unit exam 1 Flashcards
What is biological diversity?
reflects an interaction between the forms that preceded them and an ongoing process of change
All species are temporary what is as much a part of nature as is the formation of new species ?
extinction
What are the requirements for evolution (by natural selection)?
- Variation in a population
these can be phenotypes, traits, ext.
- in between variation and increased survival or reproduction is SELECTIVE PRESSURE this is needed for evolution, this can be seen in terms of availability or avoid being the food
- increased survival or reproduction
- Inheritance of traits
this can be inheritance to next generation/offspring
- from inheritance of traits to variation in a population is MUTATIONS
- mutations increase evolution/population
- repeats back to variation
- variation shrinks overtime due to selective traits
what is the definition of genetics?
study of heredity and variation in cells, individuals and populations
what is the definition of a gene?
functional unit of heredity and variation (hence genetics is simply the study of genes)
- also the DNA sequence that is involved in making RNA and protein
what is molecular genetics?
is the “study of structure and function of genes at the molecular level”
what is the definition of alleles?
variant forms of a gene caused by differences in DNA sequence (e.g variation in eye colour, height)
what is the definition of a genotype ?
gene(s) inherited by an organism
what is the definition of a phenotype?
visible traits (e.g body plan, behaviour, illnesses/diseases)
what is the definition of a genome?
entire DNA sequence (ACGT) of an organism
what is gene expression?
Genes: found on chromosomes and are parts of the genome that encode RNA and protein
gene expression= “turning on” a gene to produce RNA and protein (coding gene)
what is protein expression? and what do protein determine?
the type and abundance of protein in the cell.
- Although DNA is the information molecule that directs protein expression, proteins ultimately determine the phenotype of the cell because they control every reaction in the cell
what are enzymes?
catalyzing the synthesis and transformation of all biomolecules
what are structural proteins?
they are the proteins used for maintenance of cell shape
what are signalling proteins?
these are proteins used for hormones and receptors
what factors make individuals different from one another?
This is known as phenotypic variation
- different alleles ( the slight difference in gene sequence can result in changes in the amino acid sequence of proteins) - the genotype
- different regulation of gene and protein expression
when will similar protein expressions and phenotypes occur?
when individuals possess common alleles and gene regulation
- this can be immediate family, relatives
what are some ways studying molecular genetics important?
human health, forensics, agriculture, environment, and evolutionary biology
differentiate the differences between proteins and nucleic acids (DNA) when the candidates is chromosomes?
PROTEINS:
-20 subunit variants (amino acids)
- majority component of chromosomes (~50-60%)
- many chemical properties and secondary structure
- enzyme activity
NUCLEIC ACIDS (DNA)
- 4 subunit variants (nucleotides)
- minority component of chromosomes (~40-50%)
- few chemical properties and low 2 degree structure
- functionally inert
What were the three classical experiments ranked in order to establish DNA as the hereditary molecule?
- Griffith: found a substance that could genetically transform streptococcus pneumonia ( one strain to another strain)
- Avery, Macleod and McCarty: identified DNA as the molecule that transforms rough S. pneumonia to the infective form
- Hershey and Chase : found the final evidence establishing DNA as the hereditary molecule
what is strepococcus pneumoniae?
bacterial pathogen that causes pneumonia in mammals
what is smooth strain (S)?
bacterium is surrounded by a polysaccharide capsule ( this interacts in respiratory trait in animals)
- the capsule protects the S strain from the immune system, thereby allowing infection
what is rough strain (R) ?
lacks polysaccharide capsule, cannot evade the immune system, thereby is known as non-virulent
- this is a mutation in the gene so it cant get in/invade the immune system
Explain the Griffith experiment? What was his conclusion?
he basically had to bacteria one that was virulent, and one that was nonvirulent.
- the mouse with virulent (SMOOTH) bacteria died of pneumonia and the mouse with the nonvirulent bacteria (ROUGH) remained healthy.
- he then heat killed the virulent bacteria. the mouse remained healthy
- he then mixed dead virulent bacteria (SMOOTH) with nonvirulent bacteria (ROUGH) this transformed the rough cells to virulent cells, it caught something in the environment changing the phenotype of these cells
CONCLUSION:
some molecules (TRANSFORMING PRINCIPLE) released when S cells were killed could transform living R cells genetically to the virulent S form
- transformation was permanent and heritable ( all progeny cells in the colony were the same type)
Explain the Avery, Macleod, and McCarty experiment?
Hypothesis, experimental approach, and conclusion
there main concept was the question what is the chemical nature of the transforming principle?
HYPOTHESIS: transforming principle could be protein, DNA or RNA- which one?
EXPERIMENTAL APPROACH: eliminate each type of molecule in S cells and see whether transformation of R cells into the S virulent form still occurs
CONCLUSION: if type of molecule is absent, and transformation is gone, then this molecule is the transforming principle
what is the life cycle of a virus (bacteriophage)?
- infection : massive reproduction of a virus resulting in host cell lysis (virulent)
- Viral DNA replicates separately from bacterial chromosome
- Lysogenic cycle replication of viral genome (latent)
- Viral DNA is integrated into the bacterial chromosome.
- Lysogeny can switch to lytic cycle if viral DNA is excised from bacterial chromosome
explain the lytic pathway in detail?
after the circularization of viral DNA, the viral DNA hijackes cellular bacteria and produce more protein
- there is a replication of viral DNA, RNA and protein; bacterial chromosome degradation
- then there is an assembly into progeny viral particles
- cell lysis and mature phage are released they rupture
explain the lysogeny pathway in detail?
- Viral DNA inserts into bacterial chromosome by recombination (Prophage)
- Prophage hitches a ride and replicates; viral genes are inactive
- prophage is inherited in bacterial daughter cells
explain the Hershey and Chase experiment?
there main concept was: Does the bacteriophage inject DNA or protein into E.coli?
- label bacteriophage DNA and proteins with radioactive isotopes 32P and 35S respectively
- allow infection of E.coli with radioactive bacteriophage
- separate attached bacteriophage and E.coli with blender (NO CELL IS RUPTURED)
- look for presence of 32P (DNA) and 35S (PROTEIN) in detached bacteriophage, E.coli cells and progeny bacteriophage (not shown)
RESULTS:
- There was no 35S in E.coli cells, 35S found in detached bacteriophages; no 35S in progeny bacteriophage (NOT HERITABLE)
- 32P in E.coli ; no 32P found in detached bacteriophages; 32P in progeny bacteriophage (HERITABLE)
Explain how gene expression produce a phenotype?
Gene expression involves the transcription of DNA into mRNA followed by translation of mRNA into proteins, determining which proteins are produced and in what quantities. Protein expression, a critical outcome of gene expression, directly influences cellular functions and processes, ultimately shaping an organism’s phenotype through the proteins’ roles in metabolism, structure, signaling, and regulation within cells and tissues. Thus, the intricate regulation and coordination of gene and protein expression are fundamental to the manifestation of observable traits and characteristics in living organisms.
explain how alleles, as well as differential regulation of gene and protein expression can cause a variation in phenotype?
Alleles are different versions of the same gene that can lead to variations in protein structure or expression levels. Differential regulation of gene and protein expression means that genes can be turned on or off, or their expression levels can be adjusted, influencing which proteins are produced and in what amounts. These variations in alleles and regulatory mechanisms can lead to differences in phenotype, such as differences in appearance, behavior, or susceptibility to diseases among individuals
What is the function of the gene involved in transforming R cells to S cells?
The gene responsible for transforming R cells to S cells is typically a gene encoding a capsule in bacteria like Streptococcus pneumoniae. The capsule gene allows bacteria to produce a protective polysaccharide capsule around themselves. This capsule enhances the bacteria’s ability to evade the host immune system by preventing phagocytosis, ultimately increasing the bacteria’s virulence and ability to cause disease
design an experiment that would test if lipids were the tranformation molecule?
To test if lipids could be the transformation molecule, you could design an experiment where R cells (non-virulent strain) are exposed to purified lipids extracted from S cells (virulent strain). Control groups could be exposed to lipids from non-virulent strains or no lipids at all. After exposure, assess the transformation by observing any phenotypic changes indicative of virulence, such as capsule formation or increased pathogenicity in animal models. Analyzing gene expression related to capsule production could also provide insights into the mechanism of transformation.
what are the components of DNA?
- PENTOSE SUGAR:
- ribose (RNA) or deoxyribose (DNA) - Nitrogenous Base
- Purine (Guanine; Adenine) or
- pyrimidine (cytosine;uracil; thymine) - Phosphate
How do pentose sugars differ from DNA to RNA?
The two sugars for RNA and DNA only differ in the type of chemical group bound to the 2’ carbon
What do the Nitrogenous bases of DNA and RNA consist of?
whats the pairing rule?
DNA: A,C,G,T
RNA: A,C,G,U
A-T
G-C
with rna its the same except
A-U
what are adenine and guanine known as, and what is thymine and cytosine known as?
adenine and guanine is known as purines
and
thymine and cytosine is known as pyrimidines
what did Watson and Crick discover ?
- two strands of the phosphate-pentose backbone spiral as a double helix about a common axis
- the two strands run antiparallel (one strand is 5’-3’ direction while the other strand is 3’-5’)
- A purine on one strand is always base-paired with a pyrimidine ( fits chargaffs rule and the 2 nm diameter of the double helix)
- studying their model, they saw that the backbone (exterior) is hyrophilic; the bases (interior) are hydrophobic
what are some factors we need to consider that makes the structure of the DNA DOUBLE HELIX?
- base pairing is COMPLEMENTARY and therefore base pair sequence on one strand can be used to specify the sequence of the other strand
- base pairs are STACKED flat lying perpendicular to the axis and contribute to stability of double helix (hyrdophobic wanderwalls)
- hydrogen bonding between bases keeps two strands intact
How many hydrogen bonds does guanine and cytosine have?
and how many adenine and thymine hydrogen bonds have?
G-C= 3 BONDS
A-T= 2 BONDS
How can we create nucleic acid hybridization?
annealing (which means heating or cooling) of single strands of DNA or RNA by forming H-bonds
- highly specific (two strands must be complementary in sequence), temperature-driven and concentration-dependent
- Hybrids can be formed through denaturing conditions such as heat, alkali
- or cooling down which is known as reannealing
- it can also denature and add RNA
- RNA hybridizes to complementary DNA strand
What was the watson and crick’s model of DNA replication?
- complementary base pairing allows parental strands to act as templates for DNA replication of new strands
- parental strands can unwind by breaking the hydrogen bonds between bases
what is semiconservative replication?
where the double helix will contain a parental strand and a newly synthesized strand
How is DNA organized in prokaryotes and eukaryotes?
-In prokaryotes, DNA is organized into a single, circular chromosome located in a region called the nucleoid. In eukaryotes, DNA is organized into multiple, linear chromosomes contained within a membrane-bound nucleus, with DNA wrapped around histone proteins to form chromatin.
what is a chromatin?
a given region of DNA with its associated proteins on a chromosome
chromonsomes can either be what?
linear or circular
prokaryotes typically have what when DNA is organized?
one chromosome (predominantly circular) and other small independent circular DNA called plasmids in the cytoplasm
eukaryotes chromosomes look like what, and where can they be found?
linear and enclosed in a nucleus
what is an essential component of eukaryotic chromosomes?
- the chromosomes need to be fully duplicated (DNA REPLICATION) and properly transmitted to each daughter cell during mitosis/meiosis
what are the three components of a eukaryotic chromosome structure ?
- origins of replication
- centromeres
- telomeres
what is the role of the origin of replication in eukaryotic chromosomes?
DNA sequences along chromosome which initiate DNA replication
what is the role of the centromere in eukaryotic chromosomes?
DNA sequences required for correct segregation of chromosomes by directing formation of the kinetochore in which the mitotic spindle attaches
what is a ploidy?
the number of chromosome sets of a cell or species
label each part
what is a constitutive heterochromatin ?
these are regions where DNA is always highly compacted. (CENTROMERES AND SUB-TELOMERIC REGIONS), THESE ARE AREAS WITH NO ACTIVE GENES PRESENT
how can you identify the 5’ and 3’ ends of a double stranded piece of DNA?
The 5’ end has a phosphate group (P) not attached to another nucleotide.
The 3’ end has a hydroxyl group (OH) on the sugar.
label the DNA structure
what is a semiconservative model of DNA replication?
each daughter strand remains paired with its complementary parental strand
what is the conservative model of DNA replication consist of?
after replication, both daughter strands pair up
what is the dispersion model of DNA replication?
daughter strands will have a mixture of parental and newly-synthesized DNA
what is the Meselson and Stahl experiment?
to determine how DNA replicates.
the method was to use nitrogen isotopes 15N and 14N to label DNA and track parental and newly synthesized strands over several generations
- initial labelling: bacteria are grown in a medium with 15N (heavy nitrogen) which gets incorporated into the DNA
- switch to 14 N medium :
bacteria are then transferred to a medium with 14N (light nitrogen) and allowed to replicate - DNA analysis after each replication
- after one round of replication: DNA is a hybrid with one strand of 15N and one strand of 14N
- after two rounds of replication: half of the DNA is hybrid (15N/14N)
and half is fully 14N (light)
key findings: after one replication cycle, DNA is hybrid. After two cycles, you get both hybrid and light DNA
what are the properties of DNA polymerases?
- synthesizes the new strand only in the 5’-3’ direction ( it can only add new bases to the 3-OH’ end of the existing strands)
- cannot synthesize a new strand
- requires a RNA primer with a 3’-OH for synthesis
- DNA polymerase has a single active site that can catalyze the incorporation of all four nucelotides
what is the job of the helicase enzyme?
An enzyme that untwists the double helix of DNA at the replication forks helix by breaking
the hydrogen bonds
- unwinds double helix, RNA primase lays down RNA primer
what is the role of the single-strand binding protein?
it stabilizes the single strands before replication by preventing reannealing so that the strands can serve as template
what is the job of the primase DNA replication enzyme?
makes a starting point (primer) for synthesis
-synthesized RNA primers for DNA polymerase
What is the DNA polymerase III as a DNA replication enzyme?
synthesizes DNA by adding nucleotides to the new DNA strand it builds new DNA
- extends RNA primer
What is the role of DNA polymerase I? as an enzyme
replaces RNA primer with DNA
- removes RNA primer and fills the gaps with DNA
- removes RNA primer of Okazaki fragments and fills in gap with dNTPs
What are the key things we need to know about the replication forks, and the sites of DNA synthesis?
- synthesizes if the two strands from the template strands occurs concurrently at the forks
- however, because DNA polymerase can only synthesize in the 5’-3’ direction
- one new strand is synthesized continuously (leading strand)
- while the other new strand is synthesized discontinuously (lagging strand) in small DNA fragments (Okazaki fragments)
what is DNA topoisomerase/gyrase as a DNA replication enzyme?
removes super coils that form ahead of the replication fork, relieves torque of mainly circular
DNA
- prevents twisting ahead of replication fork during unwinding
lable the parts of DNA of bacterial chromosomes
Draw out how DNA replication is happening at a fork for eukaryotic?
- leading is always from 3’ to 5; but synthesises 5’ to 3’
- lagging is the opposite way going from 5’ to 3’ but in lagging strands or okazaki fragments
what is a polymerase chain reaction or PCR?
Polymerase Chain Reaction (PCR) is a technique used to amplify a specific segment of DNA, making millions of copies from a small initial sample. It involves repeated cycles of heating to separate the DNA strands, cooling to allow primers to attach, and using DNA polymerase to replicate the DNA. This process enables researchers to analyze the amplified DNA in various applications, such as genetic testing and research.
what is the dilemma to replicate ends of linear chromosomes ?
- RNA primer : DNA synthesis needs an RNA primer to start, which creates a problem at the 3’ ends of linear chromosomes
Gap at chromosome ends: no DNA polymerase can fill in the gaps where the RNA primers were removed at the ends of chromosomes - Additive loss: each round of DNA replication leads to a loss of a small portion of DNA from the ends of chromosomes (telomeres)
what is the solution to end the replication problem (telomeres)?
- noncoding single stranded DNA added to the 3’ end of chromosomes by Telomeres
- usually repeats of 5-8 G’s and T’s
- telomeres will be worn away after each DNA/ cell division
- when the telomere region is gone, the cell stops dividing
what are the proofreading activities of DNA polymerases?
- synthesis direction - DNA polymerase III synthesizes new DNA in the 5’ to 3’ direction
- optimal conformation: the active site of DNA polymerase III is shaped to add the correct nucleotide
- Error detection and removal: DNA polymerase III can detect mistakes (mismatched nucleotides)
- it uses its proofreading activity to remove the incorrect nucleotide - Correction and continuation
- after removing the wrong nucleotide, DNA polymerase III adds the correct one and continuous DNA synthesis - High fidelity: polymerases with proofreading abilities significantly reduce the error rate
what is a nucelotide?
nucleoside molecule and a phosphate
- the phosphate group is attached to a carbon- 5 of the ribose and deoxyribose sugars
