IBIO exam 1

SSB Protein

Prevents reannealing of DNA strands

DNA Polymerase III

Synthesizes new DNA

Kilobase (kb)

(in expressing the lengths of nucleic acid molecules) 1,000 bases.

PCR occurs in 3 steps:

-Denaturation: In this step the double stranded DNA is get converted into single stranded DNA when heated at 94•C. -Annealing: The two forward and reverse primers bind to the complementary region of the DNA template. This step occurs at 45-55•C. -Extension: This is the last step of PCR PCT in which dNTPs are added at the free 3'OH of primer by the Taq polymerase. This step occurs at 70-74•C.

Place the events that take place during translation and protein synthesis in the correct order.

-The mRNA strand binds with the smaller subunit of the ribosome, which moves along the mRNA. -The anticodon of a tRNA molecule carrying an amino acid matches with the complementary codon on the mRNA strand. -New amino acids are added to the polypeptide chain by the ribosome. -The tRNA molecules that have contributed amino acids to the protein chain leave the ribosome.

Apply Chargaff's rule by giving the complementary sequence of a given DNA sequence, including the polarity of the strands. Textbook section 13.1

5'-ACTGATGCCCGTA-3' 3'-TGACTACGGGCAT-5'

Define a DNA library

A DNA library is a collection of DNA fragments that have been cloned into vectors so that researchers can identify and isolate the DNA fragments that interest them for further study. There are basically two kinds of libraries: genomic DNA and cDNA libraries.

Complementary DNA (cDNA) library

A cDNA library is a combination of cloned cDNA (complementary DNA) fragments inserted into a collection of host cells, which constitute some portion of the transcriptome of the organism and are stored as a "library".

Partial diploid (merodiploid, merozygote)

A cell carrying two copies of some, but not all, of its genes. In bacteria where one copy of the genes of interest is carried on the chromosome, a second copy may be introduced on a plasmid. The cells therefore carry one complete set of genes and a duplicated copy of part of the genome.

Telomere

A compound structure at the end of a chromosome.

Consensus sequences

A consensus sequence is a sequence of DNA, RNA, or protein that represents aligned, related sequences. The consensus sequence of the related sequences can be defined in different ways, but is normally defined by the most common nucleotide(s) or amino acid residue(s) at each position.

Sticky ends

A fragment of DNA (often produced by a staggered cut on the DNA using restriction enzymes) in which the terminal portion has a stretch of unpaired nucleotides, and the strands are not of the same length.

Recognize that genes come in multiple forms; recall the name of these forms.

A gene can exist in different forms or different alleles These different alleles can control the phenotypic differences we see These alleles are inherited from the parents

Identify the gene as the fundamental unit of heredity

A gene is a unit of heredity which is transferred from a parent to the offspring and is held to determine some characteristics of the offspring Is also a distinct sequence of nucleotides forming part of a chromosome and the order in which the monomers are placed will determine the synthesis. Create phenotypes we see

lethal mutation

A gene mutation whose expression results in the premature death of the organism carrying it. Dominant lethals kill both homozygotes and heterozygotes, recessive lethals kill homozygotes only.

Plasmid

A genetic structure in a cell that can replicate independently of the chromosomes, typically a small circular DNA strand in the cytoplasm of a bacterium or protozoan. Plasmids are much used in the laboratory manipulation of genes.

Genomic library

A genomic library is a collection of the total genomic DNA from a single organism. The DNA is stored in a population of identical vectors, each containing a different insert of DNA.

Identify sequences of ssDNA, dsDNA, and RNA that will form secondary structures, including: Hairpins

A hairpin loop is an unpaired loop of messenger RNA (mRNA) that is created when an mRNA strand folds and forms base pairs with another section of the same strand. The resulting structure looks like a loop or a U-shape. Hairpins are a common type of secondary structure in RNA molecules.

Describe the function of a molecular probe.

A molecular probe is a group of atoms or molecules used in molecular biology or chemistry to study the properties of other molecules or structures

Multiple cloning site (MCS)

A multiple cloning site (MCS, or Polylinker region) is a DNA region within a Plasmid that contains multiple unique Restriction enzyme cut sites. Plasmids are very useful in biotechnology and one key feature of their use is the multiple cloning site, which allows for foreign DNA to be inserted into the plasmid.

Identify mutation as the raw material for evolutionary change.

A mutation is a change in the sequence of an organism's DNA. What causes a mutation? Mutations can be caused by high-energy sources such as radiation or by chemicals in the environment.

Northern blotting

A northern blot is a laboratory method used to detect specific RNA molecules among a mixture of RNA. Northern blotting can be used to analyze a sample of RNA from a particular tissue or cell type in order to measure the RNA expression of particular genes.

Identify sequences of ssDNA, dsDNA, and RNA that will form secondary structures, including: Palindromes

A palindromic sequence is a sequence made up of nucleic acids within double helix of DNA and/or RNA that is the same when read from 5' to 3' on one strand and 5' to 3' on the other, complementary, strand. It is also known as a palindrome or an inverted-reverse sequence.

Population

A population is defined as a group of individuals of the same species living and interbreeding within a given area.

Genetics Protein

A protein is composed of one or more long chains of amino acids, the sequence of which corresponds to the DNA sequence of the gene that encodes it. Proteins play a variety of roles in the cell, including structural (cytoskeleton), mechanical (muscle), biochemical (enzymes), and cell signaling (hormones).

Recipient cell (F- cell)

A recipient F- cell has only a chromosome and no F plasmid. The donor cell uses its pilus to attach to the recipient cell, and the two cells are pulled together. A channel forms between the cytoplasms of the two cells, and a single strand of the F plasmid is fed through.

Replication bubble

A replication bubble is an unwound and open region of a DNA helix where DNA replication occurs. Helicase unwinds only a small section of the DNA at a time in a place called the origin of replication. In eukaryotes, there are several origins of replication on each chromosome.

Restriction map

A restriction map is a map of known restriction sites within a sequence of DNA. Restriction mapping requires the use of restriction enzymes. In molecular biology, restriction maps are used as a reference to engineer plasmids or other relatively short pieces of DNA, and sometimes for longer genomic DNA.

Deoxyribonucleic acid (DNA)

A self-replicating material that is present in nearly all living organisms as the main constituent of chromosomes. It is the carrier of genetic information. The fundamental and distinctive characteristics or qualities of someone or something, especially when regarded as unchangeable.

Interrupted mating

A technique used to MAP bacterial genes by determining the sequence in which donor genes enter recipient Cells. A gene MAPping technique in which bacterial conjugation is disrupted after specified time intervals.

Chromosome

A threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.

Mitosis

A type of cell division that results in two daughter cells each having the same number and kind of chromosomes as the parent nucleus, typical of ordinary tissue growth.

Gain-of-function mutation

A type of mutation in which the altered gene product possesses a new molecular function or a new pattern of gene expression. Gain-of-function mutations are almost always Dominant or Semidominant.

Gene

A unit of heredity is transferred from a parent to offspring and is held to determine some characteristic of the offspring.

Conservative DNA replication

According to the conservative replication model, the entire original DNA double helix serves as a template for a new double helix, such that each round of cell division produces one daughter cell with a completely new DNA double helix and another daughter cell with a completely intact old (or original) DNA double helix.

Conceptual replication

Alter the methodology, design and tools of the study to test the generalisability of the results of the original study. These studies corroborate the underlying concept or theory or hypothesis, and try to find out the extent to which the study results can be generalised to new situations.

Bidirectional DNA replication

Bidirectional replication is a method of DNA replication found in organisms from each of the main kingdoms. Bidirectional replication involves replicating DNA in two directions at the same time resulting in a leading strand (were replication occurs more rapidly) and a lagging strand (with slower replication).

Describe how an Hfr chromosome forms

An F-plasmid is integrated into the bacterial chromosomes, leading to an Hfr chromosome.

Identify sequences of ssDNA, dsDNA, and RNA that will form secondary structures, including: Inverted repeats

An inverted repeat (or IR) is a single stranded sequence of nucleotides followed downstream by its reverse complement. ... These repeated DNA sequences often range from a pair of nucleotides to a whole gene, while the proximity of the repeat sequences varies between widely dispersed and simple tandem arrays.

Inverted repeat

An inverted repeat (or IR) is a single stranded sequence of nucleotides followed downstream by its reverse complement. The intervening sequence of nucleotides between the initial sequence and the reverse complement can be any length including zero. For example, 5'---TTACGnnnnnnCGTAA---3' is an inverted repeat sequence.

Model genetic organisms

An organism suitable for studying a specific trait, disease, or phenomenon, due to its short generation time, characterized genome, or similarity to humans; examples are a fly, fish, rodent, or pig, whose biology is well known and accessible for laboratory studies.

Origin of transfer (oriT)

An origin of transfer (oriT) is a short sequence (up to 500 bp) that is necessary for transfer of the DNA that contains it from a bacterial host to recipient during bacterial conjugation.

Eukaryotic

Are organisms whose cells have a nucleus enclosed within a nuclear envelope.

Predict results from a described experiment using screening with antibiotic resistance and lac Z (blue/white screening)

Blue-white screening is a rapid and efficient technique for the identification of recombinant bacteria. It relies on the activity of β-galactosidase, an enzyme occurring in E. coli, which cleaves lactose into glucose and galactose.

Differentiate blunt from sticky ends

Blunt A straight cut with no overhang. Sticky also called cohesive ends; create a staggered cut that leaves an overhang; complementary to each other and can spontaneously pair

Apply Chargaff's rule to problems on base composition.

Chargaff's rules state that DNA from any species of any organism should have a 1:1 stoichiometric ratio (base pair rule) of pyrimidine and purine bases and, more specifically, that the amount of guanine should be equal to cytosine and the amount of adenine should be equal to thymine.

Differentiate minimal medium from complete medium

Complete medium contains all the substances required by bacteria for growth and reproduction. Minimal medium contains only nutrients necessary for prototrophic (wild-type) bacteria.

Describe the use of minimal and complete media to screen bacterial colonies for mutants

Complete medium contains all the substances required by bacteria for growth and reproduction. Minimal medium contains only nutrients necessary for prototrophic (wild-type) bacteria. To isolate auxotrophic mutants that require leucine, bacteria are first grown on complete medium.

Define conjugation

Conjugation is the process by which one bacterium transfers genetic material to another through direct contact. During conjugation, one bacterium serves as the donor of the genetic material, and the other serves as the recipient. The donor bacterium carries a DNA sequence called the fertility factor, or F-factor.

Donor cell (bacterial donor)

Conjugation is the process by which one bacterium transfers genetic material to another through direct contact. During conjugation, one bacterium serves as the donor of the genetic material, and the other serves as the recipient. The donor bacterium carries a DNA sequence called the fertility factor, or F-factor.

Conjugation pilus (conjugation tube)

Conjugative pili allow for the transfer of DNA between bacteria, in the process of bacterial conjugation. They are sometimes called "sex pili", in analogy to sexual reproduction, because they allow for the exchange of genes via the formation of "mating pairs"

DNA Ligase

Connects the separated DNA segments

Identify sequences of ssDNA, dsDNA, and RNA that will form secondary structures, including: Cruciform

Cruciform DNA is a form of non-B DNA, or an alternative DNA structure. ... These inverted repeats contain a sequence of DNA in one strand that is repeated in the opposite direction on the other strand. As a result, inverted repeats are self-complementary and can give rise to structures such as hairpins and cruciforms.

Cruciform

Cruciform structures consist of a branch point, a stem and a loop, where the size of the loop is dependent on the length of the gap between inverted repeats (Figure 1). Direct inverted repeats lead to formation of a cruciform with a minimal single-stranded loop

Outline the Central Dogma of Genetics.

DNA (Transcription) mRNA rRNA RNA (Translation) AA tRNA Protein i. Amino Acid

DNA clone

DNA cloning is the process of making multiple, identical copies of a particular piece of DNA. In a typical DNA cloning procedure, the gene or other DNA fragment of interest (perhaps a gene for a medically important human protein) is first inserted into a circular piece of DNA called a plasmid.

Recall that genetic information is encoded in DNA and RNA.

DNA encodes RNA (with the help of mRNA and rRNA) RNA encodes Protein (with the help of tRNA and amino acids)

Sticky end again

DNA ends refer to the properties of the end of DNA molecules, which may be sticky or blunt based on the enzyme which cuts the DNA. The restriction enzyme belongs to a larger class of enzymes called exonucleases and endonucleases.

Describe the structure of DNA, including: composition of nucleotides, types of bonds, and polarity of strands.

DNA is made from the base pairing of adenine, guanine, thymine, and cytosine. Adenine pairs with Thymine Creates two hydrogen bonds and will be easier to break in a DNA molecule Thymine is 30% Adenine is 30% Guanine pairs with Cytosine Creates three hydrogen bonds and will be much harder to break because G and C is held together with more bonding and more energy and ATP will be used to break apart than the AT pairing Guanine is 20% Cytosine is 20% Purines Adenine Guanine Pyrimidines Thymine

DNA ligase important term

DNA ligase is an enzyme which can connect two strands of DNA together by forming a bond between the phosphate group of one strand and the deoxyribose group on another. It is used in cells to join together the Okazaki fragments which are formed on the lagging strand during DNA replication.

DNA polymerase (pol I, pol III, 5'- to 3' polymerase activity)

DNA polymerase is responsible for the process of DNA replication, during which a double-stranded DNA molecule is copied into two identical DNA molecules.

Replication fork RNA primer

DNA primase forms an RNA primer, and DNA polymerase extends the DNA strand from the RNA primer. DNA synthesis occurs only in the 5' to 3' direction. On the leading strand, DNA synthesis occurs continuously. ... Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA.

Describe what it means to say that DNA replication is semiconservative and bidirectional (bidirectional)

DNA replication in both/two directions from the starting point and two replication forks are formed spontaneously. These two replication forks moved in the opposite direction and leading and lagging strands at the two replication forks are also on opposite sides of the DNA strand starting at the origin of replication.

DNA replication (semiconservative, conservative, dispersive)

DNA replication is the process by which DNA makes a copy of itself during cell division. The first step in DNA replication is to 'unzip' the double helix structure of the DNA

Describe the stages of DNA replication, including enzymes and other proteins involved.

DNA replication requires other enzymes in addition to DNA polymerase, including DNA primase, DNA helicase, DNA ligase, and topoisomerase. In order to fit within a cell's nucleus, DNA is packed into tightly coiled structures called chromatin, which loosens prior to replication, allowing the cell replication machinery to access the DNA strands Stages Initiation Elongation

Polymerase chain reaction is an efficient way to increase the copy number of desired DNA molecule in-vitro. PCR require five major component to amplify the DNA in a tube

DNA template Taq polymerase Primers dNTPs Buffers

Dideoxynucleotide triphosphates (ddNTPs)

DdNTP refers to Dideoxynucleotides triphosphates which are used in Sanger dideoxy method to produce different lengths of DNA strands for DNA sequencing. DdNTP includes ddATP, ddTTP, ddCTP and ddGTP.

Dideoxy DNA sequencing

Dideoxynucleotides are chain-elongating inhibitors of DNA polymerase, used in the Sanger method for DNA sequencing. They are also known as 2',3' because both the 2' and 3' positions on the ribose lack hydroxyl groups, and are abbreviated as ddNTPs (ddGTP, ddATP, ddTTP and ddCTP)

Restriction Enzyme:

Enzyme that recognizes particular base sequences in DNA and makes double-stranded cuts nearby; also called a restriction endonuclease Recognize specific nucleotide sequences in DNA and make double-stranded cuts at restriction sites. Produced by bacteria and are used in defense against viruses All molecular genetics work is done with type II restriction enzymes Recognizes 4 to 8b Form sticky and blunt cuts

Elongation (transcription)

Elongation is the addition of nucleotides to the mRNA strand. RNA polymerase reads the unwound DNA strand and builds the mRNA molecule, using complementary base pairs. There is a brief time during this process when the newly formed RNA is bound to the unwound DNA. During this process, an adenine (A) in the DNA binds to an uracil (U) in the RNA.

Telomere shortening

Eukaryotic cells face a special problem in replicating the ends of their linear DNA molecules. Following removal of the RNA primer from the extreme 5' end of the lagging strand, there is no way to fill in the remaining gap with DNA. Consequently, in most normal human somatic cells, telomeres shorten with each successive cell division. Once telomeres are shortened beyond some critical length, the cell is no longer able to divide and is said to be senescent. In germ cells and other stem cells, as well as in cancer cells, telomeres do not shorten and the cells do not senesce. This is a result of the presence of a ribonucleoprotein, telomerase, which maintains telomere length in these cells.

What is the role of F factor in conjugation?

F factor contains a number of genes that take part in the conjugation process, including genes necessary for the synthesis of the sex pilus. The F factor also has an origin of replication that enables the factor to be replicated in the conjugation process.

Describe how an F' cell forms

F' Cells are Derivatives of Hfr cells where F plasmid has disintegrated from host chromosome and picks up some host genes next to F plasmid integration sites at 06:07. F plasmid is an episome so once it gets integrated into host chromosomal DNA, it can also disintegrate itself back from the host chromosome.

Identify the stages of the cell cycle.

G1 (Interphase) Increases in cell size Growth S (Interphase) Synthesis of DNA G2 (Interphase) Preparation for division M Division and mitosis

Give the phenotype and genotype of the donor and recipient cells after F+ x F- conjugation

G: F+ thr+/thr+ F- thr+/thr- P: F- and F+ can both synthesize threonine

Gel electrophoresis

Gel electrophoresis is a technique used to separate DNA fragments according to their size. DNA samples are loaded into wells (indentations) at one end of a gel, and an electric current is applied to pull them through the gel. DNA fragments are negatively charged, so they move towards the positive electrode.

Describe the association between genes and chromosomes.

Genes are segments of deoxyribonucleic acid (DNA) that contain the code for a specific protein that functions in one or more types of cells in the body. Chromosomes are structures within cells that contain a person's genes. Genes are contained in chromosomes, which are in the cell nucleus. Genes and alleles make up our chromosomes!

Define transformation

Genetic transformation is a process that involves the introduction and expression of foreign genes in a host organism. This expression can result from the extrachromosomal, or episomal, presence of genes in nuclei that may persist if the introduced DNA has a mechanism for replication.

Helicase important term

Helicases are enzymes that bind and may even remodel nucleic acid or nucleic acid protein complexes. There are DNA and RNA helicases. DNA helicases are essential during DNA replication because they separate double-stranded DNA into single strands allowing each strand to be copied.

Hybridization (of molecular probe)

Hybridization is the idea that atomic orbitals fuse to form newly hybridized orbitals, which in turn, influences molecular geometry and bonding properties. Hybridization is also an expansion of the valence bond theory.

Relate the cell cycle and its checkpoints to DNA repair.

If the checkpoint mechanisms detect problems with the DNA, the cell cycle is halted, and the cell attempts to either complete DNA replication or repair the damaged DNA. If the damage is irreparable, the cell may undergo apoptosis, or programmed cell death 2.

Identify mutations as changes in genetic information.

In biology, a mutation is an alteration in the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Can cause disease or phenotypic changes in the individual

Evolution

In biology, evolution is the change in the characteristics of a species over several generations and relies on the process of natural selection. The theory of evolution is based on the idea that all species? are related and gradually change over time.

Transmission

In medicine, public health, and biology, the transmission is the passing of a pathogen causing communicable disease from an infected host individual or group to a particular individual or group, regardless of whether the other individual was previously infected.

Translation

In molecular biology and genetics, translation is the process in which ribosomes in the cytoplasm or endoplasmic reticulum synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus. The entire process is called gene expression.

Transformation

In molecular biology transformation is genetic alteration of a cell resulting from the direct uptake, incorporation and expression of exogenous genetic material (exogenous DNA) from its surroundings and taken up through the cell membrane(s)

DNA proofreading (3'- to 5' exonuclease activity)

In proofreading, the DNA pol reads the newly added base before adding the next one, so a correction can be made. The polymerase checks whether the newly added base has paired correctly with the base in the template strand. If it is the right base, the next nucleotide is added.

Conditional mutation

In the class of conditional mutations, a mutant allele causes a mutant phenotype in only a certain environment, called the restrictive condition, but causes a wild-type phenotype in some different environment, called the permissive condition. Geneticists have studied many temperature-conditional mutations.

Initiation (transcription)

Initiation is the beginning of transcription. It occurs when the enzyme RNA polymerase binds to a region of a gene called the promoter. This signals the DNA to unwind so the enzyme can ''read'' the bases in one of the DNA strands. The enzyme is now ready to make a strand of mRNA with a complementary sequence of bases.

Recognize that some traits are influenced by multiple genes and environmental factors.

Internal and external environmental factors, like gender and temperature, influence gene expression. Similarly, drugs, chemicals, temperature, and light are among the external environmental factors that can determine which genes are turned on and off, thereby influencing the way an organism develops and functions.

Describe how data from an interrupted mating experiment are used to create a map of bacterial genes

Interrupted mating experiment involves an experiment to determine the gene order on Hfr (high frequency recombination) bacterial chromosomes. Hfr strains are those donor strains, which have integrated F-plasmids that can be transferred to recipients with high efficiency.

Differentiate between the products of mitosis and meiosis.

Mitosis Two identical daughter cells Meiosis Four sex cells

Recombinant clone

It is recombinant in the sense that it is composed of DNA from two different sources. Thus, it is a type of DNA that would be impossible naturally and is an artifact created by DNA technology. The next step in the cloning process is to cut the vector with the same restriction enzyme used to cut the donor DNA.

F- cell

Lacks fertility factor

Lagging strand

Lagging strand. The lagging strand is the strand of nascent DNA whose direction of synthesis is opposite to the direction of the growing replication fork. Because of its orientation, replication of the lagging strand is more complicated as compared to that of the leading strand.

Meiosis

Meiosis is a process where a single cell divides twice to produce four cells containing half the original amount of genetic information. These cells are our sex cells - sperm in males, eggs in females. During meiosis, one cell divides twice to form four daughter cells.

Recall that chromosomes are duplicated and separated from their duplicates via mitosis and meiosis.

Mitosis (genetic division) A type of cell division that results in two daughter cells each having the chromosomes as the parent nucleus, typical of ordinary tissue growth. Meiosis (sexual division) Meiosis is a process where a single cell divides twice to produce four cells containing half the original amount of genetic information. These cells are our sex cells - sperm in males, eggs in females. During meiosis, one cell divides twice to form four daughter cells.

Molecular genetics

Molecular genetics is the study of the molecular structure of DNA, its cellular activities (including its replication), and its influence in determining the overall makeup of an organism. Molecular genetics relies heavily on genetic engineering

Neutral mutation

No phenotypic change Theoretically, the evolutionary change of phenotypic characters can be generated by neutral or nearly neutral mutations that may be fixed in the population by chance. ... Large random phenotypic evolution may also be generated when geological changes such as mass extinction and continental drift occur.

Okazaki fragment

Okazaki fragments are short sequences of DNA nucleotides (approximately 150 to 200 base pairs long in eukaryotes) which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA replication.

Allele

One of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome.

PCR primers

PCR primers are short pieces of single-stranded DNA, usually around 20 nucleotides in length. ... That is, they are given sequences that will make them bind to opposite strands of the template DNA, just at the edges of the region to be copied. The primers bind to the template by complementary base pairing.

Describe what it means to say that DNA replication is semiconservative and bidirectional (semiconservative)

Presented by watson and crick In semiconservative replication each strand of the original DNA molecule serves as a template for the production of its counterpart/complementary and produced two daughter double stranded ds DNA molecules each of them has one original template strand and and one newly synthesized DNA.

Primase

Primase is an enzyme that synthesizes short RNA sequences called primers. These primers serve as a starting point for DNA synthesis. Since primase produces RNA molecules, the enzyme is a type of RNA polymerase.

The phrases or terms below describe different fundamental processes of nuclei acids. Sort each phrase or term as relating to replication, transcription, or translation.

Replication Both DNA strands are duplicated, described as semi-conservative, DNA polymerase Transcription Single DNA strand is used to produce mRNA Translation Amino acids added to peptide chain, requires RNA, ribosome

Define STRs (short tandem repeats) and describe how these might vary among different alleles for a single gene.

Short tandem repeats (STRs), which are sometimes referred to as microsatellites or simple sequence repeats (SSRs), are accordion-like stretches of DNA containing core repeat units of between two and seven nucleotides in length that are tandemly repeated from approximately a half dozen to several dozen times

Prokaryotic

Prokaryotes are single-celled organisms of the domains Bacteria and Archaea. All prokaryotes have plasma membranes, cytoplasm, ribosomes, a cell wall, DNA, and lack membrane-bound organelles.

Differentiate between prokaryotic and eukaryotic cells in terms of cell size (see figure 2.1), complexity, and presence/absence of nuclear membrane and membrane-bound organelles.

Prokaryotic No membrane-bound nucleus Smaller Has no membrane-bound organelles Unicellular/Circular One chromosome is present, but more than one chromosome plasmid Eukaryotic Larger/Linear Has a membrane bound nucleus Has membrane-bound organelles Many chromosomes Multicellular

Initiation (translation)

Protein synthesis begins with the formation of an initiation complex. In E. coli, this complex involves the small 30S ribosome, the mRNA template, initiation factors and a special initiator tRNA. The initiator tRNA interacts with the start codon AUG. Guanosine triphosphate (GTP), which is a purine nucleotide triphosphate, acts as an energy source during translation Both at the start of elongation and during the ribosome's translocation. Once the appropriate AUG is identified, the 50S subunit binds to the complex of Met-tRNAi, mRNA, and the 30S subunit. This step completes the initiation of translation.

Describe the structure of RNA, including: composition of nucleotides, types of bonds, and polarity of strands.

RNA consists of four nitrogenous bases: adenine, cytosine, uracil, and guanine. Uracil is a pyrimidine that is structurally similar to thymine, another pyrimidine that is found in DNA. Like thymine, uracil can base-pair with adenine Held by two H bonds

Loss-of-function mutation

Recessive mutations lead to a loss of function, which is masked if a normal copy of the gene is present. For the mutant phenotype to occur, both alleles must carry the mutation. Dominant mutations lead to a mutant phenotype in the presence of a normal copy of the gene.

Explain how recombinant DNA technology is used to clone genes using plasmid vectors.

Recombinant DNA technology enables individual fragments of DNA from any genome to be inserted into vector DNA molecules, such as plasmids, and individually amplified in bacteria. Each amplified fragment is called a DNA clone.

DNA Topoisomerase

Relaxes the supercoiled DNA

Define restriction fragment length polymorphism (RFLP), and describe the utility of RFLP analysis in identifying individuals

Restriction Fragment Length Polymorphism (RFLP) is a molecular method of genetic analysis that allows individuals to be identified based on unique patterns of restriction enzyme cutting in specific regions of DNA

RFLP

Restriction fragment length polymorphism (RFLP) is a type of polymorphism that results from variation in the DNA sequence recognized by restriction enzymes. These are bacterial enzymes used by scientists to cut DNA molecules at known locations. RFLPs (pronounced "rif lips") are used as markers on genetic maps

Identify the products of meiosis.

Results in four sex cells

Identify the products of mitosis.

Results in two IDENTICAL daughter cells

Ribonucleic acid (RNA)

Ribonucleic acid, a nucleic acid present in all living cells. Its principal role is to act as a messenger carrying instructions from DNA for controlling the synthesis of proteins, although in some viruses RNA rather than DNA carries the genetic information.

Placing the events in chronological order, starting from the poisoning of ricin and ending with the death of the victim.

Ricin enters the victim's body Ricin absorbed into the blood and enters the body cells Ricin binds to the ribosome in the cytoplasm Ricin inactivates the 28S rRNA in the large subunit of the ribosomes Ribosomes are unable to add new amino acids to polypeptides Protein synthesis halts in many tissues Multiple organ systems fail The victim dies

SNP

SNP stands for "Single Nucleotide Polymorphism". A SNP is the most common type of genetic variation, and may occur every 100 to 300 bases.

How sanger allows for sequencing of DNA

Sanger sequencing involves making many copies of a target DNA region. Its ingredients are similar to those needed for DNA replication in an organism, or for polymerase chain reaction (PCR), which copies DNA in vitro. They include: -A DNA polymerase enzyme. -Sanger sequencing results in the formation of extension products of various lengths terminated with dideoxynucleotides at the 3′ end. -The extension products are then separated by Capillary Electrophoresis. -The molecules are injected by an electrical current into a long glass capillary filled with a gel polymer. -Dideoxynucleotides are chain-elongating inhibitors of DNA polymerase, used in the Sanger method for DNA sequencing -> This can lead to the termination of the DNA sequence. Thus, these molecules form the basis of the dideoxy chain-termination method of DNA sequencing, which was developed by Frederick Sanger in 1977.

Palindrome

Sequence that reads the same backward as forward

Diagram/identify/describe the major events in the phases of meiosis.

Since cell division occurs twice during meiosis, one starting cell can produce four gametes (eggs or sperm). In each round of division, cells go through four stages: prophase, metaphase, anaphase, and telophase.

Deoxynucleoside 5'- triphosphates (dNTPs)

Since the purpose of the technique is to synthesize new DNA, dNTP provides nucleotides to the "unzipped" strand using the template of a single side. This turns a single strand of DNA into two, and can continue exponentially as long as reagents remain present until the final hold stage.

Define single nucleotide polymorphism (SNP), and describe the utility of SNPs in identifying individuals

Single nucleotide polymorphisms, frequently called SNPs (pronounced "snips"), are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block, called a nucleotide. Most SNPs have no effect on health or development.

Single-stranded binding (SSB) protein

Single-stranded DNA-binding protein (SSB) binds to single-stranded regions of DNA. ... During DNA replication, SSB molecules bind to the newly separated individual DNA strands, keeping the strands separated by holding them in place so that each strand can serve as a template for new DNA synthesis.

Differentiate somatic from germ-line mutations, and state which type is heritable.

Somatic mutations - occur in a single body cell and cannot be inherited (only tissues derived from mutated cell are affected) ... Germline mutations - occur in gametes and can be passed onto offspring (every cell in the entire organism will be affected)

Polymerase chain reaction (PCR)

Sometimes called "molecular photocopying," the polymerase chain reaction (PCR) is a fast and inexpensive technique used to "amplify" - copy - small segments of DNA. Because significant amounts of a sample of DNA are necessary for molecular and genetic analyses, studies of isolated pieces of DNA are nearly impossible without PCR amplification.

Southern blotting

Southern blotting is a laboratory technique used to detect a specific DNA sequence in a blood or tissue sample. A restriction enzyme is used to cut a sample of DNA into fragments that are separated using gel electrophoresis. The DNA fragments are transferred out of the gel to the surface of a membrane.

Describe the stages of DNA replication, including enzymes and other proteins involved.

Step 1 Sequences of recognition complex are recognized by pre RC components and form initiation complex which then attach helicase which melt the DNA . Step 2 Single strand binding protein (ssb) binds the separated strands and prevents them from rejoining . Step 3 Topoisomerase is also bound to relax the load of unwrapping then DNA polymerase III binds the strands and makes polymerization by adding nucleotides in leading strands; it happens in 5 ' to 3' direction. In the other strand First, primase add some DNA primer in the 5 to 3 ' direction and then DNA polymerase II acts in synthesizing short okazaki fragments Then, finally both have to be treated by primase and then RNA pol ii removes the RNA primer and fills the gaps by DNA bases and ligases to ligate the okazaki fragments.

Systematic replication

Studies also use different procedures to replicate the original study, but has some logical connections with the original procedure. They attempt to extend the study findings to other settings

Direct replication

Studies use the same experimental procedures as used by the original study as far as possible, that is more or less the same tools, design and method of statistical analysis. Thus, these kinds of replication studies have more confirmatory power. Such studies help in controlling the sampling errors and artifacts, and adds on to the information regarding the reliability and validity of the original work.

Regulatory mutation

Such a mutation - loss of an enhancer element - is called a regulatory mutation. It affects the spatial or temporal regulation of the gene without causing universal loss of the gene product.

Bacterial chromosome

The bacterial chromosome is one long, single molecule of double stranded, helical, supercoiled DNA. In most bacteria, the two ends of the double-stranded DNA covalently bond together to form both a physical and genetic circle.

Describe the stages of transcription, including enzymes and other proteins involved. Textbook section 15.5

Summary The process in which cells make proteins is called protein synthesis. It actually consists of two processes: transcription and translation. Transcription takes place in the nucleus. It uses DNA as a template to make an RNA molecule. RNA then leaves the nucleus and goes to a ribosome in the cytoplasm, where translation occurs Translation reads the genetic code in mRNA and makes a protein. Transcription is the first part of the central dogma of molecular biology: DNA → RNA. It is the transfer of genetic instructions in DNA to messenger RNA (mRNA). During transcription, a strand of mRNA is made that is complementary to a strand of DNA. Figure 1 shows how this occurs.

Describe the stages of translation, including enzymes and other proteins involved

Summary Translation reads the genetic code in mRNA and makes a protein. As with mRNA synthesis, protein synthesis can be divided into three phases: initiation, elongation, and termination. The process of translation is similar in prokaryotes and eukaryotes.

Termination (transcription)

Termination is the ending of transcription, and occurs when RNA polymerase crosses a stop (termination) sequence in the gene. The mRNA strand is complete, and it detaches from DNA.

Termination (translation)

Termination of translation occurs when a stop codon, or nonsense codon (UAA, UAG, or UGA) is encountered. Upon aligning with the A site, these stop codons are recognized by release factors in prokaryotes and eukaryotes that instruct peptidyl transferase to add a water molecule to the carboxyl end of the P-site amino acid. This reaction forces the P-site amino acid to detach from its tRNA, and the newly made protein is released. The small and large ribosomal subunits dissociate from the mRNA and from each other; they are recruited almost immediately into another translation initiation complex. After many ribosomes have completed translation, the mRNA is degraded so the nucleotides can be reused in another transcription reaction.

Central Dogma

The 'Central Dogma' is the process by which the instructions in DNA are converted into a functional product. It was first proposed in 1958 by Francis Crick, discoverer of the structure of DNA

Elongation (translation)

The 50S ribosomal subunit of E. coli consists of three compartments A (aminoacyl) site Binds incoming charged aminoacyl tRNAs. The P (peptidyl) site Binds charge tRNAs carrying amino acids that have formed peptide bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA. The E (exit) site Releases dissociated tRNAs so that they can be recharged with free amino acids. This creates an initiation complex with a free A site ready to accept the tRNA corresponding to the first codon after the AUG. Elongation proceeds with charged tRNAs entering the A site and then shifting to the P site followed by the E site with each single-codon "step" of the ribosome. Ribosomal steps are induced by conformational changes that advance the ribosome by three bases in the 3′ direction. The energy for each step of the ribosome is donated by an elongation factor that hydrolyzes GTP. Peptide bonds form between the amino group of the amino acid attached to the A-site tRNA and the carboxyl group of the amino acid attached to the P-site tRNA. The formation of each peptide bond is catalyzed by peptidyl transferase, an RNA-based enzyme that is integrated into the 50S ribosomal subunit. The energy for each peptide bond formation is derived from GTP hydrolysis, which is catalyzed by a separate elongation factor. The amino acid bound to the P-site tRNA is also linked to the growing polypeptide chain. As the ribosome steps across the mRNA, the former P-site tRNA enters the E site, detaches from the amino acid, and is expelled

Using the codon table, what conclusions can be drawn about the genetic code?

The 64 codons are roughly evenly distributed between amino acid codons and stop codons. Many amino acids are encoded by multiple codons.

Mutation

The changing of the structure of a gene, resulting in a variant form that may be transmitted to subsequent generations, caused by the alteration of single base units in DNA, or the deletion, insertion, or rearrangement of larger sections of genes or chromosomes.

F (fertility) factor (F plasmid)

The donor bacterium carries a DNA sequence called the fertility factor, or F-factor. The F-factor allows the donor to produce a thin, tubelike structure called a pilus, which the donor uses to contact the recipient.

F' cell (F' donor)

The donor cell usually the "default"

Blunt ends

The end of a DNA fragment resulting from the breaking of DNA molecule in which there are no unpaired bases, hence, both strands are of the same length.

Minor groove

The minor groove occurs where they are close together.

Genotype

The genetic constitution of an individual organism.

Genome

The haploid set of chromosomes in a gamete or microorganism, or in each cell of a multicellular organism. The complete set of genes or genetic material present in a cell or organism.

Leading strand

The leading strand is a single DNA strand that, during DNA replication, is replicated in the 3' - 5' direction (same direction as the replication fork). DNA is added to the leading strand continuously, one complementary base at a time

Major groove

The major groove occurs where the backbones are far apart. The grooves twist around the molecule on opposite sides. Certain proteins bind to DNA to alter its structure or to regulate transcription (copying DNA to RNA) or replication (copying DNA to DNA).

Origin of replication

The origin of replication (also called the replication origin) is a particular sequence in a genome at which replication is initiated. ... This can either involve the replication of DNA in living organisms such as prokaryotes and eukaryotes, or that of DNA or RNA in viruses, such as double-stranded RNA viruses.

Define a partial diploid

The partial diploid has one copy of most genes (on the chromosome) but has two copies of a few genes. For these few genes, there is one copy of the gene(s) on the chromosome and one copy on the extra DNA.

Erwin Chargaff's experiments on the composition of DNA provided clues about the structure of DNA. Select the statements that describe what Chargaff discovered about the base pair composition of DNA.

The proportions of A:T base pairs and C:G base pairs are similar for members of the same species and vary between species DNA molecules contain similar numbers of A and T bases and similar numbers of G and C bases

Which of the events occur during eukaryotic translation initiation?

The small ribosomal subunit binds with a specific tRNA to the mRNA and scans for a start codon.

Hairpin/stem-loop

The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop.

Genetics

The study of heredity and the variation of inherited characteristics.

Sugar-phosphate backbone

The sugar phosphate backbone is an important structural component of DNA. It consists of 5-carbon deoxyribose sugars and phosphate groups. These sugars are linked together by a phosphodiester bond, between carbon 4 of their chain, and a CH2 group that is attached to a phosphate ion.

Conjugation

The temporary union of two bacteria or unicellular organisms for the exchange of genetic material.

Describe how genes are related to phenotype.

The term "phenotype" refers to the observable physical properties of an organism; these include the organism's appearance, development, and behavior. An organism's phenotype is determined by its genotype, which is the set of genes the organism carries, as well as by environmental influences upon these genes. Mutations in genes can cause phenotypic changes in an individual

Western blotting

The western blot (sometimes called the protein immunoblot), or western blotting, is a widely used analytical technique in molecular biology and immunogenetics to detect specific proteins in a sample of tissue homogenate or extract. In brief, the sample undergoes protein denaturation, followed by gel electrophoresis.

Telomerase

This complex contains a protein (Tert) that acts as a reverse transcriptase and a short piece of RNA (Terc) that acts as a template. The CA-rich RNA template base-pairs with the GT-rich, single-stranded 3' end of telomeric DNA. The reverse transcriptase uses the RNA template to synthesize DNA in the usual 5 →3 direction, extending the already longer 3' end. Telomerase then translocates to the newly synthesized end, and the process is repeated. Once the GT-rich strand has been lengthened, the primase activity of DNA pol α can use it as a template to synthesize an RNA primer. The RNA primer is extended by DNA pol α, and then removed.

Time-of-entry mapping

Time of entry mapping can be used to order genes for a particular Hfr strain. By combining results from multiple Hfr strains it is possible to construct a detailed map ordering the genes. The F factor may sometimes carry pieces of bacterial DNA with it if it leaves the E

Topoisomerase

Topoisomerases (or DNA topoisomerases) are enzymes that participate in the overwinding or underwinding of DNA. The winding problem of DNA arises due to the intertwined nature of its double-helical structure. During DNA replication and transcription, DNA becomes overwound ahead of a replication fork.

Transcription

Transcription is the process by which the information in a strand of DNA is copied into a new molecule of messenger RNA (mRNA). DNA safely and stably stores genetic material in the nuclei of cells as a reference or template.

Helicase

Unwinds the DNA double helix

F+ cell (F+ donor)

We know plasmid is an extrachromosomal DNA that can replicate independently. It is called F plasmid because it has F factor which is a Fertility factor. This fertility factor contains the genes required for the transfer or conjugation. F+ Cells = Cells containing F plasmid (F plasmid = Plasmid containing F factor)

Restriction endonuclease (restriction enzyme)

an enzyme produced chiefly by certain bacteria, having the property of cleaving DNA molecules at or near a specific sequence of bases.

Describe the classes of RNA. Replication Textbook section 12.3

rRNA Ribosomal RNA Assists in the translation of RNA to protein rRNA is a ribozyme that carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits tRNA Transfer RNA Assists in the translation of RNA to protein Transfer ribonucleic acid (tRNA) is a type of RNA molecule that helps decode a messenger RNA (mRNA) sequence into a protein. tRNAs function at specific sites in the ribosome during translation, which is a process that synthesizes a protein from an mRNA molecule mRNA Messenger RNA Assists in the transcription of DNA to RNA mRNA molecules carry the genetic information needed to make proteins. They carry the information from the DNA in the nucleus of the cell to the cytoplasm where the proteins are made.

Differentiate plasmids from the bacterial genome

​Plasmid A plasmid is a small, often circular DNA molecule found in bacteria and other cells. Plasmids are separate from the bacterial chromosome and replicate independently of it. They generally carry only a small number of genes, notably some associated with antibiotic resistance.