DNA structure and replication

Explain the purpose for each of the enzymes involved in DNA replication helicase

- unwind and separate the hydrogen bonds

Identify the location where RNA processing occurs

-inside the nucleus

Describe the process of DNA replication

1. helicase unwinds and separates the DNA strands breaking the hydrogen bonds 2. topoisomerase prevents supercoiling on the other side of the replication fork 3. Primase adds RNA nucleotides forming the primer on both continuous and discontinuous strands 4. DNA polymerase adds nucleotides on both leading/lagging strands synthesizing them in the 5' to 3' direction 4. DNA Ligase covalently bonds the okazaki fragments 5. proofreading of the synthesized strands

Identify the base pairing rule

A pairs with T and C pairs with G explain- a purine must pair with a pyrimidine so it is the correct width . A must pair with T because it is the correct width and correct number of hydrogen bonds holding them together (both require 2 hydrogen bonds) G and C must pair together for the correct width (purine to pyrimidine) and the correct number of hydrogen bonds (both need 3)

Describe what occurs to the pre- mRNA to process it into a mature mRNA

Addition of a poly-A tail, Addition of a GTP cap, Excision of introns and splicing and retention of exons.

Describe the differences between DNA and RNA

DNA double stranded, RNA single stranded DNA contains the pyrimidine T while RNA contains U DNA contains the sugar deoxyribose while RNA contains the sugar ribose

identify the building blocks of DNA

DNA is a molecule made up of four chemical bases: adenine (A), cytosine (C), guanine (G), and thymine (T). For the two strands of DNA to zip together, A pairs with T, and C pairs with G.

Identify the direction DNA polymerase reads the template strand AND EXPLAIN why the template strand is read in that direction

DNA polymerase reads the template strand 3' to 5' and synthesizes the new strand 5' to 3'. ( it must lay down the new nucleotides by adding them to the exposed 3' end)

EXPLAIN why a newly synthesized DNA strand is made from both continuous and discontinuous DNA synthesis

DNA replication is semi conservative. since there are two template strands from the original DNA, the one template strand is read towards the replication fork and is made continuously while the other template strand is made away from the replication fork and made discontinuously

Identify the phase in which DNA replication takes place and EXPLAIN the importance of DNA replication

DNA replication occurs during the "S" phase of interphase prior to mitosis and meiosis. this ensures that there is the correct amount of DNA in the daughter cells after cell division

DESCRIBE a purine and IDENTIFY the purines in DNA

Describe- Purines are nucleotides with double ringed nitrogenous bases. identify- A and G are purines

DESCRIBE what is occurring at each step in translation to produce a polypeptide Elongation

Elongation- growth of polypeptide chain tRNA continues to bring the corresponding amino acid over to the growing polypeptide chain amino acids peptide bonded together process continues along the mRNA until a stop codon is reached

Explain the importance of the hydrogen bonds in the DNA molecule

In addition to holding the DNA strands together, the hydrogen bonding between the complementary bases also sequester the bases in the interior of the double helix. Therefore, the hydrogen bonding between the bases reinforces the hydrophobic effects that stabilize the DNA. holds the antiparallel strands tgthrh

DESCRIBE what is occurring at each step in translation to produce a polypeptide Initiation

Initiation- assembling all the RNA's involved in protein synthesis at the codon start sequence small ribosomal subunit attaches to mRNA at start codon sequence tRNA carries the correct amino acid over based on the codon large ribosomal subunit attaches

Identify the number of chromosomes (as single or multiple) that exist in prokaryotes and eukaryotes and Describe their shape (circular or linear)

Prokaryote- 1 double helix chromosome that is circular eukaryotes- multiple double helix chromosomes that are linear

Identify the enzyme used in transcription and EXPLAIN its role in transcription

RNA polymerase is the enzyme used in transcription which synthesizes the new RNA strand by using the DNA template to produce the RNA strand

Describe the process of transcription

RNA polymerases use a single template strand of DNA to direct the inclusion of bases in the newly formed RNA molecule. RNA polymerase attaches to the promoter region on the DNA strand, adds RNA nucleotides to the new strand, and stops adding nucleotides when it gets to the termination sequenceThe enzyme RNA polymerase synthesizes mRNA molecules in the 5' to 3' direction by reading the template DNA strand in the 3' to 5' direction.

Explain what is meant by the phrase " DNA replication is a semiconservative process"

Replication is a semiconservative process—that is, one strand of DNA serves as the template for a new strand of complementary DNA.

Explain how the selection of which DNA strand will serve as the template Identify the mRNA strand that would be produced from the following DNA strand A T A C C G T G A C T A

Selection of which DNA strand serves as the template strand depends on the gene being transcribed. the transcription factors will attach to the DNA strand that will be transcribed and translated U A U G G C A C U G A U

DESCRIBE what is occurring at each step in translation to produce a polypeptide Termination

Termination- polypeptide is done being assembled separation of the types of RNA from the polypeptide chain result is a polypeptide in its primary structure which will then go on to fold into secondary, tertiary, quaternary structure based on the amino acids present

Identify the number of DNA strands found in a DNA molecule and Explain the orientation of the DNA strands

The chromosomes of many organisms are composed of two DNA strands: one strand is oriented in the 5′-3′ direction with respect to the carbon atoms on the sugar (deoxyribose) and the complimentary strand is in the opposite 3′-5′ direction. antiparallel

Identify the direction in which RNA polymerase synthesizes mRNA molecules and EXPLAIN why the RNA polymerase must synthesize mRNA in this direction

The enzyme RNA polymerase synthesizes mRNA molecules in the 5' to 3' direction by reading the template DNA strand in the 3' to 5' direction.the noncoding strand is the template/nonsense strand bc it is complementary to the RNA. it does not contain the code for the protein The DNA strand acting as the template strand is also referred to as the noncoding strand, minus strand, or antisense strand.

Identify the direction in which DNA is synthesized

The new strand is synthesized 5' to 3'

DESCRIBE how the same transcription factor can regulate/active gene expression of multiple genes

The same transcription factor can bind to multiple different promoter regions activating different genes. this coordinates their production at the same time coordinating activity in the body. (the transcription factor can also at the same time bind to different promoters causing gene expression to stop... this is not pictured in the diagram to the right)

Describe how the process of transduction brings about genetic variation in prokaryotes

a bacteriophage( virus that infects bacteria) transfers DNA from one bacteria to another bacteria as in infects the bacteria.

DRAW a plasmid and DESCRIBE its structure.***

a plasmid is a double helix that is separate from the chromosome. It can contain gene sequences that benefit survival such as genes that code for the resistance of antibiotics there is a promoter region

Explain the purpose for each of the enzymes involved in DNA replication Primase

adds RNA nucleotides forming the primer

**EXPLAIN the role of tRNA in protein synthesis and IDENTIFY and label both the anticodon and amino acid on the tRNA

carry over the amino acids to the growing polypeptide chain

Explain the uses of gel electrophoresis

compare relationships of individuals or species diagnose genetic disorders evidence in crime scenes or paternity cases

IDENTIFY the components of a eukaryote chromosome and DESCRIBE the arrangement of the components in the chromosome

contains multiple histones (a group of 8 proteins) with DNA wrapped around each histone. the combination of histone and DNA is called a nucleosome. histones that are tightly packed together is heterochromatin histones that are separated (loosely packed) is euchromatin

Explain the purpose of the operator region

control protein synthesis. site where repressor can bind to stopping protein synthesis which conserves energy

Explain the purpose for each of the enzymes involved in DNA replication Ligase

covalently bonds the okazaki fragments on the lagging strand

DESCRIBE a pyrimidine and IDENTIFY the pyrimidines in DNA/RNA

describe- pyrimidines are nucleotides with single ring bases identify- T and C are pyrimidines

DESCRIBE the process of conjugation in prokaryotes and EXPLAIN the benefits to the prokaryotes

describe- transfer of DNA from one prokaryote to another through a structure called a pili. when a plasmid with antibiotic resistance is passed to a prokaryote, the prokaryote now is resistant giving it a survival advantage

Explain why the analysis of DNA to compare individuals results in a greater estimate of genetic variability than does analysis of amino acid sequences

different DNA sequences can code for the same amino acid

Since each cell contains all the genes of the organism, EXPLAIN how cells can express different phenotypes

different cells express different genes resulting in the production of different proteins

Explain why the central dogma ((this just means the process of DNA → mRNA → Protein) )does not apply to retroviruses EXPLAIN why During the infection cycle for a typical retrovirus, such as HIV, which uses RNA as genetic material, the genetic variation in the resulting population of new virus particles is very high

does not apply to retroviruses retroviruses start with RNA not DNA for their genetic content because retroviruses produce DNA from RNA during reverse transcription, there is no proofreading so errors are introduced into the DNA strand and not corrected

DESCRIBE how nondisjunction happens in MEIOSIS I and EXPLAIN how it impacts the chromosome number in the gametes

during anaphase I homologous chromosomes failed to separate resulting in all gametes having the incorrect chromosome number. two gametes will have an extra chromosome and two gametes will have a missing chromosome. the incorrect chromosome number will produce changes in the phenotype

Explain why the DNA fragments move through the gel

electricity pulls the DNA since DNA has a negative charge

Explain epigenetics

epigenetics is the change to gene expression without changing the genetic code. ( it can allow gene expression to occur or stop gene expression)

identify the process that would produce errors in the DNA sequence and EXPLAIN why the errors in the DNA could have an impact on the phenotype

errors can occur in DNA replication or DNA proofreading which could result in the wrong amino acid in the polypeptide sequence. changing in the polypeptide would change the secondary/tertiary/quaternary folding resulting in a different phenotype

EXPLAIN how transcription and translation varies between prokaryotes and Eukaryotes Explain why transcription and translation can happen at the same time in Prokaryotes but not Eukaryotes

eukaryotes have RNA processing after transcription while prokaryotes do not have RNA processing transcription occurs in eukaryotes inside the nucleus and must do RNA processing before moving out of the nucleus to the ribosomes. prokaryotes do not have to do RNA processing and transcription occurs in the cytosol where the ribosomes are located

EXPLAIN how the same pre m-RNA strand can result in different mature mRNA strands

excision (removal)of introns and splicing and of exons can generate different versions of the resulting mRNA molecule; this is known as alternative splicing.

Explain why DNA bands appear at different locations in the gel

fragments are different sizes, vary in number of nucleotides

DESCRIBE heterochromatin and euchromatin and EXPLAIN the importance of each type of folding

heterochromatin is tightly packeded so gene expression does not occur in heterochromatin euchromatin is loosely packed so gene expression can occur

Describe how the repressor protein regulates gene expression in prokaryotes

if protein synthesis is not needed for the genes, the repressor protein, if it has he correct shape, can bind to operator region preventing RNA polymerase from functioning so transcription cannot occur preventing protein synthesis from occuring

he Lac operon is an inducible operon. Explain what is means to be an inducible operon.

if the operon is inducible, that means it can be induced or turned on. so in its normal state it is turned off

Explain how gene expression can occur in an inducible operon and EXPLAIN how lactose is involved in the inducible operon

in an inducible operon, since it is normally turned off, the repressor is bound to the operator region preventing RNA polymerase from doing transcription. when lactose is present, allolactose (isomer of lactose) binds to the repressor changing the shape of the repressor. the shape change causes the repressor to stop binding to the operator region. RNA polymerase is then able to do transcription

DESCRIBE how nondisjunction happens in MEIOSIS II and EXPLAIN how it impacts the chromosome number in the gametes

in anaphase II sister chromatids failed to separate. the result would be two gametes having the correct chromosome number and the other two would be incorrect. one gamete would have an extra chromosome and one would be missing a chromosome.

Explain the impact these epigenetic changes have on gene expression

it controls whether gene expression can occur. In some cases, methyl tags are removed from genes that should not be expressed which can negatively impact the organism like producing cancerous cells

Explain why the leading strand is referred to as the continuous strand

it is made towards the replication fork as the helicase separates the DNA strands. the leading strand does not have any breaks in the strand

Identify which type of fragments stay closest to the well

largest fragments because they have the most nucleotides so harder to move through gel

Explain the importance of the promoter region

location for RNA polymerase to bind to

Explain the purpose of restriction enzymes

looks for specific recognition sequences and cut DNA into fragments

**Explain the role of mRNA in protein synthesis, DETERMINE the number of nucleotides that make up a codon AND DRAW a circle around each codon

mRNA contains the code from DNA which will be used to produce the amino acid sequence. 3 nucleotides make up 1 codon

Explain the role for each of the following types of RNA mRNA

mRNA molecules carry information from DNA to the ribosome.

Explain why the lagging strand is referred to as the discontinuous strand

made away from the replication fork. must be made in fragments (okazaki fragments) as the replication fork unwinds dna polymerase adds new nucleotides away from the fork. the fragments then need to be covalently bonded to make it a continuous complete strand

PREDICT the impact a mutation to the gene coding for the repair enzyme would have on the cell AND JUSTIFY your prediction

multiple errors would be present in the DNA that as synthesized during interphase. a mutation to the repair enzyme would not correct mutations which would produce proteins with the incorrect amino acid sequence and incorrect folding

Explain the purpose for each of the enzymes involved in DNA replication topoisomerase

on the other side of the replication fork. as helicase unwinds the DNA strands topoisomerase will prevent supercoiling (over winding) of the DNA strands upstream of the replication fork

Sickle cell anemia is caused by a point mutation that results in the red blood having an altered shape. PREDICT the impact this mutation would have on an individual AND JUSTIFY your prediction.

predict- individuals would not be able to transport oxygen justify- if the protein has an altered shape, oxygen cannot bind so the cells will not get enough oxygen for cellular respiration

HIV infects cells that contain a CCR5 protein on surface of the plasma membrane. Some individuals have a mutation in the CCR5 gene resulting in a smaller protein that remains on the inside. If a person with the gene mutation was exposed to HIV, PREDICT the impact the exposure would have on these individuals. JUSTIFY your prediction

predict- these individuals would be immune to HIV justify- since the CCR5 protein is not on the outside of the cell, HIV would not have the protein to bind to. If HIV cannot bind, it cannot infect the cells making the individual immune to HIV. (in this case, the mutation produced a positive change in phenotype)

Explain the importance of the regulatory gene in the prokaryote and IDENTIFY the molecule that is produced from the regulatory gene

produces a protein called the repressor that controls protein synthesis.

DESCRIBE how transformation occurs in prokaryotes (bacteria) and EXPLAIN the positive impact it has on prokaryotes

prokaryotes take in naked DNA (plasmid, or segment of DNA) from its surrounding environment and incorporate the DNA into its own DNA/plasmid explain- for prokaryotes, this allows from variation which could be a resistant gene allowing them to survive exposure to antibiotics

Identify the structures that make up a lac operon

promoter region, operator region, structrual genes (which will be transcribed and translated into proteins)

Promoter regions on DNA are involved with gene expression. Identify the location of promoters and EXPLAIN their involvement with gene expression

promoter regions are upstream ( not part of) from the region where transcription occurs. the promoter region can active or turn off gene expression

Explain the role for each of the following types of RNA rRNA

rRNA molecules are functional building blocks of ribosomes.Describe how the phenotype of an organism is determined by its genotype.

Explain why the banding pattern for each individual is different even though the same restriction enzyme is used

restriction enzyme is used -nucleotide sequence is different for each individual (except for identical twins)

identify the genetic contents of a retrovirus

retroviruses have RNA as their genetics content

Viruses, just like prokaryotes and Eukaryotes, use their genetic content to produce proteins. Describe the processes retroviruses must go through to produce a protein

retroviruses must first make a DNA strand before protein synthesis can occur. RNA🡪 DNA🡪 RNA🡪 protein

Describe the overall structure of ribosomes AND EXPLAIN what ribosomes are made up of

ribosomes are made of rRNA and proteins. site of protein synthesis. allows mRNA codon to pair with tRNA anticodon and formation of peptide bonds between amino acids

Describe the overall structure of RNA

single stranded nucleic acid made of nucleotides. nucleotides made of phosphate, ribose sugar, nitrogenous bases. (A-U, C-G)

Identify which fragments are able to move the furthest in the gel and EXPLAIN why they are able to move the furthest

smallest are able to move through the gel because they have the fewest nucleotides and easier to move through gel

Explain the purpose for each of the enzymes involved in DNA replication DNA polymerase

synthesizes the new DNA strands on both the continuous and discontinuous strands

Explain the role for each of the following types of RNA tRNA

tRNA molecules bind specific amino acids and have anti-codon sequences that base pair with the mRNA. tRNA is recruited to the ribosome during translation to generate the primary peptide sequence based on the mRNA sequence.

***Draw a circle around the coding strand and EXPLAIN why it is the coding strand

the coding strand is the sense strand bc it is the code for the amino acid sequence which will determine the protein produced

Explain how signal transduction is involved in phenotypic expression

the environmental signal (ligand) causes signal transduction which produces a response to activate the transcription factors. (the transcription factors are inactive so no gene expression can occur until signal transduction activates the transcription factors)

Explain what non disjunction is

the failure of the chromosomes or sister chromatids to separate in anaphase

Explain the importance for RNA processing

the introns are noncoding segments so must be removed . if not removed the wrong amino acids would be in the protein and produce the wrong shape protein. the poly a tail is added so enzymes do not degrade it while moving through cytosol. the GTP cap helps attach to ribosome

****Draw a circle around the noncoding (template) strand and EXPLAIN why it is the noncoding strand

the noncoding strand is the template/nonsense strand bc it is complementary to the RNA. it does not contain the code for the protein The DNA strand acting as the template strand is also referred to as the noncoding strand, minus strand, or antisense strand.

Explain what is meant by the 5' and 3' ends of the nucleotide

the numbers refer to the carbon that is in that position. the 5' end is the 5th carbon which has a phosphate attached and the 3' end is the 3rd carbon in the structure which has a OH (hydroxyl group) attached

Explain the importance of the 5' and 3' end in a DNA molecule

the orientation of the 3' and 5' end determine which direction DNA and RNA polymerase will lay down nucleotides. DNA replication- DNA polymerase synthesizes the new strand in the 5' - 3' direction (so it reads the template strand 3'-5') transcription- RNA polymerase also must synthesize the new RNA strand in the 5' to 3' direction (so it reads the DNA template strand 3' to 5')

Explain why some DNA mutations are harmful while other DNA mutations are beneficial

the phenotypes that result from the mutation will be harmful or beneficial depending on the environment the organism is exposed to

Describe how this regulatory gene is involved in the operons

the regulatory gene will be transcribed and translated into the regulatory repessor protein which is capable on binding to the operator region and stoping protein synthesis

Describe the impact non disjunction has on individuals

the resulting daughter cells will have either too many to too few chromosomes Changes in chromosome number often result in human disorders with developmental limitations, including Down syndrome/ Trisomy 21 and Turner syndrome.

Describe the involvement of transcription factors in the expression of genes

transcription factors bind to the promoter region activating or inactivating transcription. if transcription factors are activating transcription, it signals RNA polymerase to attach and begin transcription of that gene

Identify the location where transcription takes place and Identify what is produced as a result of Transcription

transcription occurs in the nucleus and produces mRNA

Describe the similarities of protein synthesis in Prokaryotes and Eukaryotes

transcription occurs using DNA as the template, and RNA polymerase as the enzyme translation occurs at the ribosomes using the 3 types of RNA's resulting in a polypeptide

Predict what would happen to gene expression if a chemical was bound to the transcription factors. JUSTIFY your prediction

transcription would not happen since the transcription factors would be unable to bind to the promoter region. RNA polymerase would not attach so transcription would not happen and no protein would be made

IDENTIFY the location where translation takes place and IDENTIFY the molecule produced at the end of translation

translation occurs at the ribosome and produces a polypeptide

Describe how the methyl group causes changes in the chromosome

when the methyl tag is present, it causes the chromatin to tightly pack into heterochromatin preventing gene expression from happening when the methyl tag is removed, chromatin is loosely packed into euchromatin so gene expression can occur