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Midterm 1 - Flashcards

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Class:BIS 002A - Introduction to Biology
Subject:Biological Sciences
University:University of California - Davis
Term:Winter 2011
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Functions of Proteins enzymes, defensive (antibodies), hormonal/regulatory (insulin), receptors, storage (amino acids), structural (collagen), transport (hemoglobin), genetic regulatory proteins
Proteins polymers made up of different proportions and sequences of 20 amino acids -consist of one or more polypeptide chains: linear polymer of covalently linked amino acids
Amino Acids alpha carbon atom containing an amino group, a carboxylic acid group and a side chain (R group) and H atom -asymmetrical, isomeric: D-amino acids and L-amino acids
Hydrophilic/hydrophobic +attracts water /-fear of water
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Disulfide Bridge help determine how a polypeptide chain folds
Peptide Linkage formed when the carboxyl group of one amino acid reacts with the amino group of another, undergoing a condensation reaction
N terminus/C terminus N: marks beginning of a polypeptide, first amino acid C: period of carboxyl group, last amino acid added
Primary Structure holds together the precise sequence of amino acids in a polypeptide chain -give molecule's final functional shape
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Secondary Structure consists of regular, repeated spatial patterns in different regions of a polypeptide chain- two types determined by hydrogen bonding 1. alpha helix: right-handed coil 2. beta pleated sheet: formed from two or more polypeptide chains that are almost completely extended and aligned
Tertiary Structure the polypeptide chain is bent at specific sites and then folded back and forth -results in a macromolecule's definitive 3D shape
Maintaining Tertiary Structure polypeptide folding: -covalent disulfide bridges -H bonds -hydrophobic side chains -van der Waals forces stabilizes hydrophobic side chains ionic bonds: forms salt bridges between amino acids
lysozyme
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denaturation when a protein is heated slowly, the heat energy will disrupt only the weak interactions causing secondary and tertiary structure to break down *returns to normal tertiary structure when cooled down -can be irreversible when caused to form new structure
Quaternary Structure results from the ways in which subunits bind together and interact ex) hemoglobin: weak nature of four forces (hydrophobic, van der Waal, H bonds and ionic bonds) permits small changes in structure to aid the function
Shape and Surface Chemistry shape and structure of protein allow specific sites on its exposed surface (R groups) to bind noncovalently to another molecule -binding is specific because only certain compatible chemical groups will bind to one another -3 types of interactions: ionic, hydrophobic, and H bonding
Environmental Effects +T : faster molecular movements, can break H bonds *alterations in PH: disrupts pattern of ionic attractions high concentrations of polar substances disrupts protein structure nonpolar substances may disrupt protein structures
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Chaperones special class of proteins in eukaryotic cells that act to counteracts threats to 3D structure
heat shock proteins general class of stress-induced chaperone proteins
nucleic acids polymers specialized for the storage, transmission between generations, and use of genetic information -two types: DNA and RNA
DNA encodes hereditary info and passes it from generation to generation -info flows from DNA to DNA during reproduction -DNA to RNA to proteins in non-reproductive activities
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RNA used as an intermediate, info from DNA is used to specify the amino acid sequences of proteins -lacks single oxygen atom found in DNA
nucleotides composes nucleic acids, consists of a pentose sugar, a phosphate group, and a nitrogen-containing base functions: -ATP, GTP: energy source -cAMP: additional bond between sugar and phosphate group (hormones and nervous system)
pyrimidine six-membered single ring structure: C, T
purine fused double ring structure: A,G
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phosphodiester linkages joins the nucleotides between the sugar of one and phosphate of the next -link carbon 3 to carbon 5 of adjacent sugar
base pairing adenine (A) - thymine (T)/ uracil (U) cytosine (C) - guanine (G)
replication DNA can reproduce itself by polymerization on a template 1) DNA unwound to two template strands, available for new base pairing 2) new nucleotides form complementary base pairs with template DNA, covalently linked together by phosphodiester bonds
transcription transfer of DNA info copied into RNA *Requires: -DNA template for complementary base pairing; 1 of 2 strands -ATP, GPT, CTP, UTP substrates -RNA polymerase enzyme STEPS 1) Initiation 2) Elongation 3) Termination
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translation nucleotide sequence in RNA can specify a sequence of amino acids in a polypeptide
genome complete set of DNA in a living organism -not all of the info in the genome is needed at all times
genes sequences of DNA that encode specific proteins are transcribed into RNA
spontaneous generation organism arose spontaneously from rich chemical envrionment
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transfection genetic transformation of eukaryotic cells by DNA
genetic marker a gene whose presence in the recipient cell confers an observable phenotype
crystals isolated and purified chemical substances
Chargaff's Rule
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Watson and Crick Structure 3D representation of DNA -helical, two polynucleotide chains, antiparallel -nucleotide bases are on the interior of the two strands -sugar phosphate backbone on the outside
5' end free 5' phosphate group (-OPO3-)
3' end free 3' hydroxyl group (-OH)
Double helical structure -genetic material is susceptible to mutations in the info -precisely replicated in the cell division cycle -expressed as the phenotype
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DNA polymerase enzyme catalyzes DNA replication
nucleoside nitrogen base attached to a sugar
semiconservative replication* each parent strand serves as a template for a new strand, and the two new DNA molecules each have one old and one new strand
conservative replication the original double helix serves a s a temple for, but does not contribute to, a new double helix -1st generation would have both high-density and low-density DNA
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dispersive replication fragments of the original DNA molecule serve as templates for assembling two new molecules, each containing old and new parts, perhaps at random -new DNA would have been intermediate
replication complex 1) primase binds to the template strand and synthesizes an RNA primer 2) DNA polymerase binds and synthesizes new DNA
origin of replication one region which the replication complex binds
primer "starter strand" short single strand of RNA and is complementary to the DNA template
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primase RNA primer is synthesized by this enzyme
DNA helicase enzyme that uses energy from ATP to unwind and separate the strands
single-strand binding proteins special proteins bind to the unwound strands to keep them from reassociating into a double helix
replication fork site(s) where DNA unwinds to expose the bases so that they can act as templates
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leading strand newly replicating strand is oriented so that it can grow continuously at its 3' end as the fork opens up
lagging strand new strand oriented so that as the fork opens up, its exposed 3' end gets farther and farther away from the fork
Okazaki fragments short fragment of DNA created on the lagging strand during DNA replication
processive DNA polymerases catalyze many polymerizations each time they bind to a DNA molecule
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sliding DNA clamp protein shaped like a screw cap binds the DNA polymerase, keeping the enzyme and the DNA associated tightly with each other
PCNA keeps DNA polymerase bound to the DNA, helps to orient the polymerase for binding to the substrates
DNA topoisomerase enzyme that separates two interlocking circular DNA molecules
telomeres region of repetitive DNA at the end of a chromosome, which protects the end of the chromosome from deterioration
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telomerase an enzyme that catalyzes the addition of any lost telomeric sequences the cells
mRNA carries a copy of a gene sequence in DAN to the site of protein synthesis at the ribosome
tRNA carries amino acids to the ribosome for assembly into polypeptides -must read mRNA codons correctly -delivers the amino acids that correspond to each mRNA codon -"charged" when carrying particular amino acid -interacts with ribosomes
rRNA catalyzes peptide bond formation and provides a structural framework for the ribosome
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Uracil the fourth base in RNA, similar to thymine but lacks the methyl group (-CH3)
codon consists of 3 consecutive nucleotides (letters) and different codons encode particular amino acids (during transcription)
transcript examining the mRNA copy of the gene
anticodon complements the codon in mRNA
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Messenger Hypothesis Crick and his colleagues proposed that an RNA molecule forms as a complementary copy of one DNA strand in a gene. The mRNA then travels from the nucleus to the cytoplasm where it serves as an informational sequence of codons.
Adapter Hypothesis Crick proposed that there must be an adapter molecule that can both bind a specific amino acid and recognize a specific sequence of nucleotides. Each tRNA recognizes a specific codon in the mRNA and simultaneously carries the amino acid corresponding to that codon.
RNA Virus RNA viruses are exceptions to central dogma, could possibly act as an info carrier and be expressed as a protein ex) HIV relies on host cell's transcription machinery to make more RNA
RNA polymerase from both prokaryotes and eukarytoes catalyze the synthesis of RNA from the DNA template -only one type in bacteria -do not require a primer/ do not have a proofreading function
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reverse transcription synthesis of DNA from RNA -such viruses are called retroviruses
promoter a special sequence of DNA to which the RN polymerase binds very tightly *TELLS RNA POLYMERASE: -where to start transcription -which strand of DNA to transcribe
Transcription Process 1) initiation site- where transcription begins: -5' on the non-template strand / 3' on the template strand 2) elongation- RNA polymerase unwinds the DNA about 10 base pairs at a time and reads the template strand in the 3'-5' direction 3) termination
genetic code relates genetic DNA to mRNA and mRNA to the amino acids that make up proteins
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start codon the initiation signal for translation (AUG)
stop codon termination signals for translation (UAA, UAG, UGA)
redundant code for almost all amino acids, there is more than one codon
ambiguous code a single codon could specify either of two or more different amino acids, and there would be doubt about which amino acid should be incorporated into a growing polypeptide chain
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Universal Genetic Code same genetic code is used by all the species on our planet, thus there must have been a common ancestor -common language for evolution -few exceptions for prokaryotes and eukaryotes
Eukaryotic genes -each gene has its own promoter -does not recognize the promoter sequence by itself, but requires help from other molecules -may contain introns, exons
prokaryotic genes -several adjacent genes sometimes share one promoter -recognizes promoter by itself
introns noncoding base sequences (intervening regions)
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exons one or more introns interspersed with the coding sequences (expressed regions)
pre-mRNA the mRNA that will be translated; cuts introns out of the pre-mRNA and splicing together the remaining exon transcripts -involves both introns and exons
RNA splicing removes the introns and splices the exons together -if not removed, a very different amino acid/nonfunctional protein would result
snRNPs after pre-mRNA is transcribed, snRNPs bind at each end
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consensus sequences short stretches of DNA that appear with little variation in many different genes
spliceosome using ATp, proteins are added to form this large RNA-protein complex; cuts the pre-mRNA, releases the introns and joins the ends of the exons to produce mature mRNA
wobble allows the alanine codons all to be recognized by the same tRNA; does not allow the genetic code to be ambiguous
ribosome molecular workbench where the task of translation is accomplished; structure enables it to hold mRNA and charged tRNs in the right positions -when not active, becomes two separate subunits
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Translation Process 1) initiation complex: consists of a charged tRNA and a small ribosomal subunit, both bound to the mRNA 2) elongation: breaks bond between the tRNA and amino acid; catalyzes the formation of a peptide bond between amino acid and tRNA => peptidyl transferase 3) termination: UAA, UAG, or UGA
proofreading mechanism corrects errors in replication as DNA polymerase makes them -occurs when DNA polymerase introduces a new nucleotide into a growing DNA strand
mismatch repair mechanism scans DNA immediately after it has been replicated and corrects any base-pairing mismatches -DNA strand is chemically modified some time after replication to detect wrong base complements
excision repair mechanism removes abnormal bases that have formed because of chemical damage and replaces them with functional bases -deals with high energy radiation, chemicals from environment, random spontaneous chemical reactions damaged DNA
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mutations inherited changes in genes -changes in the nucleotide sequence of DNA that are passed on from one cell, or organism to another
somatic mutations occur in body cells; passed on to the daughter cells during mitosis and so on but passed on to sexually produced offspring
germ line mutations occur in the cells of the germ line- the specialized cells that give rise to gametes; passes it on to a new organism at fertilization
silent mutations DO NOT affect protein function; in noncoding DNA such as repeat sequences or coding portion of DNA
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loss of function mutations AFFECT protein function; may lead to nonfunctional proteins that no longer work as structural proteins or enzymes and always show recessive inheritance
gain of function mutation leads to a protein with an altered function; shows dominant inheritance ex) cancer cells
conditional mutations cause their phenotypes only under certain restrictive conditions; not detectable under other permissive conditions
point mutation results from the gain, loss, or substitution of a single nucleotide
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chromosomal mutations more extensive than point mutations; may change the position or orientation of a DNA segment without actually removing any genetic info, or they may cause a segment of DNA to be duplicated or irretrievably lost -deletions, duplications, inversions, translocations
mutagen substances that cause mutations such as radiation or certain chemicals -can be natural or artificial
silent mutations have no effect on amino acid sequences; often found in noncoding DNA because of the redundancy of the genetic code
missense mutation base substitutions change the genetic code such that one amino acid substitutes for another in a protein -might reduce the functional efficiency rather than completely inactivating a protein ex) sickle cell disease
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nonsense mutations involves a base substitution that causes a stop codon (for translation) to form somewhere in the mRNA -results in shortened protein, usually not functional
frame-shift mutations single or double bases may be inserted into or deleted from DNA because they interfere with the translation of the genetic message by throwing it out of register
deletions removal of part of the genetic material; can be severe unless they affect noncoding DNA or unnecessary genes
duplications produced at the same time as deletions; arise if homologous chromosomes broke at different positions and then reconnected to the wrong partners
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inversions breaking and rejoining of chromsomes; if break site includes part of a DNA segment the resulting protein will be drastically altered and almost certainly nonfunctional
translocation when segment of a chromosome breaks off and is inserted into a different chromosomes; often lead to duplications and deletions and may result in sterility
spontaneous mutations permanent changes in the genetic material that occur without any outside influence; because cellular processes are imperfect -nucleotide bases of DNA have different structures -bases may change because of chemical reactions -DNA polymerase can make errors in replication -meiosis is not perfect
induced mutations when some agent from outside the cell- a mutagen- causes a permanent change in DNA -some chemicals can alter the nucleotide bases -some chemicals add groups to the bases -radiation damages the genetic material
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benefits/costs of mutations +Mutations are the raw material of evolution: without mutation, there would be no evolution -Germ line and somatic mutations can be harmful: mutations in germ line cells that get carried to the next generation are often deleterious
restriction enzymes cut double-stranded DNA molecules into smaller, noninfectious fragments
restriction digestion breaking the bonds of the DNA backbone between the 3' hydroxyl group of one nucleotide and the 5' phosphate group of the next nucleotide
recognition sequence/ restriction site specific sequence of bases where restriction enzymes cleaves DNA
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gel electrophoresis convenient way to separate or purify DNA fragments *gives us 3 types of info: -number of fragments -sizes of fragments -relative abundance of a fragment
prion infectious agent composed of protein in a misfolded form -violation of the central dogma
multifactorial diseases that are caused by the interactions of many genes and proteins with one or more factors in the environment
gene flow migration of individuals and movements of gametes between populations, can change allele frequencies in a population
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genetic drift change in the frequency of a gene variant in a population due to random sampling -may cause large changes in small population
population bottleneck populations that are normally large may occasionally pass through a period in which only a small number of individuals survive
founder effect resulting change in genetic variation, is equivalent to that in a large population reduced by a bottleneck
molecular evolution investigates the mechanisms and consequences of the evolution of macromolecules
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nucleotide substitution sometimes result in amino acid replacements that can change the charge, the structure (2nd or 3rd) and other chemical/physical properties of the encoded protein
sequence alignment we compare two amino acid sequences from homologous proteins in different organism
similarity matrix a measure of the minimum number of changes that have occurred during the divergence between each pair of organisms
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 Functions of Proteinsenzymes, defensive (antibodies), hormonal/regulatory (insulin), receptors, storage (amino acids), structural (collagen), transport (hemoglobin), genetic regulatory proteins
 Proteinspolymers made up of different proportions and sequences of 20 amino acids
-consist of one or more polypeptide chains: linear polymer of covalently linked amino acids
 Amino Acidsalpha carbon atom containing an amino group, a carboxylic acid group and a side chain (R group) and H atom
-asymmetrical, isomeric: D-amino acids and L-amino acids
 Hydrophilic/hydrophobic+attracts water /-fear of water
 Disulfide Bridgehelp determine how a polypeptide chain folds
 Peptide Linkageformed when the carboxyl group of one amino acid reacts with the amino group of another, undergoing a condensation reaction
 N terminus/C terminusN: marks beginning of a polypeptide, first amino acid
C: period of carboxyl group, last amino acid added
 Primary Structureholds together the precise sequence of amino acids in a polypeptide chain
-give molecule's final functional shape
 Secondary Structureconsists of regular, repeated spatial patterns in different regions of a polypeptide chain- two types determined by hydrogen bonding
1. alpha helix: right-handed coil
2. beta pleated sheet: formed from two or more polypeptide chains that are almost completely extended and aligned
 Tertiary Structurethe polypeptide chain is bent at specific sites and then folded back and forth
-results in a macromolecule's definitive 3D shape
 Maintaining Tertiary Structure polypeptide folding:
-covalent disulfide bridges
-H bonds
-hydrophobic side chains
-van der Waals forces stabilizes hydrophobic side chains
ionic bonds: forms salt bridges between amino acids
 lysozyme 
 denaturationwhen a protein is heated slowly, the heat energy will disrupt only the weak interactions causing secondary and tertiary structure to break down
*returns to normal tertiary structure when cooled down
-can be irreversible when caused to form new structure
 Quaternary Structureresults from the ways in which subunits bind together and interact
ex) hemoglobin: weak nature of four forces (hydrophobic, van der Waal, H bonds and ionic bonds) permits small changes in structure to aid the function
 Shape and Surface Chemistryshape and structure of protein allow specific sites on its exposed surface (R groups) to bind noncovalently to another molecule
-binding is specific because only certain compatible chemical groups will bind to one another
-3 types of interactions: ionic, hydrophobic, and H bonding
 Environmental Effects+T : faster molecular movements, can break H bonds
*alterations in PH: disrupts pattern of ionic attractions
high concentrations of polar substances disrupts protein structure
nonpolar substances may disrupt protein structures
 Chaperonesspecial class of proteins in eukaryotic cells that act to counteracts threats to 3D structure
 heat shock proteinsgeneral class of stress-induced chaperone proteins
 nucleic acidspolymers specialized for the storage, transmission between generations, and use of genetic information
-two types: DNA and RNA
 DNAencodes hereditary info and passes it from generation to generation
-info flows from DNA to DNA during reproduction
-DNA to RNA to proteins in non-reproductive activities
 RNAused as an intermediate, info from DNA is used to specify the amino acid sequences of proteins
-lacks single oxygen atom found in DNA
 nucleotidescomposes nucleic acids, consists of a pentose sugar, a phosphate group, and a nitrogen-containing base
functions:
-ATP, GTP: energy source
-cAMP: additional bond between sugar and phosphate group (hormones and nervous system)
 pyrimidinesix-membered single ring structure: C, T
 purinefused double ring structure: A,G
 phosphodiester linkagesjoins the nucleotides between the sugar of one and phosphate of the next
-link carbon 3 to carbon 5 of adjacent sugar
 base pairingadenine (A) - thymine (T)/ uracil (U)
cytosine (C) - guanine (G)
 replicationDNA can reproduce itself by polymerization on a template
1) DNA unwound to two template strands, available for new base pairing
2) new nucleotides form complementary base pairs with template DNA, covalently linked together by phosphodiester bonds
 transcriptiontransfer of DNA info copied into RNA
*Requires:
-DNA template for complementary base pairing; 1 of 2 strands
-ATP, GPT, CTP, UTP substrates
-RNA polymerase enzyme
STEPS
1) Initiation
2) Elongation
3) Termination
 translationnucleotide sequence in RNA can specify a sequence of amino acids in a polypeptide
 genomecomplete set of DNA in a living organism
-not all of the info in the genome is needed at all times
 genessequences of DNA that encode specific proteins are transcribed into RNA
 spontaneous generationorganism arose spontaneously from rich chemical envrionment
 transfectiongenetic transformation of eukaryotic cells by DNA
 genetic markera gene whose presence in the recipient cell confers an observable phenotype
 crystalsisolated and purified chemical substances
 Chargaff's Rule 
 Watson and Crick Structure3D representation of DNA
-helical, two polynucleotide chains, antiparallel
-nucleotide bases are on the interior of the two strands
-sugar phosphate backbone on the outside
 5' endfree 5' phosphate group (-OPO3-)
 3' end free 3' hydroxyl group (-OH)
 Double helical structure-genetic material is susceptible to mutations in the info
-precisely replicated in the cell division cycle
-expressed as the phenotype
 DNA polymeraseenzyme catalyzes DNA replication
 nucleoside nitrogen base attached to a sugar
 semiconservative replication*each parent strand serves as a template for a new strand, and the two new DNA molecules each have one old and one new strand
 conservative replicationthe original double helix serves a s a temple for, but does not contribute to, a new double helix
-1st generation would have both high-density and low-density DNA
 dispersive replicationfragments of the original DNA molecule serve as templates for assembling two new molecules, each containing old and new parts, perhaps at random
-new DNA would have been intermediate
 replication complex1) primase binds to the template strand and synthesizes an RNA primer
2) DNA polymerase binds and synthesizes new DNA
 origin of replicationone region which the replication complex binds
 primer"starter strand" short single strand of RNA and is complementary to the DNA template
 primaseRNA primer is synthesized by this enzyme
 DNA helicaseenzyme that uses energy from ATP to unwind and separate the strands
 single-strand binding proteinsspecial proteins bind to the unwound strands to keep them from reassociating into a double helix
 replication forksite(s) where DNA unwinds to expose the bases so that they can act as templates
 leading strandnewly replicating strand is oriented so that it can grow continuously at its 3' end as the fork opens up
 lagging strandnew strand oriented so that as the fork opens up, its exposed 3' end gets farther and farther away from the fork
 Okazaki fragmentsshort fragment of DNA created on the lagging strand during DNA replication
 processiveDNA polymerases catalyze many polymerizations each time they bind to a DNA molecule
 sliding DNA clampprotein shaped like a screw cap binds the DNA polymerase, keeping the enzyme and the DNA associated tightly with each other
 PCNAkeeps DNA polymerase bound to the DNA, helps to orient the polymerase for binding to the substrates
 DNA topoisomeraseenzyme that separates two interlocking circular DNA molecules
 telomeresregion of repetitive DNA at the end of a chromosome, which protects the end of the chromosome from deterioration
 telomerasean enzyme that catalyzes the addition of any lost telomeric sequences the cells
 mRNAcarries a copy of a gene sequence in DAN to the site of protein synthesis at the ribosome
 tRNAcarries amino acids to the ribosome for assembly into polypeptides
-must read mRNA codons correctly
-delivers the amino acids that correspond to each mRNA codon
-"charged" when carrying particular amino acid
-interacts with ribosomes
 rRNAcatalyzes peptide bond formation and provides a structural framework for the ribosome
 Uracilthe fourth base in RNA, similar to thymine but lacks the methyl group (-CH3)
 codonconsists of 3 consecutive nucleotides (letters) and different codons encode particular amino acids
(during transcription)
 transcriptexamining the mRNA copy of the gene
 anticodoncomplements the codon in mRNA
 Messenger HypothesisCrick and his colleagues proposed that an RNA molecule forms as a complementary copy of one DNA strand in a gene. The mRNA then travels from the nucleus to the cytoplasm where it serves as an informational sequence of codons.
 Adapter HypothesisCrick proposed that there must be an adapter molecule that can both bind a specific amino acid and recognize a specific sequence of nucleotides. Each tRNA recognizes a specific codon in the mRNA and simultaneously carries the amino acid corresponding to that codon.
 RNA VirusRNA viruses are exceptions to central dogma, could possibly act as an info carrier and be expressed as a protein
ex) HIV relies on host cell's transcription machinery to make more RNA
 RNA polymerasefrom both prokaryotes and eukarytoes catalyze the synthesis of RNA from the DNA template
-only one type in bacteria
-do not require a primer/ do not have a proofreading function
 reverse transcriptionsynthesis of DNA from RNA
-such viruses are called retroviruses
 promotera special sequence of DNA to which the RN polymerase binds very tightly
*TELLS RNA POLYMERASE:
-where to start transcription
-which strand of DNA to transcribe
 Transcription Process1) initiation site- where transcription begins:
-5' on the non-template strand / 3' on the template strand
2) elongation- RNA polymerase unwinds the DNA about 10 base pairs at a time and reads the template strand in the 3'-5' direction
3) termination
 genetic coderelates genetic DNA to mRNA and mRNA to the amino acids that make up proteins
 start codonthe initiation signal for translation (AUG)
 stop codon termination signals for translation (UAA, UAG, UGA)
 redundant codefor almost all amino acids, there is more than one codon
 ambiguous codea single codon could specify either of two or more different amino acids, and there would be doubt about which amino acid should be incorporated into a growing polypeptide chain
 Universal Genetic Codesame genetic code is used by all the species on our planet, thus there must have been a common ancestor
-common language for evolution
-few exceptions for prokaryotes and eukaryotes
 Eukaryotic genes-each gene has its own promoter
-does not recognize the promoter sequence by itself, but requires help from other molecules
-may contain introns, exons
 prokaryotic genes-several adjacent genes sometimes share one promoter
-recognizes promoter by itself
 intronsnoncoding base sequences (intervening regions)
 exonsone or more introns interspersed with the coding sequences (expressed regions)
 pre-mRNAthe mRNA that will be translated; cuts introns out of the pre-mRNA and splicing together the remaining exon transcripts
-involves both introns and exons
 RNA splicingremoves the introns and splices the exons together
-if not removed, a very different amino acid/nonfunctional protein would result
 snRNPsafter pre-mRNA is transcribed, snRNPs bind at each end
 consensus sequencesshort stretches of DNA that appear with little variation in many different genes
 spliceosomeusing ATp, proteins are added to form this large RNA-protein complex; cuts the pre-mRNA, releases the introns and joins the ends of the exons to produce mature mRNA
 wobbleallows the alanine codons all to be recognized by the same tRNA; does not allow the genetic code to be ambiguous
 ribosomemolecular workbench where the task of translation is accomplished; structure enables it to hold mRNA and charged tRNs in the right positions
-when not active, becomes two separate subunits
 Translation Process1) initiation complex: consists of a charged tRNA and a small ribosomal subunit, both bound to the mRNA
2) elongation: breaks bond between the tRNA and amino acid; catalyzes the formation of a peptide bond between amino acid and tRNA => peptidyl transferase
3) termination: UAA, UAG, or UGA
 proofreadingmechanism corrects errors in replication as DNA polymerase makes them
-occurs when DNA polymerase introduces a new nucleotide into a growing DNA strand
 mismatch repairmechanism scans DNA immediately after it has been replicated and corrects any base-pairing mismatches
-DNA strand is chemically modified some time after replication to detect wrong base complements
 excision repairmechanism removes abnormal bases that have formed because of chemical damage and replaces them with functional bases
-deals with high energy radiation, chemicals from environment, random spontaneous chemical reactions damaged DNA
 mutationsinherited changes in genes
-changes in the nucleotide sequence of DNA that are passed on from one cell, or organism to another
 somatic mutationsoccur in body cells; passed on to the daughter cells during mitosis and so on but passed on to sexually produced offspring
 germ line mutationsoccur in the cells of the germ line- the specialized cells that give rise to gametes; passes it on to a new organism at fertilization
 silent mutationsDO NOT affect protein function; in noncoding DNA such as repeat sequences or coding portion of DNA
 loss of function mutationsAFFECT protein function; may lead to nonfunctional proteins that no longer work as structural proteins or enzymes and always show recessive inheritance
 gain of function mutationleads to a protein with an altered function; shows dominant inheritance
ex) cancer cells
 conditional mutationscause their phenotypes only under certain restrictive conditions; not detectable under other permissive conditions
 point mutationresults from the gain, loss, or substitution of a single nucleotide
 chromosomal mutationsmore extensive than point mutations; may change the position or orientation of a DNA segment without actually removing any genetic info, or they may cause a segment of DNA to be duplicated or irretrievably lost
-deletions, duplications, inversions, translocations
 mutagensubstances that cause mutations such as radiation or certain chemicals
-can be natural or artificial
 silent mutationshave no effect on amino acid sequences; often found in noncoding DNA because of the redundancy of the genetic code
 missense mutationbase substitutions change the genetic code such that one amino acid substitutes for another in a protein
-might reduce the functional efficiency rather than completely inactivating a protein
ex) sickle cell disease
 nonsense mutationsinvolves a base substitution that causes a stop codon (for translation) to form somewhere in the mRNA
-results in shortened protein, usually not functional
 frame-shift mutationssingle or double bases may be inserted into or deleted from DNA because they interfere with the translation of the genetic message by throwing it out of register
 deletionsremoval of part of the genetic material; can be severe unless they affect noncoding DNA or unnecessary genes
 duplicationsproduced at the same time as deletions; arise if homologous chromosomes broke at different positions and then reconnected to the wrong partners
 inversionsbreaking and rejoining of chromsomes; if break site includes part of a DNA segment the resulting protein will be drastically altered and almost certainly nonfunctional
 translocationwhen segment of a chromosome breaks off and is inserted into a different chromosomes; often lead to duplications and deletions and may result in sterility
 spontaneous mutationspermanent changes in the genetic material that occur without any outside influence; because cellular processes are imperfect
-nucleotide bases of DNA have different structures
-bases may change because of chemical reactions
-DNA polymerase can make errors in replication
-meiosis is not perfect
 induced mutationswhen some agent from outside the cell- a mutagen- causes a permanent change in DNA
-some chemicals can alter the nucleotide bases
-some chemicals add groups to the bases
-radiation damages the genetic material
 benefits/costs of mutations+Mutations are the raw material of evolution: without mutation, there would be no evolution
-Germ line and somatic mutations can be harmful: mutations in germ line cells that get carried to the next generation are often deleterious
 restriction enzymescut double-stranded DNA molecules into smaller, noninfectious fragments
 restriction digestionbreaking the bonds of the DNA backbone between the 3' hydroxyl group of one nucleotide and the 5' phosphate group of the next nucleotide
 recognition sequence/ restriction sitespecific sequence of bases where restriction enzymes cleaves DNA
 gel electrophoresisconvenient way to separate or purify DNA fragments
*gives us 3 types of info:
-number of fragments
-sizes of fragments
-relative abundance of a fragment
 prioninfectious agent composed of protein in a misfolded form
-violation of the central dogma
 multifactorialdiseases that are caused by the interactions of many genes and proteins with one or more factors in the environment
 gene flowmigration of individuals and movements of gametes between populations, can change allele frequencies in a population
 genetic driftchange in the frequency of a gene variant in a population due to random sampling
-may cause large changes in small population
 population bottleneckpopulations that are normally large may occasionally pass through a period in which only a small number of individuals survive
 founder effectresulting change in genetic variation, is equivalent to that in a large population reduced by a bottleneck
 molecular evolution investigates the mechanisms and consequences of the evolution of macromolecules
 nucleotide substitutionsometimes result in amino acid replacements that can change the charge, the structure (2nd or 3rd) and other chemical/physical properties of the encoded protein
 sequence alignmentwe compare two amino acid sequences from homologous proteins in different organism
 similarity matrixa measure of the minimum number of changes that have occurred during the divergence between each pair of organisms
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