrane or transport vesicles.
Degradation: proteins are generally degraded by an ATP-dependent proteolytic system. In eukaryotic cells, the proteins are first tagged by linking them to ubiquitin.