Week 1 Textbook Reading pt 2 Flashcards
cells
small membrane-enclosed units filled with a concentrated aqueous solution of chemicals and provided with the ability to make copies of themselves by growing and dividing in two
Diverse in their chemical requirements
Some cells are so specialized that they stop reproducing
nucleotides
In all organisms, genetic info, genes, are carried in DNA molecules
In every cell, long polymer chains of DNA are made from the same set of 4 monomers, called nucleotides, attached together in different sequences
RNA
The info encoded in these DNA molecules is read out, or transcribed into a related set of polynucleotides called RNA
protein
Although some of these RNA molecules have their own regulatory, structural or chemical activities, most are translated into a different type of polymer called protein
central dogma
This flow of info(from DNA to RNA to protein) is so important to life that it’s called the central dogma
parts of the central dogma and how they make self-replication possible
DNA encodes info that directs the assembly of proteins: the sequence of nucleotides in a molecule of DNA controls (“dictates”) the sequence of amino acids in a protein
Proteins catalyze the replication of DNA and its transcription into RNA, and they participate in the translation of RNA into proteins
This feedback loops between proteins and polynucleotides supports the self-reproducing behaviour of living things
how is life an autocatalytic process
self-sustaining process where 2 or more ecological processes form a closed cycle, where each process makes the other one easier
DNA and RNA provide the sequence information(green arrows) that’s used to produce proteins and to copy themselves
Proteins, provide the catalytic activity (red arrows) needed to synthesize DNA, RNA, and themselves
Black arrows represent the biochemical processes by which new DNA, RNA, and proteins are manufactured in cells
All together, these feedback loops create the self-replicating systems that provides living cells with their ability to reproduce
what makes viruses different than living cells
Only living cells can perform self replication
Viruses don’t have the ability to reproduce on their own
Instead, they parasitize the reproductive machinery of the cells they invade to make copies of themselves
Without a host cell to help them, viruses are inert and are considered not living
These are sometimes harmful… once viruses gain entry, they can exert a malign influence over a cell or an organism, as shown by the coronavirus responsible for the covid-19 pandemic
how do mutations arise
When a cell copies its DNA in prep for cell division, the copying is not always perfect
Sometimes, the instructions aren’t read correctly or become damaged by mutations that change the sequence of nucleotides in the DNA
For this reason, daughter cells are not exact copies of their parent
Mutations can make offspring that make them worse off (less able to survive and reproduce), better off (better able to survive and reproduce) or changed in a neutral way (genetically different but equally viable)
how is the pattern of heredity complicated for many organisms
For many organisms, the pattern of heredity is complicated by sexual reproduction, in which 2 cells of the same species fuse, combining their DNA
In the process, the genes from each parent are combined and then passed on in new combos to the next gen, to be tested again for their ability to promote survival and reproduction
eukaryote vs prokaryote
e- with nucleus
p-w/o nucleus
Why does the bacterium E.coli serve as an important model organism?
Rod-shaped (bacillus) Gram-negative bacterium that is frequently used as a model organism
Factors such as its ability to grow fast using cheap media and availability of molecular tools to perform genetic manipulations are favorable for using E. coli as a model organism in molecular genetics
How does bacteria play a unique and fundamental part in the nutritional “economic” of life on Earth?
Some bacteria perform photosynthesis, using energy from sunlight to produce organic molecules from CO2, other derive energy from the chemical reactivity of inorganic substances in the environment
Use energy from the sun to produce organic molecules and take energy from the chemical reactivity of inorganic substances in the environment
Other living organisms depend on the organic compounds that these cells produce from inorganic molecules
How is bacteria harmful?
In the middle ages, bacteria that caused the bubonic plague wiped out half the pop of Europe
Today, different bacteria cause a variety of human diseases from cholera and whooping cough to tuberculosis
How is bacteria beneficial?
Bacteria that reside on our skin and in our gut promote a healthy immune response
Organelles that generate energy in eukaryotic cells are thought to have evolved from aerobic bacteria that used to reside inside anaerobic ancestral cells
Our own metabolism can be seen as a product of the activity of an organelle whose evolutionary birthright we can trace to a bacteria cell
Why is archaea the most poorly understood domain?
Most of its members have been identified only by DNA sequencing of environmental samples
The only ones we know about are small and lack the internal, membrane-enclosed organelles that distinguish the eukaryotes
Discovered that their genomes are more closely related to those of eukaryotes
How do bacteria and archaea store their genetic info differently from eukaryotes?
They store their genetic info in the form of DNA; however these cells do not keep their DNA tightly packed inside a nuclear envelope, separated from the rest of the cell contents
mitochondria
Mitochondria generate usable energy from food molecules
Mitochondria are present in all eukaryotic cells and are present in the cytoplasm
Individuals are found enclosed in 2 separate membranes, with the inner membrane formed into folds that project into the interior of the organelle
how are mitochondria generators of chemical energy for the cell
Generators of chemical energy for the cell
Harness the energy from the oxidation of food molecules, such as sugars to produce adenosine triphosphate(ATP)- the basic chemical fuel that powers most of the cell’s activities
what would happen to eukaryotes and plants without mitochondria?
Because the mitochondrion consumes oxygen and releases CO2 in the process, the entire process is called cellular respiration
Without mitochondria, eukaryotes and plants would be unable to use oxygen to extract the energy they need from the food molecules that nourish them
How does the resemblance of mitochondria to bacteria provide evidence that mitochondria evolved from an aerobic bacterium that was engulfed by an anaerobic ancestor of present day eukaryotic cells?
Mitochondria contain their own DNA and reproduce by dividing
Their strong resemblance (both in appearance and in DNA sequence) to modern day bacteria provides evidence
This engulfing event created a symbiotic relationship that provided both partner cells with metabolic support, allowing them to survive and reproduce
why are mitochondria believed to have evolved from engulfed bacteria
The surface protrusions of an ancient archaea expanded and surrounded an aerobic bacterium → symbiotic relationship
Protrusions fused with one another, trapping the bacterium as an endosymbiont within the body of the archaeon where it remained enclosed by an internal membrane by the archaea membrane
At some point, the symbiont escaped and entered cell’s cytoplasm, where it evolved into a mitochondria containing DNA and its membranes derived from the engulfed bacterium
The archaeal plasma membrane that folded inward during protrusion, expansion and fusion is proposed to have formed both the nuclear envelope and the internal membrane-enclosed organelles, such as ER
Structure and function of the inner membrane of mitochondria?
Inner membrane contains most of the proteins responsible for energy production in eukaryotic cells
Highly folded to provide a large surface area for this activity
chloroplasts capture energy from sunlight
Chloroplasts are large, green organelles that are found in the cells of plants and algae, but not in the cells of animals or fungi and capture the energy of sunlight
Possess internal stacks of membranes containing the green pigment chlorophyll
Carry out photosynthesis→ trapping the energy of sunlight in their chlorophyll molecules and using this energy to drive the production of energy-rich sugar molecules
Release oxygen as molecular by-product
Plant cells can extract this stored chemical energy when they need it like animal cells → by oxidizing these sugars and their breakdown products, mainly i the mitochondria
Golgi apparatus
Golgi apparatus, stacks of flattened, membrane-enclosed sacs that modify and package molecules made in the ER that are destined to be either secreted or transported from cell
Endoplasmic reticulum
Endoplasmic reticulum is an irregular maze of interconnected spaces enclosed by a membrane
Site where most cell-membrane components and materials destined for export from the cell, are made
lysosomes
Lysosomes are small, irregularly shaped organelles in which intracellular digestion occurs, releasing nutrients from ingested food particles into the cytoplasm and break down unwanted molecules for recycling or excretion
peroxisomes
Peroxisomes are small, membrane-enclosed vesicles that provide an isolated environment for a variety of rxns in which hydrogen peroxide is used to inactivate toxic molecules
endocytosis
process where portions of the plasma membrane tuck inward and pinch off to form vesicles that carry material captured from the external medium into the cell
exocytosis
vesicles from inside the cell fuse with the plasma membrane and release their contents into the external medium
Most of the hormones and signal molecules that allow cells to communicate with one another are secreted from cells by exocytosis
cytosol
The cytosol is a concentrated aqueous gel of large and small molecules
Cytosol→ the part of the cytoplasm that is not contained within intracellular membranes
Site of many chemical rxns that are fundamental to the cell’s existence
cytoskeleton
Cytoskeleton is responsible for directed cell movements
3 major filament types of cytoskeleton
Cytoskeleton is a system of protein filaments, and composed of 3 major filament types
Thinnest of these filaments are the actin filaments; occur largely in muscle cells and serve as a central part of the machinery responsible for muscle contraction
Thickest filaments are microtubules because they have the form of minute hollow tubes
in dividing cells, they become reorganized into an array that helps pull the duplicated chromosomes apart and distributes them equally to the 2 daughter cells
Intermediate in thickness are intermediate filaments, which serve to strengthen animal cells
These 3 together with other proteins form a system that gives the cell its mechanical strength, controls its shape and guides its movements
Suggest a reason why it might have been advantageous for eukaryotic cells to have evolved elaborate internal membrane systems that allow them to import substances from the outside
Due to efficient nutrient uptake and storage(import nutrients), increase cellular complexity and specialization (enables execution of diverse metabolic processes), protection against external threats, signal and communication
protozoans
Protozoans→ free-living, motile, unicellular eukaryotes
Range from predators, can be photosynthetic or carnivorous, motile or sedentary(inactive)
Which cellular component separates the DNA of eukaryotic cells from the cytosol?
nuclear membrane
model organisms
a living thing selected for study as a representative of a large group of species (mouse→mammals, yeast→unicellular eukaryote, E.coli→bacteria)
E. coli model organism
Used to explore how cells regulate gene expression
Also revealed how cells replicate their DNA and how they decode the instructions contained in DNA to make proteins
Studies of enzymes produced by this bacterium led to the development of tools that started the “recombinant DNA” revolution, allowing us to be able to manipulate genes and DNA
Also harnessed to produce large quantities of therapeutic proteins, including insulin
Brewer’s yeast is a simple eukaryote
Can grow and divide almost as rapidly as a bacterium and carries out all the basic tasks that every eukaryotic cell must do and can even mate with the opposite sex of the same species
Arabidopsis as a Model Plant
Provided a deep understanding of the mechanisms that allow plants to grow toward sunlight, to flower in spring, and to coordinate their development with the cycle of the seasons
Model animals include worms, flies, fish and mice
Nematode worm develops with precision from a fertilized egg cell into an adult that has 959 body cells
Some human genes have some resemblance in this worm
Studies of nematode development have led to a better understanding of apoptosis, a form of programmed cell death by which animals get rid of extra cells
This process is also important in the development of cancer
fruit fly as a model organism
backbone of study of animal genetics
Provided proof that genes are carried on chromosomes
Shows how genetic instructions encoded in DNA molecules direct the development of a fertilized egg cell into an adult multicellular organism
Fruit fly mutants with body parts misplaced have provided the key to identifying the genes needed to make a properly structured adult body
Defines how each cell will behave in its social interactions with its sisters and cousins
zebra cells
transparent for their 1st 2 weeks of life and are ideal for observing how cells behave during development in a living animal
Provided key insights into the development of the heart and blood vessels
in vitro vs in vivo
Experiments using cultured cells are sometimes carried out in vitro(“in glass”) or in vivo (“in the living”)
Because cultured cells are maintained in a controlled environment, they are accessible to study in ways not possible in vivo
hydrogen bonds
Hydrogen bonds are important noncovalent bonds for many biological molecules
In each molecule of water, the 2 covalent H-O bonds are highly polar because the O is strongly attractive for electrons whereas the H is only weakly attractive
When a positively charged region of one water molecule(H atom) comes close to a negatively charged region (O) of a 2nd water molecule, the electrical attraction b/w them can establish a weak bond called a hydrogen bond
Weaker than covalent bonds and are easily broken by random thermal motions
It’s because of these bonds that water at room temp is a liquid- with a high BP and high surface tension
nucleotides
Nucleotides are the subunits of DNA and RNA
DNA and RNA are built from subunits called nucleotides
Consist of a nitrogen containing ring linked to a 5 carbon sugar(ribose or deoxyribose) that has a phosphate group attached to it
Nucleotides with ribose → ribonucleotides and deoxyribose → deoxyribonucleotides
nucleotide bases
4 nucleotide bases
Cytosine, thymine, uracil → pyrimidines, all derive from a six-membered pyrimidine ring
Guanine, adenine → purines, have a 2nd five-membered ring fused to the six-membered ring
nucleoside
Base plus its sugar (w/o any phosphate group attached) → nucleoside
Nucleoside di- and triphosphates can act as short-term carriers of chemical energy
ATP
ATP participates in the transfer of energy in metabolic rxns and formed through rxns that are driven by the energy released from the breakdown of food
role of nucleotides
Nucleotides have an important role in the storage and retrieval of biological information
Serve as building blocks for the construction of nucleic acids- long polymers in which nucleotide subunits are linked by the formation of covalent phosphodiester bonds
b/w the phosphate group attached to the sugar of 1 nucleotide and a hydroxyl group on the sugar of the next nucleotide
nucleic acid types
Based on ribose → ribonucleic acids or RNA
Based on deoxyribose → deoxyribose or DNA
Linear sequence of nucleotides in a DNA or RNA molecule encodes genetic info
DNA acts as a long-term repository for hereditary info
RNA serves as short-term carriers of molecular instructions
Covalent bonds are formed by the sharing of electrons. In the cell, how are covalent bonds broken?
By enzyme catalysis that’s specific for a protein and its substrate
N-glycosidic bond→
covalent bond that forms b/w a nitrogenous base and a sugar, and is found in nucleotides and nucleosides
base-sugar linkage
N-glycosidic bond links the bases of DNA and RNA to the sugar-phosphate backbone
AMP= adenosine monophosphate and DP=diphosphate, TP=triphosphate
nucleoSide vs nucleoTide
Base + sugar = nucleoside
Base + sugar + phosphate = nucleotide
phosphodiester bonds
To form nucleic acid polymers, nucleotides are joined together by phosphodiester bonds b/w the 5’ and 3’ carbon atoms of adjacent sugar rings
As nucleoside di- and triphosphates, they carry chemical energy in their easily hydrolyzed phosphoanhydride bonds
-They combine with other groups to form
coenzymes
-They are used as small intracellular signaling
molecules in the cell
what did the structure of DNA help determine
Structure of DNA determined by Watson and Crick and revealed how DNA might be copied, or replicated and it provided the first clues about how a molecule of DNA might encode the instructions for making proteins
This structure immediately suggested both how DNA could encode the instructions necessary for life, and how these instructions could be copied and passed along when cells divide
structure of DNA
DNA molecule consists of 2 complementary chains of nucleotides
DNA consists of 2 long polynucleotide chains
Each chain is composed of 4 types of nucleotide subunits and the 2 strands are held together by hydrogen bonds b/w the base portions of the nucleotides
Nucleotide subunits held together by phosphodiester bonds
Subunits within a DNA strand held together by the bonds link the 5’ end of one sugar with the 3’ end of the next
Each purine pyrimidine pair is called a base pair and this complementary base-pairing allows the base pairs to be packed in the energetically most favourable arrangement along the interior of the double helix
Can only pair like this if the 2 polynucleotide chains that contain them are antiparallel
major vs minor groove
The 2 DNA strands wind around each other to form a right-handed helix
Their coiling creates 2 grooves in the double helix
The wider groove is called the major groove
Smaller one is called the minor groove
Why are G-C base pairs more stable than A-T base pairs?
G and C form 3 hydrogen bonds and A and T form 2 hydrogen bonds, since G and C have an additional hydrogen bond, they are more stable and require more energy to break
Genetic code:
set of rules by which the info contained in the nucleotide sequence of a gene and its corresponding RNA molecule is translated into the amino acid sequence of a protein
gene expression
the process by which the nucleotide sequence of a gene is transcribed into the nucleotide sequence of an RNA molecule and then, in most cases, translated into the amino acid sequence of a protein
