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DNA and Proteins Cheat Sheet by

DNA and Proteins Revision

PROTEIN STRUCTURE AND FUNCTION

The folding of a polype­ptide (PP) to form a protein with a unique 3D shape is determined by its sequence of amino acids (AA).
 
STRUCTURE
Primary Structure: A linear sequence of AA.
Secondary Structure: Hydrogen bonds of the peptide backbone causes the AA to fold into a repeating pattern. Most common type is alpha-­helix and beta-s­heet.
Tertiary Structure: 3D folding pattern of a protein due to chemical intera­ctions and repulsions between AA.
Quaternary Structure: More than one PP chain.
EXAMPLE OF PROTEINS
Enzymes, hormone receptors, some hormone receptors and antibo­dies.
IMPORTANCE OF STRUCTURE
Retains the important genetic inform­ation, base pairings in PP strands can separate for replic­ation and transc­rip­tion.
H bonds between comp. bases ensure DNA molecule does not form an irregular shape that will affect its function in the cell.

ENZY­MES

Enzymes are specific for their substrate and increase rate of reaction by lowering activation energy.
Induce­d-Fit Model: As an enzyme's active site binds with its specific and comple­mentary substrate, their 3D shape changes to allow a perfect comple­mentary fit between the active site and substrate.
FACTORS
Temper­ature
Low:Slow moveme­nt-Less collis­ion­s-D­ecr­eased reaction rate
Optimal: Fast moveme­nt-More collis­ion­s-I­ncr­eased reaction rate/until plateau
High: Decreased reaction rate-T­ertiary structure destab­ili­sed­-De­nat­urated (can be reversed if minimal damage and moved to optimal)
pH
Non-op­timal: Changes charge of AA-Alters shape 3D so cannot bind to comp. substr­ate­-De­creased reaction rate
Optimal: Increased reaction rate
Inhibitors
Non-co­mpe­titive: Attaches to enzyme­-Ch­emi­cally alters enzyme's active site-S­ubs­trate cannot bind
Compet­itive: Competes with substr­ate­-Im­itates 3D shape of substr­ate­-Stops substrate from binding
Co-factors
Required to complete enzyme's active site to help substrate bind.
Concen­tration of enzyme
Increased concen­tra­tio­n-More active sites-More collis­ion­s-I­ncr­eased reaction rate/until plateau
Concen­tration of substrate
Increased concen­tra­tio­n-More collis­ion­s-I­ncr­eased reaction rate/until plateau

DNA STRUCT­URE

Stores and transmits genetic info. and functions the same way in all living organisms.
DNA is a helical double­-st­randed molecule.
Eukaryotes
Prokar­yotes
Bound to histones in linear chromo­somes- Found in nucleus, chloro­plasts and mitoch­ondria.
Unbound, circular, single chromo­some- Found in the nucleoid.
Simple Genome
Complex Genome
1 copy of gene
2 copies of gene
No homologous pairs
Chromo­somes in homologous pairs-­obs­erved as karyotypes
Made of only DNA
Made of chromatin, nucleo­protein
Copies its chromo­somes and divides immedi­ately after
Copies chromo­somes, then cells grow, goes through mitosis, organise chromo­somes into 2 equal groups

ISSUES OF COLLECTING GENETIC INFO.

Discri­min­ation
Insurance companies and employers discri­minate based on genetic health.
Ownership
Genetic info. collected should be legal property of the individual obtained from.
Privac­y/C­onf­ide­nti­ality
Shared with other people without permis­sion.
Emotional Impact
Results can be distre­ssing, leading to counse­lling for incurable genetic illnesses.
Family Members
Could expose infide­lities within the family, causing emotional damage.
Young children
Cannot consent to being tested.
Social Implic­ations
Results can make an individual socially awkward due to stigmas against genetic illnesses.
Reprod­uctive Choices
Genetic illnesses affecting reprod­uctive organs affect people having kids. Influenced by society, culture and religion.
Limita­tions
Does not predict severity of genetic illnesses or age. Enviro­nment affects develo­pment of genetic diseases.
Inaccu­racies
Possib­ility of misint­erp­reted or inaccurate results. False info. about indivi­dual's genetic health.
Reliab­ility
Can be unreliable indicator for genetic diseases, other studies required to assess reliab­ility of genetic testing in the accurate diagnosis of genetic disease.

GENES

A unique sequence of nucleo­tides that code for a functional protein or RNA molecule.
Exons:
Code for protein
Introns:
Do not code for protein
RNA SPLICING
Immature mRNA contains exons and intron­s-I­ntrons are remove­d-Exons spliced togeth­er-­Forms mature MRNA

PROTEIN SYNTHE­SIS

Transc­ription of mRNA-T­ran­slation of mRNA into an AA sequence at ribosomes.
TRANSC­RIPTION (In the Nucleus)
1. RNA unwinds DNA strand­s-T­emplate and Coding strand­-Bases are exposed
2. Free RNA nucleo­tides BP to comp. bases on T strand
3. RNA Polymerase join positioned bases to form mRNA (messenger RNA)
4. mRNA peels away- DNA rewinds
TRANSL­ATION
1. mRNA leaves nucleus via nuclear pores-attaches to ribosome in cytopl­asm-2 codons inside at a time
2. tRNA carries specific AA and anticodon comp. to codon-form H bond between anticodon and codon
3.mRNA moves to next codon-2nd tRNA transfers AA to riboso­me-­peptide bonds join AA togeth­er-­forming PP chain
4.tRNA keeps bringing AA to ribosome until STOP codon on mRNA-PP releas­ed-­forms protein
 

DNA REPLIC­ATION

Allows for genetic info. to be inherited.
Base pairings (BPs) and method of DNA replic­ation are universal
Structure: A phosphate group, deoxyr­ibose sugar, nucleotide base (A,T,C,G).
H Bonds: Very weak bond between strands of DNA allow for replic­ation.
Importance of BP:
A only binds to T. C only binds to G. Ensures the genetic info. is completely and correctly transf­erred to next genera­tion.
Semi-c­ons­erv­ative Replic­ation:
1 OG DNA=2 daughter DNA-He­licase separates OG strands to become template for newly synthe­sised strands of DNA-Each daughter molecule has one OG strand.

DNA PROFIL­ING

DNA EXTRAC­TIONS FROM TARGET CELL
Cell lysis: Detergents added-­Breaks down cell and nuclear membra­nes­-Re­leases DNA
Protein Removal: Protease and RNAase added-­Removes proteins and RNA-Ce­ntr­ifu­ge-­Forms a pellet of cell debris
DNA Precip­itation: Add ice-cold ethano­l-DNA precip­itates from solution
DNA Purifi­cation: DNA is washed­-Re­moves impurities
POLYMER CHAIN REACTION (PCR): Amplifies target gene
Requires: DNA Polyme­rase, Free nucleo­tides, Primers, Target gene
Process
Denatu­ration: Heated-H bonds break-DNA unwind­s-Bases are exposed
Annealing: Cooled­-Pr­imers bind to separated strands of target DNA through H bonds between comp. bases-DNA nucleo­tides bind to exposed bases
Extension: Heated- DNA Polymerase joins nucleo­tides to produce new DNA
Repeated 25-30 times until sufficient amount of DNA fragments
ELECTR­OPH­ORESIS
Used to separate DNA molecu­les­/fr­agments of different sizes.
Process
DNA fragments are negatively charge­d-A­ttr­acted to positi­ve-­Length travelled determines size of fragment- Marker DNA determines (Small­er=­Faster & Larger­=Sl­owe­r)-­Flu­ore­scent dye used for DNA Profile
Is a DNA-based pattern composed of a series of bands correspond to DNA fragments of different sizes.
DNA profile is unique to each indivi­dual. Approx. half from mother and half from father.
Introns contain highly repetitive sequences of bases called Short Tandem Repeats (STRs) .
STRs can determine: number of repeats in each allele at a locus, total length of STR
STRs containing variable numbers of repeating nucleo­tides are called Variable Number Tandem Repeats (VNTRs) (6-100bp).
VNTRs has 2 types: Minisa­tel­lites (10-70 nucleo­tides) and Micros­ate­llites (Less than 10 nucleo­tides))
Single Nucleotide Polymo­rphism (SNPs): Detects types of changes due to mutations from one generation to next.
Found throughout genome­-Looks at allele and determines sequence change between 2 genes.
If less than 1% of population does not carry the same nucleotide at same position in DNA sequen­ce-­Cla­ssified as SNPs.

DNA SEQUEN­CING

Nucleotide base sequence of target DNA molecule can be determ­ined.
Chain termin­ation method
ddNTPs (deoxy­nuc­leo­tides)
Modified DNA nucleo­tide- cannot form sugar phosphate bond with other dNTPs or ddNTP-last nucleotide on fragme­nt-­ter­min­ating the strand
dNTPs
Normal DNA nucleotide
Process
1. 4 test tubes- many copies of target DNA molecule
2. All 4 dNTPs added to each tube in excess
3.Different ddNTP added to each tube
4.Primers & DNA polymerase added
5.Thermo­cycler
6. DNA replic­ation stops when ddNTPs joins to strand­-pr­oduces many incomplete template DNA
7.Contents poured into 4 separate wells in gel-se­parated through electr­oph­ore­sis­-re­lative DNA sequence of target DNA revealed
ELECTR­OPH­EROGRAM
Can determine base sequence of unknown segment of DNA-Ob­serve change in base sequence of different genomes for genetic diseas­es-For forensics, disease detection, paternity
Follows same principle of electr­oph­ore­sis­-gel, DNA fragments etc.
Capillary Tubes inside a DNA sequen­cer­-Di­fferent colour associated with ddNTPs­-Fr­agments pass through light-­ddNTPs absorb light then emits light which enters a detector
Detector graphs light into an electric curren­t-p­rod­ucing Electr­oph­ero­gra­m-h­eight represents amount of light absorbed and emitte­d-r­epr­esents sequence of target DNA molecule

TERMS

Allele
An individual inherits two alleles, one from each parent, for any given genomic location where such variation exists. If the two alleles are the same, the individual is homozygous for that allele. If the alleles are different, the individual is hetero­zygous.
Genome
Entire set of DNA found in a cell.
Locus
Particular position or place where something occurs or is situated.
rRNA
Molecule in ribosome and is exported to the cytoplasm to help translate the inform­ation in mRNA into protein.
Coding vs. Template
Coding strand determines the correct nucleotide sequence of mRNA. Template strand acts as a base for mRNA transc­rip­tion.
DNA vs. RNA Codon
The DNA codons are identical to the RNA codons, except for the one base thymine (T), which replaces uracil (U) in the RNA codons.

EPIG­ENE­TICS

GENE EXPRESSION
Genes are used to direct protein synthesis. Housek­eeping Genes are expressed contin­uously, involved with general cellular mainte­nance and energy provision. Others are switched on or off in certain cells at particular times according to the function of the cell. Others are perman­ently switched off.
CELL DIFFER­ENT­IATION
Results from the regulation of gene expres­sion. All organisms that reproduce sexually start life as a fertilised egg or zygote. As this single cell begins to divide, stem cells differ­entiate into specia­lised cells e.g. nerve cells, epithelial cells, muscle cells, sex cells etc.
DNA METHYL­ATION
A methyl group (CH3) is added to cytosine bases in the DNA strand-switches off a gene by blocking RNA polymerase and preventing transc­ription. Demeth­ylation activates a gene and allows transc­ription to occur.
HISTONE MODIFI­CATION
DNA is packaged with histone proteins to form chromatin. When chromatin is tightly wound and packaged RNA polymerase is unable to bind to DNA and as such, transc­ription cannot occur and the gene is ‘switched off’. When acetyl groups are added to histones, chromatin is unwound so that RNA polymerase can bind, transc­ription can occur and the genes are ‘switched on’. Acetyl groups can be added and removed.
TRANSC­RIPTION FACTORS
Transc­ription factors are proteins that control the rate of transc­rip­tion. These proteins either promote or prevent the binding of RNA polymerase to the gene to be transc­ribed which changes the gene expres­sion. Some transc­ription factors, called activators bind to DNA and activate or increase the rate of transc­rip­tion, whereas others, called repressors bind to DNA and slow or stop transc­rip­tion.
TRANSL­ATION FACTORS
Class of proteins that control the rate of transl­ation through the activation or inhibition of ribosomes. Non-coding RNAs (ncRNA) act on mRNA already transc­ribed and modify or destroy mRNA molecules so that they are not transl­ated. For example: Micro RNAs prevent transl­ation by bonding with comple­mentary bases on target mRNA molecu­les­-Small interf­ering RNA causes mRNA to be degraded after transc­rip­tio­n-Long non-coding RNA regulates the activity of proteins involved in the transc­ription of genes.
PROCESSING IMMATURE MRNA MOLECULES
Regulating the production of RNA molecules with different splicing of RNA sections: Some transc­ripts can underg­o a­lte­rnative splicing, making different mRNAs and proteins from the same RNA transc­ript.
       
 

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  • Published: 20th March, 2023

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