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Molecular Cell Biology Master

Molecular Cell Biology Master

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Molecular Cell Biology Core Concept Master Cheat SheetO1: Introduction Molecular Cell Biology
 
Molecular Biology
is the study of the replication,transcription, & translation of genetic material within a cell.Manipulation of these processes is also known as m
olecularbiology or recombinant DNA techniques.
 
 
Macromolecules-
there are four main classes of macromolecules: lipids, proteins, carbohydrates, and nucleicacids.
 
Deoxyribonucleic acid (DNA)-
double helix chains of paired bases containing thymine, cytosine, guanine, andadenine.
 
Ribonucleic acid (RNA)-
the intermediate between DNAand proteins.Proteins- chains of amino acids coded for bygenes in the DNA.
Transcritpion:
DNA is transcribed into RNA and specialpairing of bases dictates which sequence is made.
02: The Cell
 
Cell:
The smallest unit of an organism that can liveindependently.
 
Cell Theory:
an explanation of the role of cells inrelationship to living things. · Prokaryotic Cell: Thesmallest unit of life for prokaryotic organisms such asbacteria and other microbes.
 
Eukaryotic Cell:
The smallest unit of life for eukaryoticorganisms such as animals.
 
Nucleolus:
a “tiny nucleus” inside the nucleus, whichcontains RNA.
 
Nuclear Envelope:
a protective layer, which surrounds thenucleus.
 
Nuclear Pore:
holes in the nuclear envelope that allow thenucleus to exchange information with the rest of the cell.
 
DNA:
a nucleic acid, an organic macromolecule.
 
RNA:
a nucleic acid, an organic macromolecule.
 
Cytoplasm:
the liquid space inside of a cell.
 
Organelles:
specialized cell structures, which performspecific functions.
 
 
Cell Membrane:
a protective bilayer of lipids, which allowsthe cell to maintain a stable internal environment.
03: Cells: The Chemical Foundations
 
Organic chemicals:
contain covalently bonded carbonbackbones.
 
Isomers:
chemicals with the same molecular formula butdifferent structural formulas.
 
 
Buffers:
solutions, which resist changes in pH upon additionof small amounts of acid or base.
 
 
Electrolytes:
chemicals that release ions into solutions.
 
 
pH:
pH represents the concentration of hydrogen ions [H+]in solution (scale 1-14, pH 7=neutral). pH = -log [H+]
 
 
Acids:
release H+ into solution, pH < 7
 
 
Bases:
release OH- that can combine with H+ to makewater, pH > 7
 
 
Enzymes:
proteins that serve as catalysts for biochemicalreactions.
 
 
Entropy:
a measure of a system's degree of disorder. Itincreases with increasing disorder.
 
 
Laws of thermodynamics: First Law:
The total energy of the universe is always conserved. Energy can neither becreated nor destroyed.
Second Law:
The universe tendstowards maximum disorder; the direction of all spontaneousprocesses serves to increase the entropy of a system plus itssurroundings.
 
04: The Macromolecules
 
Macromolecule:
A molecule having a molecular weight inthe range of a few thousands to many millions.
 
Functional group:
The specific atom or group of atoms thatconfers a particular chemical property on a biomolecule.
 
Organic Compounds:
Molecules containing covalentlybonded carbon backbones are called organic compounds.
 
Monosaccharide:
A carbohydrate consisting of a singlesugar unit.
 
Disaccharide:
A carbohydrate consisiting of two covalently joined monosaccharide units.
 
Polysaccharide:
A linear or branched polymer of monosaccharide units linked by glycosidic bonds.
NucleusMitochondriaGolgi ApparatusRibosomesRoughEndoplasmicReticulumPlasma MembraneLysosomeSmoothEndoplasmicReticulum
 
Energy of activation (E
a
) = the free energy necessary to start a reaction.Enzymes act as catalysts to lower E
a
, but they do not change
Δ
G.
ReactantsProducts
   F  r  e  e  e  n  e  r  g  y
+ EnzymeNo Enzyme
Δ
G
E
a
E
a
 
PotentialMonomersA,B,C,DABCD BACDCABD DABCABDC BADCCADB DACB
 
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05: Protein Structure and Function
 
Antibody
:
 
A specific protein that interacts with a foreignsubstance (antigen) in a specific way.
 
Beta-sheet (ß-sheet):
A sheet like structure formed by theinteraction between two or more extended polypeptidechains.
 
Cytoskeleton:
The filamentous skeleton, formed in theeukaryotic cytoplasm that is largely responsible forcontrolling cell shape.
 
Dalton:
A unit of mass equivalent to the mass of ahydrogen atom (1.66 x 10-24 g)
 
Disulfide Bridge:
A covalent linkage formed between twocysteine-SH groups either in the same polypeptide chain orin different polypeptide chains.
 
Enzyme:
A molecule, most often a protein that contains acatalytic site for a biochemical reaction.
 
Globular protein:
A folded protein that adopts anapproximately globular shape. May also be called solubleproteins.
06: Gene and Chromosomes
 
Karyotype:
A complete set of all metaphase chromosomesin a cell. Species-specific and is used for genetic diagnosis.
 
 
G band and Q band:
Bands shown on chromosomes aftervarious treatments and staining technique. Samechromosome from one specieis always show same bandingpattern.
 
 
FISH:
fluorescence in site hybridization. A fluorescencelabeled DNA fragment (probe) is hybridized to achromosome therefore a gene can be located to achromosome.
 
 
Nucleosome:
A bead-string structure formed by DNA andhistones, the basic DNA structure in a chromatin.
 
 
Chromatin:
The general structure of any chromosome, thebasic units is nucleosomes.
 
 
Chromatid:
One-half of a replicated chromosome.
 
 
Histone:
structure proteins for nucleosome, including H1,H2A, H2B, H3 and H4 types.
 
 
Chromosome:
The unit of inheritance with the basicstructure of arms, a centromere and two telomeres
.
 
Euchromatin:
Chromatin region stained lightly, usually arelightly packed and transcriptionally active.
 
 
Heterochromatin:
Chromatin region stained dark, usuallyare heavily packed and transcriptionally inactive.
 
 
Telomere:
The DNA-protein strucuture at the ends of eachchromosome plays critical role in DNA replication and aging.
07: DNA Structure and Function
 
Nucleoside:
Compounds with a ribose or deoxyribose and abase. Base includes four types G, C, A and T (or U).
 
 
Nucleotide:
Compounds with a ribose or deoxyribose, a baseand a phosphate group, it is the basic building unit for DNA(monomers of DNA).
 
 
Pyrimidines:
A type of base, including both cytosine andthymidine.
 
 
Purines:
A type of base, including both guanine andadenine.
 
 
Tm:
Melting temperature of DNA. DNA is a double helixmolecule, when heated, the two strand separate from eachother (melting) and the absorbance at 260 nm increases.When half of the DNA is in single strand status, thetemperature is called the DNA’s Tm.
 
 
Denature:
The hydrogen bonds break between the twostrands of the DNA molecule, can be caused by heat or pH.
 
 
Renature:
The denatured DNA restore the double helixstructure and re-form hydrogen bonds.
08: Transcription, Translation and TheGenetic Code
 
mRNA:
A messenger between DNA and protein, made fromDNA template (transcription) and then directs the proteinsynthesis.
 
 
tRNA:
Transfer RNA, carry amino acid to protein synthesissite.
 
 
rRNA:
Structure RNA of ribosomes where proteins aresynthesized.
 
 
microRNA:
miRNA, have mismatch to mRNA, but they bindto mRNA, leading to mRNA degredation or block mRNAtranslation.
 
 
Template strand:
The transcribed DNA strand, withsequence complementary to mRNA sequence.
 
 
Non-template strand:
Not transcribed, sequence is identicalto mRNA, also called coding strand.
 
 
Promoter:
A DNA sequence having a regulatory functionover the transcription of an adjacent gene, and to which RNApolymerase binds prior to transcription.
 
R1R2R3
Peptide bond
Residue nResidue n+1
 
DegredationBlock TranslationmiRNADicer
 
DegredationBlock TranslationmiRNADicer
 
 
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09: Control of Gene Expression inProkaryotes
 
Promoter:
A DNA sequence having a regulatory functionover the transcription of an adjacent gene, and to whichRNA polymerase binds prior to transcription.
 
 
Pribnow Box:
A conserved promoter sequence located at-10 position of mRNA, usually is TATAA, also called TATA box,the function is for transcription factor binding.
 
 
Operon:
consist of two or more adjacent coding regionsthat are controlled by the same transcription factors
.
 
Polycistronic:
The structure genes of an operon aretranscribed as a single mRNA molecule containing multiplegenes.
 
 
Structure genes:
The genes in an operon that encodes theenzymes necessary for a metabolic pathway.
 
 
Regulatory genes:
The genes in an operon that playregulatory roles, acting as either repressors or activators.
 
 
Cis-acting element:
DNA sequences in the vicinity of thestructural portion of a gene that are required for geneexpression. Operator sequence and promoter sequence arecis-acting elements
.
 
Trans-acting elements:
Factors that bind to the cis-actingsequences to control gene expression, for example, RNApolymerase, TFs, repressors.
 
10: Regulation of Gene Expression inEukaryotes
 
Promoter:
A DNA sequence having a regulatory functionover the transcription of an adjacent gene, and to whichRNA polymerase binds prior to transcription.
 
Enhancer:
a short region of DNA that can be bound withproteins to promote expression of a distal or proximal gene.
 
TATA Box:
Binds to transcription factor for regulating geneexpression, usually within 30bp of the transcription startsite.
 
Basal Transcription Factor:
Transcription factors that arerequired for all transcriptions, they unwind DNA and assistRNA polymerase to bind to transcription initiation sites.
 
Modulatory Transcription Factor:
Transcription factorsthat regulate time/space expression, may bind to enhancersor to promoter regions to enhance or suppress geneexpression under certain conditions.
 
DNA binding domain:
A domain found in all transcriptionfactors, used to bind DNA, inclding three types: Zinc-finger,HLH and leucine zipper.
 
Zinc-Finger:
A structure found in a number of transcriptionfactors, has repetitive two cystein and two histidine to bind aZn, and form a “finger” structure.
 
Leucine-zipper:
A structure found in a number of transcription factors, characterized by leucine residue atevery other turn of helix, 7 amino acid apart.
11: Recombinant DNA Technology
 
Recombinant DNA:
a DNA molecule that is made from twodifferent sources and often manipulated in a test tube and ahost cell.
 
cDNA:
complementary DNA, the DNA synthesized from amature mRNA template. cDNA is often used to clone genes.
 
Genomic DNA:
DNA isolated from organisms, containing allDNA in the genome of a cell or an organism
.
 
 
PCR:
polymerase chain reaction, a molecular biologytechnique using DNA polymerase, template DNA and primersto synthesize specific DNA fragments.
 
Restriction Endonuclease:
an enzyme that cuts double-stranded DNA within the molecule.
 
DNA vector:
an agent that can carry a DNA fragment into ahost cell and ensure its replication and sometimes,expression.
 
Cloning vector:
A vector that carries DNA into a host cell forreplication.
 
Expression vector:
A vector that carries DNA into a hostcell and express the DNA into its final protein product.
12: Genomics
 
Genomics:
the study of an organism's entire genome,usually starts with whole genome sequencing.
 
BAC:
bacterial artificial chromosomes, which is based on Fplasmid and can tolerate large inserts, widely used ingenomic DNA library construction.
 
BAC library:
large genomic DNA fragments ligated into BACvectors.
 
Shot gun sequencing:
Genomic DNA from a BAC clone isfragmented into smaller size, typically 1kb, and inserted intoa sequencing plasmid. These sequences are then assembledbased on the overlapping fragments.
 
Sequence assembly:
a computer-based approach to puttogether all the genomic DNA sequence together, starting toput together a BAC sequence first.
 
Human Genome Project (HPG):
Divided into two groupsbased on different funding resource: public sector and Celeraprivate sector. The purpose is to obtain all geneticinformation from humans.
 
Functional Genomics:
Use the sequence data to explorehow DNA and proteins work with each other and theenvironment to create complex, dynamic living systems.
 
p
TrpL TrpB TrpATrpC TrpD TrpE TrpR 
p
TrpL TrpB TrpATrpC TrpD TrpE 
p
TrpL TrpB TrpATrpC TrpD TrpE TrpR TrpR 
mRNARepressor RmRNARepressor R
no Trp,no bindmRNATrpsynthesis
 
EnhancerPromoterTATABoxExonIntronTranscription startsEnhancer
 
Digest with same restriction enzyme BamHI
Sticky ends
Annealseal with DNA ligaseRecombinant DNA
 
Procedure Overview
Step 1: BAC libraryconstruction
Step 2: Shot gunsequencing
Step 3: SequenceassemblyBAC libraryChromosomeShot Gun SequencingSequence Assembly
 

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