MindMap Gallery Structure and function of biological macromolecules
1. Chemical structure and classification of amino acids that make up proteins. 2.Physical and chemical properties of amino acids. 3. Peptide bonds and peptides. 4. Primary structure and higher-order structure of proteins. 5. The relationship between protein structure and function. 6.Physical and chemical properties of protein. 7. General principles and methods for separating and purifying proteins. 8. The composition of nucleic acid molecules, mainly the chemical structures of purine and pyrimidine bases, and nucleotides. 9. Primary structure of nucleic acids. Spatial structure and function of nucleic acids, classification and functions of other non-coding RNAs. 10.Physical and chemical properties and applications of nucleic acids. 11. The basic concepts of enzymes, holoenzymes, cofactors, vitamins involved in composing coenzymes, and active centers of enzymes. 12. The mechanism of action of enzymes, enzyme reaction kinetics, types and characteristics of enzyme inhibition. 13. Regulation of enzymes
Edited at 2024-04-08 14:47:42One Hundred Years of Solitude is the masterpiece of Gabriel Garcia Marquez. Reading this book begins with making sense of the characters' relationships, which are centered on the Buendía family and tells the story of the family's prosperity and decline, internal relationships and political struggles, self-mixing and rebirth over the course of a hundred years.
One Hundred Years of Solitude is the masterpiece of Gabriel Garcia Marquez. Reading this book begins with making sense of the characters' relationships, which are centered on the Buendía family and tells the story of the family's prosperity and decline, internal relationships and political struggles, self-mixing and rebirth over the course of a hundred years.
Project management is the process of applying specialized knowledge, skills, tools, and methods to project activities so that the project can achieve or exceed the set needs and expectations within the constraints of limited resources. This diagram provides a comprehensive overview of the 8 components of the project management process and can be used as a generic template for direct application.
One Hundred Years of Solitude is the masterpiece of Gabriel Garcia Marquez. Reading this book begins with making sense of the characters' relationships, which are centered on the Buendía family and tells the story of the family's prosperity and decline, internal relationships and political struggles, self-mixing and rebirth over the course of a hundred years.
One Hundred Years of Solitude is the masterpiece of Gabriel Garcia Marquez. Reading this book begins with making sense of the characters' relationships, which are centered on the Buendía family and tells the story of the family's prosperity and decline, internal relationships and political struggles, self-mixing and rebirth over the course of a hundred years.
Project management is the process of applying specialized knowledge, skills, tools, and methods to project activities so that the project can achieve or exceed the set needs and expectations within the constraints of limited resources. This diagram provides a comprehensive overview of the 8 components of the project management process and can be used as a generic template for direct application.
Structure and function of biological macromolecules
protein
Classification
naturally occurring
Participate in protein synthesis
20 basic amino acids (With codons, involved in protein synthesis)
Except for glycine, all are L-α-amino acids
Features
nature
non-polar/hydrophobic
Isobrilliant, bright, methyl sulfide, benzene acrylic, sweet, preserved, valerian (one or two fake biscuits for diarrhea)
polarity neutral
Su, silk, glutamine, cysteine, asparagus (Su Shi cried for a long time)
Acidity and alkalinity
Polypeptides and proteins have both amino and carboxyl groups, so they are both amphoteric.
含氨基多→呈碱性 含羧基多→呈酸性
碱性氨基酸带正电:人体ph相对于氨基酸是酸性环境
Acidic
Valley, Tiandong (dog days of summer)
alkaline
Lai, jing, group (pick it up for intensive reading)
group
Aromatic amino acids/conjugated double bonds
The content of aromatic amino acids determines the ability of proteins to absorb ultraviolet light
在280nm波长有特征性吸收峰的氨基酸 色氨酸、酪氨酸
Styrene, color, cheese (original color)
Sulfur-containing amino acids
imino acid
Hydroxy-containing amino acids
Threonine, tyrosine, serine (rob Mr. Su)
branched chain amino acids
Valine, leucine, isoleucine
(Use a stand) to dry your shoes
one carbon unit amino acid
Serine, tryptophan, histidine, glycine (alms bamboo pole)
Glucogenic and ketogenic
Isoleucine, phenylalanine, tyrosine, tryptophan, threonine (an old dormitory book)
ketogenic amino acids
Leucine, lysine (leucine ketone)
essential amino acids
Methionine, histidine, valine, lysine Isoleucine, phenylalanine, leucine, tryptophan, threonine
Group A brought a bright book
modified form before translation
selenocysteine
No codons to form a protein
Constituent of human proteins, but non-protein biosynthetic raw materials, in post-translationally modified form
Cystine, hydroxylysine, hydroxyproline (just grab Laifu)
Not involved in protein synthesis/not present in proteins (no codon)
Ornithine, citrulline, argininosuccinic acid, Homocysteine (not found in natural proteins)
Birds and melons walk together, tigers are stunned
synthetic
Lysine, hydroxyproline
Conformation
The ester bond (phosphodiester bond) is the chemical bond that connects the nucleotide backbone (stabilizes the nucleotide conformation)
Grading
Level 1
definition
Refers to the sequence of amino acids in a protein from N-terminal to C-terminal
structure
Peptide bond (amide group), disulfide bond
Level 2
definition
Refers to the local spatial structure of a certain peptide chain in a protein
structure
hydrogen bond
α-helices, β-sheets, β-turns and Ω-loops
alpha helix
alpha helix ①The spiral direction is clockwise right-hand spiral ②The amino acid side chain extends toward the outside of the helix, with 3.6 amino acid residues rising in one turn (0.15nm), and the helical pitch is 360° ③The N-H of each peptide bond in the α-helix forms a hydrogen bond with the carbonyl oxygen of the fourth peptide bond, and the direction of the hydrogen bond is parallel to the long axis of the helix DNA ①DNA double helix structure has a diameter of 2.37nm and a pitch of 3.54nm. ②The deoxyribose phosphate group is hydrophilic, and the skeleton is located on the outside of the double helix structure, while the base is hydrophobic and located on the inside. ③ Each pair of helices has 10.5 base pairs, the rotation angle of each base pair is 36°, and the vertical distance between the planes of two adjacent base pairs is 0.34nm. ④The stable base stacking force of the double helix structure, hydrogen bonding, is more important.
beta sheet
1. An extended peptide chain structure 2. The peptide bond plane is folded into a zigzag shape and can be formed by two peptide segments arranged in parallel in a forward or reverse direction. 3. When two peptide segments move in opposite directions, the carbonyl oxygen and imino hydrogen of the peptide bond between the peptide chains form hydrogen bonds to stabilize the β-sheet structure
Structural motif (super secondary structure)
structure
Calcium ion binding protein, fibrin receptor binding peptide, zinc finger structure, leucine zipper
Level three
definition
Refers to the relative spatial position of all amino acid residues on the entire peptide chain
structure
Hydrophobic bonds, salt bonds, hydrogen bonds and van der Waals forces
domain
Level 4
definition
Refers to the spatial arrangement of each subunit in a protein molecule with two or more polypeptide chains and the layout and interaction of subunit contact sites
structure
Hydrogen and salt bonds (ionic bonds)
Disease caused
Madman Ahern
Mad cow disease (alpha helix → beta sheet) human striatal myelopathy Alzheimer's disease Huntington's disease
transsexual
definition
Refers to the destruction of its specific spatial conformation under the action of certain physical and chemical factors. Loss of physical and chemical properties and biological activity
Features
Solubility decreases, viscosity increases, crystallization ability disappears, biological activity is lost, and it is easily hydrolyzed by proteases
protein denaturation
空间构象破坏→疏水基团暴露
溶解度降低(易析出)
分子不对称性增加
粘度增加
易被酶破坏
规则析出的能力无→结晶能力消失
Protein detection
biuret
The phenomenon of purple or red reaction between peptide bonds and copper sulfate when heated together
Ninhydrin
The phenomenon that ninhydrin hydrate generates a blue-purple compound when heated with amino acids in a weakly acidic solution
280nm UV absorption method
Nucleic acid 260nm absorption
Detect the maximum absorption value of tyrosine and tryptophan containing conjugated double bonds under 280nm ultraviolet light to indirectly determine the protein content.
nucleic acid
Classification
DNA
composition
primary structure
polynucleotide sequence
ribose base = nucleoside nucleoside phosphate = nucleotide
deoxyribose base phosphate
RNA ribose base phosphate A-U, C-G
A-T, C-G
Chargaff rules: ①The DNA of different biological individuals has different base compositions ②DNA in different organs or tissues of the same individual has the same base composition; ③For the DNA of a specific tissue, its base composition does not change with its age, nutritional status and environment; ④For a specific organism, A=T, C=G, A C=50%
secondary structure
double helix
The stable longitudinal direction of the DNA structure is maintained by the hydrophobic stacking force between the base planes. Horizontally maintained by hydrogen bonds between the bases of the two strands
Double-stranded deoxyribonucleotide chains are antiparallel B-DNA is the most classic right-handed double helix structure of DNA, containing 10.5 base pairs per week A-DNA is a right-handed double helix structure containing 11 base pairs per week The Z-DNA helix is a left-handed helix, and the number of base pairs in each helix is 12.
The connection between bases is hydrogen bonding, two pairs A-T and three pairs C-G The connection between ribose and bases is a glycosidic bond. The connection between nucleoside and phosphate is ester bond (3',5'-phosphodiester bond)
Phosphate, deoxyribose → external base → internal
tertiary structure
Chromatin (basic unit - nucleosome)
core particles
core histones
histone octamer
Two each of H2A, H2B2, H3 and H4
H1
At the entrance and exit of the DNA double strands coiled around core histones, Play a role in stabilizing the nucleosome structure
Core DNA
The DNA double strand, which is approximately 146 bp in length, coils 1.75 times around the core histone protein.
connection area
Connector DNA
A stretch of DNA connecting adjacent nucleosomes, 20-60bp
non-histone binding
other
Chromatin fibers, hollow solenoids, supersolens, chromatids, etc.
effect
Store and transmit genetic information
RNA
coding RNA
messenger RNA,mRNA
structure
5'-cap
Trans-7-methylguanine-nucleoside triphosphate (m7GpppNmpNmp is the most common)
Connected to it is the 5’ untranslated region
open reading frame ORF
From the first start codon from the 5’-end of mature mRNA to The nucleotide sequence between the stop codons, which determines the amino acid sequence of the polypeptide chain
3'-tail
The polytail structure is added after the mRNA transcription is completed
Polyadenylate AAA consisting of 80-250 adenosine linked together
Connected to it is the 3’ untranslated region
Function
Contains genetic code to directly guide the synthesis of polypeptide chains
non-coding RNA
constitutive
transfer RNA, tRNA
structure
secondary structure (Clover structure)
Has four stems and three rings
5'
DHU loop anticodon loop TψC loop
Anticodon determines type
DHU loop: recognizes aminoacyl tRNA TψC loop: recognition of ribosomes
3'
-CCA-OH structure
combined with amino acids
tertiary structure
Inverted L shape
Function
Used to recognize the genetic code (transcribed DNA) and direct protein synthesis
Ribosomal RNA, rRNA
Function
Together with ribosomal proteins, they constitute ribosomes, which provide a place for protein biosynthesis.
Regulatory
Long non-coding RNA (lncRNA)
200~100000 nucleotides
Small non-coding RNA (sncRNA)
mRNA: most types, least quantity, shortest half-life, template tRNA: Rare bases are most transported rRNA: the most abundant location hn: mRNA precursor, heterogeneous, one nucleus sn: small in the nucleus, located in the nucleus, cutting hnRNA sno: small nucleolus, localized in nucleolus, cleaves rRNA si: small interference, cut exogenous RNA sc: signal peptide recognizes cytoplasmic small mi: Inhibits gene expression regulation,,minimum ribozyme: RNA splicing, catalysis
Ribosome (ribosome)
rRNA ribosomal protein
subunit
The original nucleus falls in love with me and wants to stay (23 5 16)
My dad was a bully and slapped me (5.8 28 5 18)
Denaturation and renaturation
transsexual
definition
Secondary structure change→Hydrogen bond cleavage causes double strand to become single strand
Tm value: the temperature at which 50% of the double strands are unraveled
影响因素
氢键越多,即C-G越多,DNA越长,Tm值越高
溶液浓度越高,Tm值越高
Features
The color-enhancing effect of DNA
After denaturation, the absorbance increases (DNA unzipping leads to exposure of conjugated double bonds)
Maximum UV absorption peak
260nm(由共轭双键决定)
280nm is protein
Restoration
DNA denaturation can be restored without changing the primary structure. The protein's primary structure has changed and is irreversible
definition
After the denaturing conditions are slowly removed, the two dissociated DNA complementary strands can re-pair to form a DNA double strand, restoring the original double helix structure.
enzyme
Classification
by structure
monomeric enzyme
enzyme composed of a peptide chain
Oligomerase
An enzyme composed of multiple identical or different peptide chains (subunits) linked by non-covalent bonds
Multi-enzyme complex/multi-enzyme system
In a certain metabolic pathway, several enzymes with different catalytic functions that catalyze a set of consecutive reactions in sequence can aggregate with each other to form a structural and functional whole.
multifunctional enzyme or tandem enzyme
Some enzymes have multiple different catalytic functions on one peptide chain at the same time
According to molecular composition
simple enzyme
Enzymes that only have amino acid components after hydrolysis and no other components
Such as urease, certain proteases, amylase, lipase, nuclease, etc.
conjugation/conjugation enzyme
Enzymes composed of enzyme proteins and cofactors
Enzyme protein and cofactors combined together are called holoenzymes. Neither the enzyme protein nor the cofactor has catalytic activity when present alone, and only the holoenzyme has catalytic activity.
cofactor
辅酶
多通过非共价键与酶蛋白相连,这种结合比较疏松,可以用透析或超滤的方法除去
酶促反应中,辅酶作为底物接受质子或基团后离开酶蛋白,参加另一酶促反应并将所携带的质子或基团转移出去,或者相反(运载体)
辅基
与酶蛋白形成共价键,结合较为紧密,不易通过透析或超滤将其除去
在酶促反应中,辅基不能离开酶蛋白
Enzyme proteins mainly determine the specificity of enzymatic reactions and their catalytic mechanism; Cofactors mainly determine the type of enzymatic reaction
isoenzyme
definition
Refers to catalyzing the same chemical reaction, but the molecular structure and physical and chemical properties of the enzyme protein or even a group of enzymes with different immunological properties
There are differences in the primary structure, but the three-dimensional structure of the active center is the same or similar, so it can catalyze the same chemical reaction.
A group of enzyme polymorphisms encoded by different genes or multiple alleles that catalyze the same reaction but exhibit different functions
Pre-mRNA transcribed from the same gene undergoes different splicing processes to generate a variety of different mRNA translation products
example
lactate dehydrogenase
LDH1 heart LDH2 white blood cells LDH3 spleen LDH4, 5 liver, skeletal muscle
creatine kinase
CK1 brain CK2 myocardium CK3 skeletal muscle
Function (catalysis)
Effective part
Enzyme active center/active site
An enzyme molecule that can specifically bind to a substrate and catalyze the conversion of the substrate into a product A region with a specific three-dimensional structure
Coenzymes and prosthetic groups are often components of enzyme active centers
essential group for enzyme
definition
There are many chemical groups in enzyme molecules, but not all of them are related to enzyme activity. Some of them are closely related to enzyme activity.
Classification
What plays the catalytic role of the enzyme is the binding group and catalytic group inside the active center.
within active center
Can be divided into binding groups and catalytic groups
The function of the former is to recognize and combine substrates and coenzymes to form an enzyme-substrate transition state complex.
The function of the latter is to affect the stability of certain chemical bonds in the substrate, catalyze the chemical reaction of the substrate, and then transform it into a product.
outside active center
Necessary to maintain the spatial conformation of the enzyme active center and/or as a binding site for regulators
mechanism
Reduce the activation energy of the reaction
It refers to the free energy required for 1 mol of a reactant to transform from the ground state to the transition state at a certain temperature, that is, the energy of the transition state intermediate is higher than that of the ground state reactant.
是决定化学反应速率的内因,是化学反应的能障
Combines with substrate to form intermediate
definition
The process of binding an enzyme to a substrate is an energy release reaction, and the released binding energy is the main energy source that reduces the activation energy of the reaction.
Whether the binding group at the active site of the enzyme can effectively bind to the substrate and convert the substrate into a transition state is the key to whether the enzyme can perform its catalytic role.
process
1. Induced fit reaction where enzyme binds to substrate
When the enzyme and the substrate are close to each other, they induce, deform and adapt to each other structurally, and then combine to form an enzyme-substrate complex.
Induced fit allows a relatively specific enzyme to bind to a group of substrate molecules whose structures are not exactly the same. The change in the enzyme conformation is conducive to its binding to the substrate and converts the substrate into an unstable transition state, which is susceptible to Enzyme catalytic attack converts into products
2. Proximity effect and directional sequencing of enzymes and substrates
In a reaction involving more than two substrates, the substrates must collide with each other in the correct direction for the reaction to occur.
During the reaction, the enzyme binds the substrates to the active center of the enzyme, bringing them close to each other and forming a correct orientation relationship that is conducive to the reaction.
3. Surface effect of enzymes
Create a hydrophobic environment that desolvates substrate molecules
It eliminates the interfering attraction and repulsion of a large number of surrounding water molecules to the functional groups in enzymes and substrate molecules, prevents the formation of hydration films, and facilitates close contact and combination of substrates and enzyme molecules.
Polycatalytic
Common acid-base catalytic reactions
Some groups on the active center of the enzyme are proton donors and some are proton acceptors. The transfer of these protons can accelerate the reaction rate.
covalent catalysis
Refers to the catalytic effect of the catalyst and the reactant forming a covalently bonded intermediate, reducing the reaction activation energy, and then transferring the transferred group to another reactant.
The nucleophilic catalytic group on its active center provides a pair of electrons to a partially electropositive atom in the substrate to form a covalent intermediate (nucleophilic catalysis)
Forming a covalent intermediate (electrophilic catalysis) through the electrophilic catalytic group on its enzyme active center and the nucleophilic atom of the substrate molecule
Pass the transferred group on the substrate to its coenzyme or another substrate
Features
High catalytic efficiency
specificity
absolute specificity
Some enzymes only act on substrate molecules of a specific structure, perform specific reactions, and generate products of a specific structure.
relative specificity
The specificity of some enzymes for substrates is not based on the entire substrate molecular structure, but on specific chemical bonds or specific groups in the substrate molecules, so they can act on a class of compounds containing the same chemical bonds or chemical groups.
Adjustability (difference from inorganic enzymes)
instability
rate
formula
Km is Michaelis constant, Vmax is the maximum reaction rate [S] is substrate concentration
When [S] is small (<<Km), ignore [S], V=(Vmax/Km)×[S], that is, a proportional relationship
When [S] is large (>>Km), ignore Km, V=Vmax, showing a quantitative relationship
Features
Km is equivalent to the substrate concentration at half Vmax
Km=[S] can be obtained
Km has nothing to do with enzyme concentration, but is related to enzyme structure, substrate structure and environment.
Km can be expressed as the affinity of the enzyme for the substrate. The greater the Km, the lower the affinity.
Influencing factors
Substrate concentration, temperature, pH
inhibitor
irreversible inhibitor
example
Organophosphorus pesticides (trichlorfon, dichlorvos, dimethoate, malathion, etc.) specifically bind to the hydroxyl group of the serine residue in the active center of cholinesterase, thereby inactivating cholinesterase
Heavy metal ions combine with the sulfhydryl groups in the sulfhydryl enzyme molecules to deactivate the enzyme
reversible inhibitor
competitive inhibitor
Features
Competes with the substrate for the receptor (active center substrate binding group)
Km increases without affecting Vmax
example
Malonate and succinate dehydrogenase, compete with succinate Sulfonamides compete with dihydropteroate synthase, which competes with para-aminobenzoic acid
noncompetitive inhibitor
Features
Binds to the enzyme, rendering the substrate-enzyme complex unable to release the substrate
Km remains unchanged, Vmax decreases
example
Leucine and arginase Ouabain and sodium pump Maltose and alpha amylase
anticompetitive inhibitor
Features
Binds to substrate-enzyme complex
Km decreases, Vmax decreases
example
Phenylalanine and placental alkaline phosphatase
activator
Substances that convert enzymes from inactive to active or increase enzyme activity
key enzyme
① Often catalyzes the first step reaction or the reaction at the branch point. It has low activity and determines the speed of the entire reaction. ② Often catalyzes one-way reactions or non-equilibrium reactions, and its activity can determine the direction of the entire metabolic pathway ③In addition to being controlled by substrates, enzyme activity is also regulated by a variety of metabolites or effectors.
regulation of enzymes
Quick adjustment
Configuration is the primary structure, conformation is the spatial structure Allosteric adjustment only changes the conformation but not the configuration zymogen activation changes configuration
Phosphorylation is common in hydroxyl-containing substances, threonine, tyrosine, serine
1. Chemical modification of enzymes: A (methylation), B (acetylation), gland (gland), sulfur (disulfide bond and sulfhydryl interconversion), phosphorus (phosphorylation) 2. Histone chemical modifications: A, B, ubiquitination (ubiquitination), sugar (glycosylation), phosphorus 3. Chemical modification of amino acids: A, B, hydroxyl (hydroxylation), sugar, selenium (selenization, modified before translation), phosphorus, sulfur (disulfide bond) 4. Ubiquitination is involved in the degradation process of eukaryotes
slow speed adjustment
Ubiquitination is a slow regulator
Changes in enzyme content
Induction and repression of enzyme protein synthesis
Enzymatic protein degradation
Classification
oxidoreductases
Lactate dehydrogenase, succinate dehydrogenase, cytochrome oxidase, catalase, peroxidase, etc.
Transferases
Methyltransferase, aminotransferase, acetyltransferase, transsulfurase, kinase and polymerase, etc.
hydrolytic enzymes
According to the substrates they hydrolyze, they can be divided into proteases, nucleases, lipases and ureases According to the action site of protease on the substrate protein, it can be further divided into endopeptidase and exopeptidase. Similarly, nuclease can also be divided into exonuclease and endonuclease.
Lyases
An enzyme that catalyzes a reaction that removes a group from a substrate and forms a double bond, or its reverse reaction
Dehydratase, decarboxylase, aldolase, hydration enzyme, etc.
Ligase
DNA ligase, aminoacyl-tRNA synthetase, glutamine synthetase, etc.