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184 Cards in this Set

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ribozymes

Some RNA molecules, called ribozymes have enzymatic activity. The ribozyme and the substrate may be two seperate RNA molecules, or two domains of the same RNA molecule.

Why do smaller animals eat more (as % of their own mass) than larger animals?

r = 1 cm, surface area to volume ratio is ~3:1


r = 10 cm, surface area to volume ratio is ~1:3



Smaller cells have greater surface area to volume ratio.


-as the radius increases, the increase in volume is faster than the increase in cell surface area


-high surface area to volume ratio means more membrane area per unit of volume: this is important for the interactions between the cell and its environment


-smaller cells can interact with their surroundings more efficiently


-smaller cells are also more likely to lose energy as heat to their surroundings


-smaller animals eat more (as % of their own mass) than larger animals

Prokaryotes are different than Eukaryotes why?

Prokaryotes (Bacteria and Aarchaea) lack a nuclear envelope, organelles, and a cytoskeleton.



Eukaryotes have a nuclear envelope (the defining feature), organelles, and a cytoskeleton.



What are some characteristics of a prokaryotic cell?

+no nucleus
+no organelles
+single chromosome (in the nucleoid area) + plasmids
+cell wall
+capsule

+no nucleus


+no organelles


+single chromosome (in the nucleoid area) + plasmids


+cell wall


+capsule

Are prokaryotes the most diverse cells?

Yes

Where do photosynthetic bacteria obtain energy?

They obtain energy from sunlight.



+these cells have an internal system of membranes where photosynthesis occurs (in photosynthetic eukaryotes such as plants, this system of membranes is the organelle chloroplast.


In the cyanobacteria Anabaena cylindrica, what are the three specialized cells?

1.  nitrogen-fixing (H, incorporate atmospheric N2 into organic compounds)
 
2.  photosynthetic (V, incorporate atmospheric CO2 into organic compounds using sunlight energy)
 
3. Also, they have S, weather resistant spores.

1. nitrogen-fixing (H, incorporate atmospheric N2 into organic compounds)



2. photosynthetic (V, incorporate atmospheric CO2 into organic compounds using sunlight energy)



3. Also, they have S, weather resistant spores.

How do Beggiatoa derive energy from their environment?

They can fix carbon dioxide but they derive energy from oxidation of hydrogen sulfide.
 
Hydrogen sulfide is an inorganic substance from the environment.  These cells can fix carbon dioxide in the dark.

They can fix carbon dioxide but they derive energy from oxidation of hydrogen sulfide.



Hydrogen sulfide is an inorganic substance from the environment. These cells can fix carbon dioxide in the dark.

What are the 3 "new" domains of life, based on molecular evolution?

What is the defining feature of Eukaryotic cells?

The nucleus. It contains most of the DNA in the cell.

What are mitochondria?

+They are membrane-enclosed organelles that are found in most eukaryotic cells and generate most of the cell's supply of usable energy.


+DNA-containing organelles (they are endosymbionts)


+enclosed by a double membrane


What are chloroplasts?

+They are organelles found in plant cells and eukaryotic algae. They harvest energy from sunlight by photosynthesis.


+Also DNA-containing organelles


+larger than mitochondria


+two membranes + a 3rd membrane system, the thykaloid, which contains the photosynthetic pigement chlorophyll.


Do mitochondria have their own DNA?

Yes

What encloses a mitochondria?

A double membrane.

What is an example of an endosymbiont?

Mitochondria and DNA

Do chloroplasts contain their own DNA?

Yes

What is larger, a mitochondria or a chloroplast?

A chloroplast is larger.

How many membranes does a chloroplast have?

two membranes + a 3rd membrane system, the thylakoid, which contains the photosynthetic pigment chlorophyll.

What is a thylakoid?

The thylakoid is the 3rd membrane of a chloroplast, which contains the photosynthetic pigment, chlorophyll.

Endocytosis

Import mediated by the formation of endocytic vesicles.

Import mediated by the formation of endocytic vesicles.

Exocytosis:

export

export

What is a model for the origin of the nucleus and the endoplastic reticulum in an ancient prokaryote?

+the bacterial chromosome is typically attached to plasma membrane of the cell
+an invagination in the membrane formed an internal double membrane structure around the chromosome
+portions of this structure also formed the endoplasmic reticulum, t...

+the bacterial chromosome is typically attached to plasma membrane of the cell


+an invagination in the membrane formed an internal double membrane structure around the chromosome


+portions of this structure also formed the endoplasmic reticulum, to which some ribosomes attached

What is some evidence for the endosymbiosis of mitochondria or chloroplasts in eukaryotic cells?

• organelles contain their own DNA (organelle genomes)
• organelles resemble present-day prokaryotes
• organelle genomic sequences resemble those of present-day
prokaryotes
• organelles can divide independently from the cell nucleus
• organelles are enclosed by double membranes


Does having organelles make a cell eukaryotic?

No, the defining feature is having a nucleus.

What are characteristics of an animal cell?

+Has nucelus


+linear nuclear chromosomes


+mitochondria


+centrioles (microtubule organizing center)


+no cell wall or capsule


What are characteristics of a plant cell?

+Has nucleus


+linear nuclear chromosomes


+mitochondria


+no centrioles


+a microtubule organizing center (but no centrioles)


+chloroplasts


+large vacuoles (fluid-filled compartments)


+cell wall

What are centrioles?

a minute cylindrical organelle near the nucleus in animal cells, occurring in pairs and involved in the development of spindle fibers in cell division.

What are vacuoles?

a space or vesicle within the cytoplasm of a cell, enclosed by a membrane and typically containing fluid


What are microtubules?

a microscopic tubular structure present in numbers in the cytoplasm of cells, sometimes aggregating to form more complex structures.

What is Giardia?

+A single-cell anaerobic parasite
+can cause gastrointestinal diseases in humans (Giardiasis)
+contains two nuclei but no mitochondria or chloroplasts.  (Remember prokaryotes don't have nucleuses).

+A single-cell anaerobic parasite


+can cause gastrointestinal diseases in humans (Giardiasis)


+contains two nuclei but no mitochondria or chloroplasts. (Remember prokaryotes don't have nucleuses).

What are Volvocaceans?

The Volvocaceae are a family of unicellular or colonial biflagellates, including the typical genus Volvox. The family was named by Ehrenberg in 1834, and is known in older classifications as the Volvocidae.

The Volvocaceae are a family of unicellular or colonial biflagellates, including the typical genus Volvox. The family was named by Ehrenberg in 1834, and is known in older classifications as the Volvocidae.

Volvox is multicellular which means?

Multicellular: true division of functions and multicellularity.

Pleodorina is "Colonial with a division of functions" which means?

Colonial with division of functions: aggregation of cells of the same species with different somatic and reproductive functions, but no recognized true multicellularity (Pleodorina).

Gonium, Pandorina, and Eudorina are all colonial which means?

Colonial: aggregation of cells of the same species but no division of functions (Gonium, Pandorina, and Eudorina)

Chlamydomonas is a single cell species, which means?

Single cell species: independent, free-living cells (Chlamydomonas)

What does haploid mean?

Haploid is the term used when a cell has only one set of chromosomes. A normal eukaryote organism is composed of diploid cells, one set of chromosomes from each parent. However, after meiosis, the number of chromosomes in gametes is halved. That is the haploid condition.

The vegetative state of Chlamydomonas is haploid, which means?

The vegetative state of Chlamydomonas is haploid, which can reproduce asexually by simple mitotic cell division. Sexual reproduction can occur when two cells of opposite mating types (+ and -) fuse to form a diploid zygote, which then undergoes me...

The vegetative state of Chlamydomonas is haploid, which can reproduce asexually by simple mitotic cell division. Sexual reproduction can occur when two cells of opposite mating types (+ and -) fuse to form a diploid zygote, which then undergoes meiosis (sporulation) to generate four haploid cells (two spores of each mating type).

What is embryogenesis?

Embryogenesis starts with the fertilization of the egg cell (ovum) by a sperm cell, (spermatozoon). Once fertilized, the ovum is referred to as a zygote, a single diploid cell. The zygote undergoes mitotic divisions with no significant growth (a process known as cleavage) and cellular differentiation, leading to development of a multicellular embryo.

What is colonial theory?
+the symbiosis of many cells of the same unicellular species
led to a multicellular organism

+increasing specialization and division of functions among
the members of the a colonial aggregate led to the transition into true multicellularity

What are epithelial cells?

+Epithelial cells are bound by tight junctions and form sheets that cover body surfaces and form the lining the internal organs.

+Epithelial cells are bound by tight junctions and form sheets that cover body surfaces and form the lining the internal organs.

What are tight junctions?

Tight junctions are the closely associated areas of two cells whose membranes join together forming a virtually impermeable barrier to fluid. It is a type of junctional complex present only in vertebrates.

Tight junctions are the closely associated areas of two cells whose membranes join together forming a virtually impermeable barrier to fluid. It is a type of junctional complex present only in vertebrates.

What are 4 connective tissues?

1. Bone and cartilage


2. adipose tissue


3. areolar tissue


4. fibroblasts

What is a fibroblast?

A fibroblast is a type of cell that synthesizes the extracellular matrix and collagen, the structural framework (stroma) for animal tissues, and plays a critical role in wound healing. Fibroblasts are the most common cells of connective tissue in ...

A fibroblast is a type of cell that synthesizes the extracellular matrix and collagen, the structural framework (stroma) for animal tissues, and plays a critical role in wound healing. Fibroblasts are the most common cells of connective tissue in animals.

What is areolar tissue?

A common type of connective tissue, also referred to as "loose connective tissue". It is strong enough to bind different tissue types together, yet soft enough to provide flexibility and cushioning.


What is adipose tissue?

Body fat or just fat is loose connective tissue composed mostly of adipocytes.

What are two blood cell types?

Red and White

What are neurons?

Neurons are cells that receive and transmit signals throughout the body and are capable of generating electrical activity.

Neurons are cells that receive and transmit signals throughout the body and are capable of generating electrical activity.

What are the three types of muscle cells (fibers)?

Skeletal, cardiac, smooth

What are muscle cells?

Multinucleated cells that generate force and movement.

What distinguishes living cells from other non-living entities?

1. Complexity: cells are highly complex and organized.



2. Genetics: cells posses a genetic program and the means to use.



3. Replication: cells are capable of producing more of themselves.



4. Metabolism: cells are capable of acquiring and utilizing energy.



5. Biochemistry: cells carry out a variety of chemical reactions.



6. Function: cells engage in numerous mechanical activities.



7. Response: cells are able to respond to external stimuli.



8. Self-regulation: cells maintain their complex state by constant self-regulation.

What happens regarding to the self-regulation of Sea urchin larva?

Two sea urchin larvae develop if the two cells are separated after the division of the zygote.

Two sea urchin larvae develop if the two cells are separated after the division of the zygote.

Study this asexual repoduction in Volvox:

The reproductive cells (gonidia) undergo embryogenesis to become juveniles, which are eventually released. The parental somatic cells undergo apoptosis (programmed cell death).

The reproductive cells (gonidia) undergo embryogenesis to become juveniles, which are eventually released. The parental somatic cells undergo apoptosis (programmed cell death).

Study this sexual repoduction in Volvox:

In the presence of a sexual inducer protein, the gonidia of males and females undergo a modified sexual development that results in the production of gametes.

In the presence of a sexual inducer protein, the gonidia of males and females undergo a modified sexual development that results in the production of gametes.

Study this:

The asexual life cycle of Dictyostelium discoideum (slime mold) is an example of multicellular organization derived from single-cell organisms.
 
In the presence of a sexual inducer protein, the gonidia of males and females undergo a modified sexu...

The asexual life cycle of Dictyostelium discoideum (slime mold) is an example of multicellular organization derived from single-cell organisms.



In the presence of a sexual inducer protein, the gonidia of males and females undergo a modified sexual development that results in the production of gametes.

What are four major families of organic molecules in the cell?

What is dehydration synthesis (condensation)?

Formation of Disaccharides.



Dehydration reactions and dehydration synthesis have the same meaning, and are often used interchangeably.



Two monosaccharides, such as glucose and fructose, can be joined together (to form sucrose) using dehydration synthesis.



The new molecule, consisting of two monosaccharides, is called a disaccharide.



The process of hydrolysis is the reverse reaction, meaning that the water is recombined with the two hydroxyl groups and the disaccharide reverts to being monosaccharides.

How are disaccharides formed?

The condensation of two monosaccharides produces one disaccharide.

The condensation of two monosaccharides produces one disaccharide.

What are two parts of a fatty acid?

1. Hydrophilic carboxylic acid head


2. Hydrophobic hydrocarbon tail

What is a triacylglycerol?

Fatty acids are stored as energy reserves (fats and oils) through an ester linkage to glycerol to form triacylglycerols. 

Fatty acids are stored as energy reserves (fats and oils) through an ester linkage to glycerol to form triacylglycerols.

What happens to the triacylglycerol when it is saturated and unsaturated?

Saturated fatty acids tend to form aggregates and deposits

inside blood vessels.




Unsaturated fatty acids:

cis unsaturated fatty acids do not form solid aggregates




trans unsaturated fatty acids behave similar to saturated fatty

...

Saturated fatty acids tend to form aggregates and deposits
inside blood vessels.



Unsaturated fatty acids:
cis unsaturated fatty acids do not form solid aggregates



trans unsaturated fatty acids behave similar to saturated fatty
acids (they tend to aggregate and form solid deposits) and
are major contributors to coronary heart disease
(atherosclerosis of coronary blood vessels)


What is a saturated fatty acid?

A carboxylic acid with an alkane R-group

A carboxylic acid with an alkane R-group

Does a trans-fatty acid or cis-fatty acid have a bend at the double bond?

a cis 

a cis

What is oleic acid?

a cis unsaturated fatty acid that comprises up to 80% of olive oil.

a cis unsaturated fatty acid that comprises up to 80% of olive oil.

What is elaidic acid?

A trans unsaturated fatty acid and a major trans fat found in partially hydrogenated vegetable oils.  

A trans unsaturated fatty acid and a major trans fat found in partially hydrogenated vegetable oils.

How is a phospholipid formed?

+two of the –OH groups in glycerol are linked to fatty acids while the third –OH group is linked to phosphoric acid (all by condensation reactions)


+the phosphate group is linked to a small polar group (an alcohol) such as choline in phosp...

+two of the –OH groups in glycerol are linked to fatty acids while the third –OH group is linked to phosphoric acid (all by condensation reactions)


+the phosphate group is linked to a small polar group (an alcohol) such as choline in phosphatidylcholine

What is the structure of a phospholipid?

What is an amino acid?

Biologically important organic compounds composed of amine (-NH2) andcarboxylic acid (-COOH) functional groups, along with a side-chain specific to each amino acid.


 


In picture: alanine, one the simplest amino acids.

Biologically important organic compounds composed of amine (-NH2) andcarboxylic acid (-COOH) functional groups, along with a side-chain specific to each amino acid.



In picture: alanine, one the simplest amino acids.

What is a polypeptide?

Naturally occurring biological molecules. They are short chains of amino acid monomers linked by peptide (amide) bonds. The covalent chemical bonds are formed when the carboxyl group of one amino acid reacts with the amino group of ano...

Naturally occurring biological molecules. They are short chains of amino acid monomers linked by peptide (amide) bonds. The covalent chemical bonds are formed when the carboxyl group of one amino acid reacts with the amino group of another.

What is ATP?

Adenosine triphosphate: a nucleotide


 


ATP transports chemical energy within cells for metabolism. It is one of the end products of 


photophosphorylati-on, cellular respiration, and fermentation


 and used by enzymes and st...

Adenosine triphosphate: a nucleotide



ATP transports chemical energy within cells for metabolism. It is one of the end products of


photophosphorylati-on, cellular respiration, and fermentation


and used by enzymes and structural proteins in many cellular processes, including


biosynthetic reactions, motility, and cell division.

A chain of sugar is called a?

polysaccharide

A chain of amino acids is called a?

Peptide, polypeptide or protein

Nucleic acids are made up of?

Nucleotides

Polysaccharides, polypeptides, and polynucleotides form from what type of bonding of their monomeric subunits?

Covalent bonding

Interactions of macromolecules are mediated by what type of bonds?

Noncovalent bonds

Noncovalent bonds

What is cAMP?

Cyclic adenosine monophosphate.  


 


cAMP is derived from adenosine triphosphate (ATP) and used for intracellular signal transduction in many different organisms, conveying the cAMP-dependent pathway.

Cyclic adenosine monophosphate.



cAMP is derived from adenosine triphosphate (ATP) and used for intracellular signal transduction in many different organisms, conveying the cAMP-dependent pathway.

The interactions of macromolecules in cells can result in what?

Macromolecular complexes


 


Pictured: The assembly of a ribosome, a cytoplasmic particle involved in translation.

Macromolecular complexes



Pictured: The assembly of a ribosome, a cytoplasmic particle involved in translation.

How are peptide bonds formed?

Dehydration synthesis

Dehydration synthesis

What are 3 types of noncovalent bonds that are strong enough to define the folded structure of a protein?

ionic bonds, hydrogen bonds, van der Waals attractions.

What are nonpolar amino acids?

Polar amino acids have a charged side chain. Nonpolar amino acids do not have a charged side chain, meaning they are hydrophobic.



In a folded polypeptide, nonpolar side chains tend to cluster at the core of the protein and away from the aqueous surrounding, leaving the polar and charged side chains at the surface. Nonpolar amino acids also form the transmembrane domains of membrane proteins.

What are polar / charged amino acids?

Polar amino acids have a charged side chain. Nonpolar amino acids do not have a charged side chain, meaning they are hydrophobic.



Polar and charged amino acids tend to be at the regions of proteins that are exposed to the aqueous surrounding.

The alpha helix and beta sheet are an example of?

Secondary structure

What are molecular chaperones?

Molecular chaperones are proteins that assist the non-covalent folding or unfolding and the assembly or disassembly of other macromolecular structures.



One major function of chaperones is to prevent both newly synthesised polypeptide chains and assembled subunits from aggregating into nonfunctional structures.



Chaperones are not present when the macromolecules perform their normal biological functions and have correctly completed the processes of folding and/or assembly.



The common perception that chaperones are concerned primarily with protein folding is incorrect.



The first protein to be called a chaperone assists the assembly of nucleosomes from folded histones and DNA and such assembly chaperones, especially in the nucleus, are concerned with the assembly of folded subunits into oligomeric structures.



.

What happens so that a protein can be transported through a membrane? (Hint: chaperone molecules)

+chaperones stabilize the newly synthesized polypeptide.


+the polypeptide is transported


+chaperones on the other side maintain the unfolded state until translocation is complete


+polypeptide is allowed to fold when it reaches its fina...

+chaperones stabilize the newly synthesized polypeptide.


+the polypeptide is transported


+chaperones on the other side maintain the unfolded state until translocation is complete


+polypeptide is allowed to fold when it reaches its final destination

What are elastin fibers?

+They are rubberlike elastic meshwork present in the extracellular matrix of some cell types.


+allow tissues such as skin, arteries, and lungs to stretch and recoil without tearing.

What type of bonds form between adjacent cysteine residues?

Disulfide bonds form between adjacent cysteine residues. They can link two domains of the same polypeptide or different polypeptide chains.

Disulfide bonds form between adjacent cysteine residues. They can link two domains of the same polypeptide or different polypeptide chains.

Cross-linking of elastin polypeptides forms what?

Elastic fibers

Elastic fibers

Denaturants (such as urea or heat) can _____ a polypeptide by breaking _____ interactions between amino acids?

Denaturants (such as urea or heat) can unfold (denature) a polypeptide by breaking non-covalent interactions between amino acids.

Denaturants (such as urea or heat) can unfold (denature) a polypeptide by breaking non-covalent interactions between amino acids.

Reducing agents (such as 2-mercaptoethanol) are necessary to _____ disulfide bonds.

Reducing agents (such as 2-mercaptoethanol) are necessary to break disulfide bonds.

Reducing agents (such as 2-mercaptoethanol) are necessary to break disulfide bonds.

Urea is produced in the liver of mammals as way to excrete ammonia (a toxic metabolic waste product). It can ______ covalent interactions between amino acids.

Urea is produced in the liver of mammals as way to excrete ammonia (a toxic metabolic waste product). It can break covalent interactions between amino acids.

Urea is produced in the liver of mammals as way to excrete ammonia (a toxic metabolic waste product). It can break covalent interactions between amino acids.

What are fibrillar collagens?

They are the major structural proteins of connective tissues, are built of triple helices of procollagen polypeptides.

What is Osteogenesis imperfecta?

A congenital bone disorder characterized by brittle bones that are prone to fracture. People with OI are born with defective connective tissue, or without the ability to make it, usually because of a deficiency of Type-I collagen.

What are TSEs? prions
+Transmissible spongiform encephalopathies.
+TSEs are a family of fatal brain diseases characterized by lesions that appear as small cavities (spongy appearance).
+infectious agent: prions (proteinaceous infectious particle)
+protein only hypothesis: diseases are caused by incorrectly folded versions of the prion protein

What are prions?

Prions (PrPsc) are variations of a normal brain protein (PrPc).




+a PrPsc can direct a PrPc to unfold and re-fold into an

identical PrPsc prion


+new prions can continue the propagation

+several strains exist (variations of the prion ...

Prions (PrPsc) are variations of a normal brain protein (PrPc).



+a PrPsc can direct a PrPc to unfold and re-fold into an
identical PrPsc prion


+new prions can continue the propagation
+several strains exist (variations of the prion protein tertiary
structure that are also infectious)


What is insulin?

+a pancreatic hormone that regulates blood glucose levels


+consists of two chains linked by disulfide bonds (between

closely placed cysteine residues)


+originally synthesized as a single polypeptide (preproinsulin)

+the signal sequence...

+a pancreatic hormone that regulates blood glucose levels


+consists of two chains linked by disulfide bonds (between
closely placed cysteine residues)


+originally synthesized as a single polypeptide (preproinsulin)
+the signal sequence is removed after translocation into the
ER and two disulfide bonds are made (result: proinsulin)


+the connecting polypeptide is then removed (result: mature insulin)



What are two levels in which protein activity are controlled?

1. Regulation of gene expression: determines the amount of protein produced by the cell by limiting transcription and/or translation.



2. Control of protein function: the protein is synthesized but its activity is restricted according to the needs of the cell.



What is allosteric regulation?

A change in the conformation of a protein that affects its activity due to the binding of a regulatory molecule (in this case, the end product of a pathway). 


 


For example:  the end product of a biosynthetic pathway inhibits the enzyme...

A change in the conformation of a protein that affects its activity due to the binding of a regulatory molecule (in this case, the end product of a pathway).



For example: the end product of a biosynthetic pathway inhibits the enzyme that catalyzes the first step of its synthesis (negative allosteric regulation), causing the entire pathway to shut down (feedback inhibition).

Allosteric inhibition of E. coli transcarbamoylase enzyme by the binding of CTP is an example of what?

Negative allosteric regulation

Negative allosteric regulation

The activation of Ras pathway is regulated by what molecule?

GTP

GTP

What is Ras?

Ras is the name given to a family of related proteins which is ubiquitously expressed in all cell lineages and organs.



All Ras protein family members belong to a class of protein called small GTPase, and are involved in transmitting signals within cells (cellular signal transduction).



Ras is the prototypical member of the Ras superfamily of proteins, which are all related in 3D structure and regulate diverse cell behaviours.

What is Guanine nucleotide exchange factor?

Guanylate nucleotide exchange factor.



Guanine Nucleotide Exchange Factors (GEFs) are proteins involved in the activation of small GTPases.



Small GTPases act as molecular switches in intracellular signaling pathways and have many downstream targets.



The most well-known GTPases comprise the Ras superfamily and are involved in essential cell processes such as cell differentiation and proliferation, cytoskeletal organization, vesicle trafficking, and nuclear transport.



GTPases are active when bound to GTP and inactive when bound to GDP, allowing their activity to be regulated by GEFs and the opposing GTPase activating proteins (GAPs).

What is phosphorylation necessary for?

Phosphorylation is necessary for the activation or inactivation of many proteins.



What are protein kinase enzymes?

Transfer a phosphate group from ATP to proteins.



+There are two types of kinases, (depending on the target amino acids).



1. Serine / threonine


2. Tyrosine



What are protein phosphatases?

Enzymes that remove phosphate groups from phosphorylated proteins.

What is ubiquitin?

A small protein that is attached to a target protein and is a label for regulation or destruction.  

A small protein that is attached to a target protein and is a label for regulation or destruction.

What is a proteasome?
Proteasomes are protein complexes inside all eukaryotes and archaea, and in some bacteria.

In eukaryotes, they are located in the nucleus and the cytoplasm.

The main function of the proteasome is to degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds.

Enzymes that carry out such reactions are called proteases.

Proteasomes are part of a major mechanism by which cells regulate the concentration of particular proteins and degrade misfolded proteins.

The degradation process yields peptides of about seven to eight amino acids long, which can then be further degraded into shorter amino acid sequences and used in synthesizing new proteins.

Proteins are tagged for degradation with a small protein called ubiquitin. The tagging reaction is catalyzed by enzymes called ubiquitin ligases.

Once a protein is tagged with a single ubiquitin molecule, this is a signal to other ligases to attach additional ubiquitin molecules. The result is a polyubiquitin chain that is bound by the proteasome, allowing it to degrade the tagged protein

What is inherited ataxia?

Inherited ataxia causes a piece of chromosome 4 to become inappropriately attached to chromosome 12.

What happens if two different closely related species breed?

They create a sterile offspring, do to differing number of chromosomes even if they have the same amount of genes.

What is meiotic failure?

When two different species with different chromosome numbers breed, they create a sterile hybrid.

What is a nucleosome?

A nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores. This structure is often compared to thread wrapped around a spool.

What is a histone?

Histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes.

What is chromatin?

Chromatin is a complex of macromolecules found in cells, consisting of DNA, protein and RNA.



The primary functions of chromatin are 1) to package DNA into a smaller volume to fit in the cell, 2) to reinforce the DNA macromolecule to allow mitosis, 3) to prevent DNA damage, and to control gene expression and DNA replication.



The primary protein components of chromatin are histones that compact the DNA. Chromatin is only found in eukaryotic cells, (a cell with a defined nucleus).



Prokaryotic cells have a different organization of their DNA (the prokaryotic chromosome equivalent is called genophore) and is localized within the nucleoid.

What is microccocal nuclease?

Micrococcal Nuclease is an endo-exonuclease that preferentially digests single-stranded nucleic acids.

What is a nuclease?

A nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids.

What is an exonuclease?

Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain.



A hydrolyzing reaction that breaks phosphodiester bonds at either the 3’ or the 5’ end occurs.



Its close relative is the endonuclease, which cleaves phosphodiester bonds in the middle (endo) of a polynucleotide chain.



What is an endonuclease?

Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as Deoxyribonuclease I, cut DNA relatively nonspecifically (without regard to sequence), while many, typically called restriction endonucleases or restriction enzymes, cleave only at very specific nucleotide sequences.

What is the highest level of of DNA organization in humans?

The condensed chromosome.

In what phase of mitosis is DNA at its maximum condensation state?

During metaphase.

The interphase heterochromatin regions of any particular chromosome are usually _____ and may be inherited.

The interphase heterochromatin regions of any particular chromosome are usually well-defined and may be inherited.

What happens to DNA during interphase?

During interphase most DNA (~90%) is decondensed: Euchromatin (true chromatin). Some DNA (~10%) remains condensed, as in metaphase: heterochromatin.

What is heterochromatin?

Condensed DNA, such as in metaphase.

What is Euchromatin?

Decondensed DNA. 90% of DNA is decondensed during interphase. (Allows for replication).

The position of a gene relative to _____ may affect its expression.

The position of a gene relative to heterochromatin may affect its expression.

In Drosphilia, what gene is necessary for normal eye pigmentation?

White gene


 


+The absence of its products results in white eyes


+if the White gene is moved close to heterochromatin DNA by a chromosomal inversion, some of the eye cells may not express the gene. 

White gene



+The absence of its products results in white eyes


+if the White gene is moved close to heterochromatin DNA by a chromosomal inversion, some of the eye cells may not express the gene.

The X chromosome that is inactivated at an early stage of development is chosen ______.

The X chromosome that is inactivated at an early stage of development is chosen randomly.

What is a barr body?

A barr body is the inactive X chromosome in a female somatic cell.

Calico and Tortoiseshell cats are always _____ females.

Calico and Tortoiseshell cats are always heterozygous females: XOXB.    They have two different Alleles for the colour gene.

Calico and Tortoiseshell cats are always heterozygous females: XOXB. They have two different Alleles for the colour gene.

What is calico?

Patches of orange and black against a white background (white skin tissue with no pigmentation).

What is tortoise shell?
Patches of orange and black with no white background.
Normal males do no exhibit calico or tortoise shell patterns (caused by a barr bodies) because?
Because normal males hemizygous: XoY (orange) or XbY (black).

+Normal males always have either patches of one colour against a white background or a single solid colour
+male Calicos or tortoiseshells can only happen if more than one X chromosome is present (as in Klinefelter's XXY)

What causes Klinefelter's syndrome?

XXY

What is a gene?

A gene is defined as a region of the chromosome that is transcribed, resulting in a functional product.


 


ALSO:


 


a segment of DNA that is transcribed and codes for a functional product:


 


such as a polypeptide or an RNA...

A gene is defined as a region of the chromosome that is transcribed, resulting in a functional product.



ALSO:



a segment of DNA that is transcribed and codes for a functional product:



such as a polypeptide or an RNA species (tRNA, rRNA) as end product.

What are exons?

Coding sequences within genes

What are introns

non-coding DNA sequences

What are regulatory sequence?

A regulatory sequence is a segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of specific genes within an organism. Regulation of gene expression is an essential feature of all living organisms and viruses.

What spacer sequences?

Spacer DNA are regions of non-transcribed DNA between tandemly repeated genes, such as ribosomal RNA genes in eukaryotes. Its function most likely involves ensuring the high rates of transcription associated with these genes.

What is the dystrophin gene?
Dystrophin is a rod-shaped cytoplasmic protein, and a vital part of a protein complex that connects the cytoskeleton of a muscle fiber to the surrounding extracellular matrix through the cell membrane.

The dystrophin gene is ~2.6 million nucleotide pairs long.

+about 0.01% of the human genome: the largest gene known
+79 exons code for a ~3600 amino acid protein +only about 0.004% of the gene is exons
+DMD patients have deletions in this gene and lack a functional dystrophin protein

Alternative splicing can create _____ versions of a gene product?

Alternative splicing can generate different versions of a gene product

Alternative splicing can generate different versions of a gene product

One or more genes may be contained within the _____ of another gene?

One or more genes may be contained within the intron of another gene.


 


This is a relatively common feature of nuclear genomes. 


 


Example: intron 27 of the human neurofibromatosis type I (NF1) gene contains three genes: OGMP, E...

One or more genes may be contained within the intron of another gene.



This is a relatively common feature of nuclear genomes.



Example: intron 27 of the human neurofibromatosis type I (NF1) gene contains three genes: OGMP, EV12B, & EV12A

The regions of two genes may _____?

The regions of two genes may overlap.



A single locus can produce more than one product by the use of different ______?

A single locus can produce more than one type of product by the use of different reading frames.

Reading frames are found in compact genomes such as ______ and ______.

Reading frames are found in compact genomes such as viruses and mitochondria. 


 


Example: ATPase-6 and ATPase-8 are in human mitochondria. 

Reading frames are found in compact genomes such as viruses and mitochondria.



Example: ATPase-6 and ATPase-8 are in human mitochondria.

What are pseudogenes?
Pseudogenes are dysfunctional relatives of genes that have lost their protein-coding ability or are otherwise no longer expressed in the cell.


 


Pseudogenes often result from the accumulation of multiple mutations within a gene w...
Pseudogenes are dysfunctional relatives of genes that have lost their protein-coding ability or are otherwise no longer expressed in the cell.

Pseudogenes often result from the accumulation of multiple mutations within a gene whose product is not required for the survival of the organism.

Although not protein-coding, the DNA of pseudogenes may be functional, similar to other kinds of non-coding DNA which can have a regulatory role.
In mitochondrial and viral genomes, why does most of the DNA code for something?
Because their genomes are really small.

Why is possible that only 1.5% of the human nuclear genome codes for something?

Humans have very large genomes compared to viruses and mitochondria. 


 


The human mtDNA (mitochondrial DNA) is 16.6 kb.  It codes for two rRNAs, 22 tRNAs, and 13 polypeptides necessary for the oxidative respiratory functions of the orga...

Humans have very large genomes compared to viruses and mitochondria.



The human mtDNA (mitochondrial DNA) is 16.6 kb. It codes for two rRNAs, 22 tRNAs, and 13 polypeptides necessary for the oxidative respiratory functions of the organelle.

Repetitive DNA sequences are noncoding sequences that are present in _______?

Repetitive DNA sequences are noncoding sequences that are present in multiple copies. 


 


+Simple sequence DNA ("satellites") are clustered repeats.


+interspersed repeats are repetitive sequences that are not clustered but are scatt...

Repetitive DNA sequences are noncoding sequences that are present in multiple copies.



+Simple sequence DNA ("satellites") are clustered repeats.


+interspersed repeats are repetitive sequences that are not clustered but are scattered throughout the genome.



What is a tandem (clustered) repeat?

Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other.



Also called, simple sequence DNA or satellites.



~19% of human genome


>40% of Drosophila genome



Example: ATT ATT ATT

What are interspersed repeats?

Interspersed repeats are repetitive sequences that are not clustered but are scattered throughout the genome.

What are restriction enzymes?

A restriction enzyme (or restriction endonuclease) is an enzyme that cuts DNA at or near specific recognition nucleotide sequences known as restriction sites.

What are the 4 steps in a reassociation assay (examining repetitive sequences)?

1.  Cut the DNA with restriction enzymes.


2.  Denature the DNA fragments by heating.


3.  Allow the DNA to cool and reassociate. 


4.  Measure the fraction of DNA remaining single strand over time (it will decrease as DNA reasso...

1. Cut the DNA with restriction enzymes.


2. Denature the DNA fragments by heating.


3. Allow the DNA to cool and reassociate.


4. Measure the fraction of DNA remaining single strand over time (it will decrease as DNA reassociates).




Pictured: E. coli DNA reassociation curve has only one component: DNA is non-repetitive (all sequences are unique)



Bovine DNA reassociation curve has a fast and a slow component: contains both repetitive and unique sequences

In a reassociation assay, highly repetitive sequences reassociate faster or slower?

Highly repetitive sequences reassociate faster.

In a reassociation assay, moderately repetitive and unique sequences reassociate faster or slower?

moderately repetitive and unique sequences reassociate slower.

E.coli DNA reassociation curves only has one component because?

DNA is non-repetitive (all sequences are unique)

Bovine DNA reassociation curve has a fast and slow component because?

Contains both repetitive and unique sequences.

What are unique DNA sequences?

Non-repetitive DNA that is in neither introns nor exons. A DNA sequence is considered to be unique if it is present in only one copy in a haploid genome.

What are Long interspersed elements (LINES)?

+example: Line1 in human


+6000 bp


+~21% of total human DNA


+Some of them are transcribed and translated, but their products have no known functions.

+example: Line1 in human


+6000 bp


+~21% of total human DNA


+Some of them are transcribed and translated, but their products have no known functions.

What are Short interspersed elements (SINES)?

+example: Alu sequences in mammalian genomes (characterized by Alu1 restriction site)


+300 bp


+~13% of total human DNA


+Some of them are transcribed but not translated.


+function unknown.


 

+example: Alu sequences in mammalian genomes (characterized by Alu1 restriction site)


+300 bp


+~13% of total human DNA


+Some of them are transcribed but not translated.


+function unknown.


What retrotransposons?

Retrotransposons (also called transposons via RNA intermediates) are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. They are a subclass of transposon.

What are transposons?

A transposable element (TE, transposon or retrotransposon) is a DNA sequence that can change its position within the genome, sometimes creating or reversing mutations and altering the cell's genome size.

The G-C base pair has more or less density than A-T base pair?

The G-C base pair has more density than the A-T base pair. G-C base pairs have 3 hydrogen bonds and A-T only have two.



If most of the of the DNA the cell had ~equal amounts of G-C and A-T (which is doesn't)



then: a high A-T sequence repeated 1000s of times will be detected in an equilibrium centrifugation because its density will be lower than the rest of the DNA



Equilibrium centrifugation of DNA using CsCl density gradient: separates DNA according to density.



Equilibrium centrifugation of DNA using CsCl density gradient: separates DNA according to _____?

Equilibrium centrifugation of DNA using CsCl density gradient: separates DNA according to density.

A strand of DNA serves as a template for the synthesis of a complimentary, antiparallel strand in the ____ direction?

A strand of DNA serves as template for the synthesis of a complementary, antiparallel strand in the 5’ to 3’ direction.

The breaking of the high energy P-P bond (phosphoanhydride) in the deoxyribonucleotide (dNTP) provides the energy required for the formation of the new _______ bond.

The breaking of the high-energy P-P bond (phosphoanhydride) in the dNTP provides the energy required for the formation of the new phosphodiester bond.

What does DNA polymerase do?

It has 3' to 5' exonuclease activity (proofreading).



If a wrong nucleotide is placed during the regular 5’ to 3’ DNA synthesis, DNA polymerase can remove it (3’ to 5’ exonuclease activity)



The enzyme then replaces it with the correct nucleotide by resuming the 5’ to 3’ polymerase activity


Synthesis of DNA in the 5' to 3' direction makes ____ possible?

Synthesis of DNA in the 5’ to 3’ direction makes proofreading possible.



During a hypothetical 3’ to 5’ DNA polymerization, the energy necessary for the formation of the phosphodiester bond would come from the breaking of the high-energy P-P bond at the 5’ end of the growing chain, but:



If the last nucleotide (the triphosphate) were removed as part of proofreading, no high energy bond would be available for the addition of the next nucleotide




The consequences of errors in DNA replication is nucleotide ______ that can lead to permanent changes if they are left unrepaired before the next round of DNA synthesis.

The consequence of errors in DNA replication is nucleotide mismatches that can lead to permanent changes if they are left unrepaired before the next round of DNA synthesis.

What is a point mutation?

A mutation affecting only one or very few nucleotides in a gene sequence.

Sickle-cell anemia is caused by a single point mutation in the ______ gene?

Beta-globin gene

How does the cell know which strand is the newly synthesized strand (and hence, which one of the two nucleotides in a mismatch pair is the wrong one?)

The recently sythesized strand has breaks (nicks).



This strand is interrupted due to discontinuous replication, resulting in Okazaki fragments.



Mismatch repair must be done before nick repair occurs.

What is an okazaki fragment?

Okazaki fragments are short, newly synthesized DNA fragments that are formed on the lagging template strand during DNA replication.

What is DNA mismatch repair?

DNA mismatch repair is a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage.



How is a DNA mismatch repaired in Eukaryotes?

DNA mismatch repair proteins recognize the mismatched pair (due to the resulting topological disturbance) and bind to it.



The DNA is scanned for a nearby nick (break in the DNA).



The nicked strand is digested all the way back from the nick back to the mismatch site.



DNA polymerase and DNA ligase complete the repair.



What is DNA ligase?

DNA ligase is a specific type of enzyme, a ligase, that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond.

Hereditary nonpolyposis colorectal cancer (HNPCC) is caused by defects in the _____ or _____ genes, which code for DNA mismatch repair proteins. It results in higher frequency of mutations in other genes, such as those that regulate cell proliferation.

MutS or MutL genes

What are 2 consequences of DNA spontaneous mutations?

1. Distorted strands


2. mismatches that include unusual bases



example: adenine to hypoxanthine from deamination

What 2 unusual base pairs in DNA caused by deamination?

1. Cytosine deamination: C-G and A-U pairs


2. Adenine deamination: A-T and hypoxantine- Cytosine pairs

Depurination is a mutation in DNA that causes?

Depurination results in an apurinic (AP) site ... no base pairing occurs

What is a purine?

A purine is a heterocyclic aromatic organic compound. It consists of a pyrimidine ring fused to an imidazole ring. 


 


Guanine and Adenine

A purine is a heterocyclic aromatic organic compound. It consists of a pyrimidine ring fused to an imidazole ring.



Guanine and Adenine

What is a pyrimidine?

A pyrimidine is an aromatic heterocyclic organic compound. It has one ring.



Thymine, Cytosine, Uracil

UV-induced mutations cause what?

Thymine-dimers, which can not pair with adenines.



This is why killing stuff with UV rays works.

What is direct reversal (direct repair) of DNA damage?

Fixes the altered molecule by reversing the chemical transformation.



Requires specific enzymes for each individual lesion.



Example: some organisms can reverse thymine dimers by using a specific photoreactivating enzyme.



What is base excision repair?

Base excision repair is a general repair mechanism for nucleotide mismatches.



+the chemical transformation is not reversed


+instead, the damaged bases are replaced


+the unpaired base is recognized and replaced before DNA replication occurs.

Step 1 base excision repair:



___________ removes the base, an __________ recognizes the site and cleaves the phosphodiester bond, and a __________ removes the remaining sugar and phosphate from the site.


DNA glycosylase removes the base, an endonuclease recognizes the site and cleaves the phosphodiester bond, and a deoxyribosephosphodiesterase removes the remaining sugar and phosphate from the site.

Step 2 and 3 of base excision repair:



________ places a new nucleotide. _______ seals the nick.

DNA polymerase places a new nucleotide. DNA ligase seals the nick.

What is DNA glycosylase?

DNA glycosylases catalyze the first step of base excision repair.



They remove the damaged nitrogenous base while leaving the sugar-phosphate backbone intact, creating an apurinic/apyrimidinic site, commonly referred to as an AP site.



This is accomplished by flipping the damaged base out of the double helix followed by cleavage of the N-glycosidic bond.