Samenvatting
Summary Essential cell biology H1-8 &10
Samenvatting van hoofdstuk 1tm8 en 10 van essential cell biology
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Voorbeeld van de inhoud
Samenvatting MCBHoofdstuk 1
- In every cell, the informaton encoded in the DNA is read out, or transcribed, into a chemically related set of
polymers called RNA. A subset of these RNA molecules is in turn translated into yet another type of polymer
called a protein.
- If cells are the fundamental units of living mater, then nothing less than a cell is can truly be called living
- A bacterium contains no organelles
- Mitochondria contain their own DNA and reproduce by dividing in two. Because they resemble bacteria in so
many ways, they are thought to have been derived from bacteria that were engulfed by some ancestor of
present-day eukaryotc cells
- The endoplasmic retculum is an irregular maze of interconnected spaces enclosed by a membrane. It is the
site where most cell-membrane components, as well as materials destned for export from the cell are
made. This organelle is enormously enlarged in cells that are specialized for the secreton of proteins
- Stacks of fatened, membrane enclosed sacs consttute the Golgi apparatus, which modifes and packaged
molecules made in the ER that are destned to be either secreted from the cell or transported to another cell
compartment.
- Lysosomes are small, irregularly shaped organelles in which intracellular digeston occurs, releasing nutrients
from ingested food partcles and breaking down unwanted molecules for either recycling within the cell or
excreton from the cell
- Cytosol is the part of the cytoplasm that is not contained within intracellular membranes
- In eukaryotc cells the cytosol is criss-crossed by long, fne flaments. This system of protein flaments, called
the cytoskeleton, is composed of three major flament types.
- The thinnest of these flaments are the actn flaments, they are abundant in all eukaryotc cells but occur in
especially large number inside muscle cells, where they serve as a central part of the machinery responsible
for muscle contracton.
- The thickest flaments in the cytosol are called microtubules, because they have the form of minute hollow
tubes. In dividing cells they become reorganized into a spectacular array that helps pull the duplicated
chromosomes in opposite directons and distribute them equally to the two daughter cells.
- Intermediate in thickness are the intermediate flaments, which serve to strengthen the cell.
- That single-celled eukaryotes can prey upon and swallow other cells is borne out by the behavior of many of
the free living, actvely motle microorganisms called protozoans
Hoofdstuk 2
- An ionic bond is formed when electrons are donated by one atom to another, whereas a covalent bond is
formed when two atoms share a pair of electrons
- A polar structure is one in which the positve charge is concentrated toward one end of the molecule and the
negatve charge is concentrated toward the other end of the molecule.
- When water is present, covalent bonds are much stronger than ionic bonds. In ionic bonds, electrons are
transferred rather than shared
- Although non-covalent bonds are individually quite weak their energies can sum to create an efectve force
between two molecules
- Molecules such as faty acids that possess both hydrophobic and hydrophilic regions are termed amphipathic
- Like sugars, all amino acids exist as optcal isomers in D- and L-forms. But only L-forms are ever found in
proteins
- Nucleosides are made of a nitrogen-containing ring compound linked to a fve-carbon sugar, which can be
either ribose or deoxyribose.
- Nucleotdes are nucleosides that contain one or more phosphate groups atached to the sugar, and they
come in two main forms: those containing ribose are known as ribonucleotdes, and those containing
deoxyribose are known as deoxyribonucleotdes
, - DNA, with its more stable, hydrogen-bonded helices, acts as a long term repository for hereditary
informaton, while single-stranded RNA is usually a more transient carrier of molecular instructons
Hoofdstuk 3
- Metabolism is the sum total of all the chemical reactons it needs to carry out to survive, grow and
reproduce
- Two opposing streams of chemical reactons occur in cells, the catabolic pathways and the anabolic
pathways.
- The catabolic pathways (catabolism) breaks down foodstufs into smaller molecules, thereby generatng
both a useful form of energy for the cell and some of the small molecules that the cell needs as building
blocks
- The anabolic pathway (anabolism) use the energy harnessed by catabolism to drive the synthesis of the
many molecules that form the cell. Together, these two sets of reactons consttute the metabolism of the
cell
- An easy way to tell whether an organic molecule is being oxidized or reduced is to count its C-H bonds:
reducton occurs when the number of C-H bonds decreases
- According to the second law of thermodynamics, a chemical reacton can proceed only if it results in a net
(overall) increase in the disorder of the universe. Disorder increases when useful energy that could be
harnessed to do the work is dissipated as heat. The useful energy in a system is known as its free energy, or
G. and because chemical reactons involve a transiton from one molecular state to another, the term that is
of most interest to chemists and cell biologists is the free energy change, or dG
- Energetcally favorable reactons, by defniton, are those that create disorder by decreasing the free energy
of the system to which they belong, in other words, they have a negatve dG
- Energetcally unfavorable reactons cannot occur spontaneously, they take place only when they are coupled
to a second reacton with a negatve dG large enough that the net dG of the entre process is negatve
- Look at page 94-99
- When Vmax is reached, the actve sites of all enzyme molecules in the sample are fully occupied by substrate
- The Km of an enzyme is defned as the concentraton of substrate at which the enzyme works at half its
maximum speed. In general, a small Km indicates that a substrate binds very tghtly to the enzyme, and a
large Km indicates weak binding
- In cells energy capture is achieved by means of a coupled reacton, in which an energetcally favorable
reacton is used to drive an energetcally unfavorable one that produces an actvated carrier or some other
useful molecule
- ATP is synthesized in an energetcally unfavorable phosphorylaton reacton, in which a phosphate group is
added to ADP. When required, ATP gives up this energy packet in an energetcally favorable hydrolysis to
ADP and inorganic phosphate Pi.
- The most important of the electron carriers are NADH and the closely related NADPH. Both carry energy in
the form of two high-energy electrons plus a proton, which together form a hydride H- ion. When these
actvated carriers pass their energy to a donor molecule, they become oxidized to form NAD and NADP
- NADPH operates chiefy with enzymes that catalyze anabolic reactons, supplying the high energy electrons
needed to synthesize energy-rich biological molecules.
- NADH, by contrast, has a special role as an intermediate in the catabolic system of reactons that generate
ATP through the oxidaton of food molecules.
- Inside the cell, the rato of NAD to NADH is kept high, whereas the rato of NADP to NADPH is kept low
- Food molecules provide the carbon skeletons for the formaton of macromolecules. The covalent bonds of
these larger molecules are produced by condensaton reactons that are coupled to energetcally favorable
bond changes in actvated carriers such as ATP and NADPH
Hoofdstuk 4
- The fnal folded structure, or conformaton, adopted by any polypeptde chain is determined by energetc
consideratons: a protein generally folds into the shape in which its free energy G, is minimized. The folding
process is thus energetcally favorable, as it releases heat and increases the disorder in the universe
,- Although a protein chain can fold into its correct conformaton without outside help, protein folding in a
living cell is generally assisted by special proteins called chaperone proteins. Some of these chaperones bind
to partly folded chains and help them to fold along the most energetcally favorable pathway. Others form
‘isolaton chambers’ in which single polypeptde chains can fold without the risk of forming aggregates in the
crowded conditons of the cytoplasm. In either case, the fnal three dimensional shape of the protein is stll
specifed by its amino acid sequence, chaperones merely make the folding process more efcient and
reliable
- A helix is a regular structure that resembles a spiral staircase. It is generated simply by placing many similar
subunits next to one another, each in the same strictly repeated relatonship to the one before. An alfa helix
is generated when a single polypeptde chain turns around itself to form a structurally rigid cylinder. A
hydrogen bond is made between every fourth amino acid, linking the C=O of one peptde bond to the N-H of
another. This gives rise to a regular righthanded helix with a complete turn every 3.6 amino acids
- Sometmes two or three alfa helices will wrap around one another to form a partcularly stable structure
known as a coiled coil. This structure forms when the alfa helices have most of their nonpolar (hydrophobic)
side chains on one side, so that they can twist around each other with these side chains facing inward,
minimizing their contact with the aqueous cytosol
- A beta sheet is made when hydrogen bonds form between segments of a polypeptde chain that lie side by
side. When the neighboring segments run in the same orientaton, the structure is a parallel beta sheet,
when they run in opposite directons, the structure is an antparallel beta sheet. Both types of beta sheets
produce very rigid, pleated structure, and they form the core of many proteins.
- A protein structure begins with its amino acid sequence, which is thus considered its primary structure. The
next level of organizaton includes the alfa helices and beta sheets that form within certain segments of the
polypeptde chain, these folds are elements of the proteins secondary structure. The full, three dimensional
conformaton formed by an entre polypeptde chain, including the alfa helices, beta sheets, random coils,
and any other loops and folds that form between the N and C termini, is sometmes referred to as the
tertary structure. Finally if the protein molecule is formed as a complex of more than one polypeptde chain,
then the complete structure is designated its quaternary structure
- A protein domain is any segment of a polypeptde chain that can fold independently into a compact, stable
structure.
- Larger proteins can contain as many as several dozen domains, which are usually connected by relatvely
unstructured lengths of polypeptde chain. Such regions of polypeptde chain lacking any defnite structure,
which contnually bend and fex due to thermal bufetng, are abundant in cells. These intrinsically
disordered sequences are ofen found as short stretches linking domains in otherwise highly ordered
proteins.
- In globular proteins the polypeptde chain folds up into a compact shape like a ball with an irregular surface.
- Fibrous proteins can span to a large distance. These proteins generally have a relatvely simple, elongated
three-dimensional structure.
- Fibrous proteins are especially abundant outside the cell, where they form the gel-like extracellular matrix
that helps bind cells together to form tssues. These proteins are secreted by the cells into their
surroundings, where they ofen assemble into sheets or long fbrils.
- The most common covalent cross-links in proteins are sulfur-sulfur bonds. These disulfde bonds are formed
before a protein is secreted by an enzyme in endoplasmic retculum that links together two SH groups from
cysteine side chains that are adjacent in the folded protein. Disulfde bonds do not change a protein’s
conformaton, but instead act as a sort of atomic staple to reinforce the protein’s most favored
conformaton
- Any substance that is bound by a protein whether it is an ion, a small organic molecule, or a macromolecule
is referred to as a ligand for that protein
- The region of a protein that associates with the ligand is the binding site
- Antbodies are immunoglobulin proteins produced by the immune system in response to foreign molecules,
especially those on the surface of an invading microorganism. Each antbody binds to a partcular target
molecule extremely tghtly, either inactvatng the target directly or marking it for destructon. An antbody
recognizes its target molecule called an antgen with remarkable specifcity.
, - A common type of control occurs when a molecule other than a substrate specifcally binds to an enzyme at
a special regulatory site, altering the rate at which the enzyme converts its substrate to product. In feedback
inhibiton, for example, an enzyme actng early in a reacton pathway is inhibited by a late product of that
pathway. Thus, whenever large quanttes of the fnal product begin to accumulate, the product binds to an
earlier enzyme and slows down its catalytc acton, limitng further entry of substrates into that reacton
pathway. Where pathways branch or intersect, there are usually multple points of control by diferent fnal
products, each of which works to regulate its own synthesis.
- Feedback is negatve regulaton.
- Many, if not most, protein molecules are allosteric: they can adopt two or more slightly diferent
conformatons, and their actvity can be regulated by a shif from one to another
- Protein phosphorylaton involves the enzyme-catalyzed transfer of the terminal phosphate group of ATP to
the hydroxyl group on a serine, threonine, or tyrosine side chain of the protein. This reacton is catalyzed by
a protein kinase. The reverse reacton, dephosphorylaton, is catalyzed by a protein phosphatase.
- In GTP, the phosphate is not enzymatcally transferred from ATP to the protein. Instead, the phosphate is
part of a guanine nucleotde, GTP, that is bound tghtly to various types of GTP-binding proteins. These
proteins act as molecular switches: they are in their actve conformaton when GTP is bound, but they can
hydrolyze this GTP to GDP, which releases a phosphate and fips the protein to an inactve conformaton.
This process is reversible
- Motor proteins generate the forces responsible for muscle contracton and most other eukaryotc cell
movements. They also power the intracellular movements of organelles and macromolecules.
- The central process in a cell is catalyzed by a highly coordinated, linked set of many proteins. In most such
protein machines, the hydrolysis of bound nucleoside triphosphates drives an ordered series of
conformatonal changes in some of the individual protein subunits, enabling the ensemble of proteins to
move coordinately. In this way, the appropriate enzymes can be positoned to carry out successive reactons
in a series, as during the synthesis of proteins on a ribosome, for example.
- The functon of a purifed protein can be discovered by biochemical analyses and its exact three-dimensional
structure can be determined by X-ray crystallography or NMR spectroscopy
Hoofdstuk 5
- A purine is a two-ring base and a pyrimidine is a single-ring base
- Each base pair has a similar width, thus holding the sugar-phosphate backbones an equal distance apart
along the DNA molecule. The members of each base pair can ft together within the double helix because the
two strands of the helix run antparallel to each other, that is, they are oriented with opposite polarites. The
antparallel sugar-phosphate strands then twist around each other to form a double helix containing 0 base
pairs per helical turn. This twistng also contributes to the energetcally favorable conformaton of the DNA
double helix
- The complex of DNA and protein is called chromatn
- A gene is ofen defned as a segment of DNA that contains the instructons for making a partcular protein or
RNA molecule
- During interphase, the chromosomes are extended as long, thin, tangled threads of DNA in the nucleus and
cannot be easily distnguished in the light microscope. We refer to chromosomes in this extended state as
interphase chromosomes.
- One type of nucleotde sequence acts as a replicaton origin, where replicaton of the DNA begins, eukaryotc
chromosomes contain repeated nucleotde sequences that are required for the ends of chromosomes to be
replicated. They also cap the ends of the DNA molecule, preventng them from being mistaken by the cell as
broken DNA in need of repair
- Eukaryotc chromosomes also contain a third type of specialized DNA sequence, called the centromere, that
allows duplicated chromosomes to be separated during the M phase. During this stage of the cell cycle, the
DNA coils up, adoptng a more and more compact structure, ultmately forming highly compacted, or
condensed, mitotc chromosomes. This is the state in which the duplicated chromosomes can be most easily
visualized. Once the chromosomes have condensed, the centromere ataches the mitotc spindle to each
, duplicated chromosome in a way that allows one copy of each chromosome to be segregated to each
daughter cell
- The nucleolus is where the parts of the diferent chromosomes carrying genes that encode ribosomal RNAs
cluster together. Here, ribosomal RNAs are synthesized and combine with proteins to form ribosomes, the
cells protein-synthesizing machines
- The proteins that bind to DNA to form eukaryotc chromosomes are traditonally divided into two general
classes: the histones and the nonhistone chromosomal proteins. Histones are present in enormous
quanttes. The complex of both classes of protein with nuclear DNA is called chromatn
- Histones are responsible for the frst and most fundamental level of chromatn packing, the nucleosome.
- An individual nucleosome core partcle consists of a complex of eight histone proteins, and a stretch of
double stranded DNA, 047 nucleotde pairs long, that winds around this histone octamer. All four of the
histones that make up the octamer are relatvely small proteins, with a high proporton of positvely charged
amino acids. The positve charges help the histones bind tghtly to the negatvely charged sugar-phosphate
backbone of DNA. These numerous electrostatc interactons explain in part why DNA of virtually any
sequence can bind to a histone octamer. Each of the histones in the octamer also has a long, unstructured N-
terminal amino acid ‘tail’ that extends out from the nucleosome core partcle. These histone tails are subject
to several types of reversible, covalent chemical modifcatons that control many aspects of chromatn
structure
- Chromatn-remodeling complexes, protein machines that use the energy of ATP hydrolysis to change the
positon of the DNA wrapped around nucleosomes. The complexes, which atach to both the histone
octamer and the DNA wrapped around it, can locally alter the arrangement of nucleosomes on the DNA ,
making the DNA either more accessible or less accessible to other proteins in the cell.
- The most highly condensed form of interphase chromatn is called heterochromatn. Heterochromatn
typically makes up about 0 % of an interphase chromosome, and in mammalian chromosomes, it is
concentrated around the centromere region and in the telomeres at the ends of the chromosomes
- The rest of the chromatn is called euchromatn
- Each type of chromatn structure is established and maintained by diferent sets of histone tail modifcatons
that atract distnct sets of non-histone proteins. The modifcatons that direct the formaton of the most
common type of heterochromatn.
- Once it has been established, heterochromatn can spread because these histone tail modifcatons atract a
set of heterochromatn-specifc proteins, including histone-modifying-enzymes, which then create the same
histone tail modifcatons on adjacent nucleosomes. These modifcatons in turn recruit more of the
heterochromatn-specifc proteins, causing a wave of condensed chromatn to propagate along the
chromosome. This heterochromatn will contnue to spread untl it encounters a barrier DNA sequence that
stops the propagaton. In this manner, extended regions of heterochromatn can be established along the
DNA.
- Most DNA that is permanently folded into heterochromatn in the cell does not contain genes. Because
heterochromatn is so compact, genes that accidentally become packaged into heterochromatn usually fail
to be expressed.
Hoofdstuk 6
- The process of DNA synthesis is begun by initator proteins that bind to specifc DNA sequences, called
replicaton origins. Here, the initator proteins pry the two DNA strands apart, breaking the hydrogen bonds
between the bases.
- DNA molecules in the process of being replicated contain Y-shaped junctons called replicaton forks. Two
replicaton forks are formed at each replicaton origin. At each fork, a replicaton machine moves along the
DNA, opening up the two strands of the double helix and using each strand as a template to make a new
daughter strand. The two forks move away from the origin in opposite directons, unzipping the DNA double
helix and replicatng the DNA as they go. DNA replicaton in bacterial and eukaryotc chromosomes is
therefore termed bidirectonal
, - The movement of a replicaton fork is driven by the acton of the replicaton machine, at the heart of which is
an enzyme called DNA polymerase. This enzyme catalyzes the additon of nucleotdes to the 3’-end of a
growing DNA strand, using one of the original, parental DNA strands as a template.
- The polymerizaton reacton involves the formaton of a phosphodiester bond between the 3’-end of the
growing DNA chain and the 5’-phosphategroup of the incoming nucleotde, which enters the reacton as a
deoxyribonucleoside triphosphate. The energy for polymerizaton is provided by the incoming
deoxyribonucleoside triphosphate itself: hydrolysis of one of its high-energy phosphate bonds fuels the
reacton that links the nucleotde monomer to the chain, releasing pyrophosphate. Pyrophosphate is further
hydrolyzed to inorganic phosphate Pi which makes the polymerizaton reacton efectvely irreversible
- DNA polymerase does not dissociate from the DNA each tme it adds a new nucleotde to the growing
strand, rather it stays associated with the DNA and moves along the template strand stepwise for many
cycles of the polymerizaton reacton.
- A new DNA chain can only be synthesized in a 5’-to-3’-directon. The DNA strand that appears to grow in the
incorrect 3’-to-5’-directon is actually mad discontnuously, in successive, separate, small pieces, with the
DNA polymerase moving backward with respect to the directon of the replicaton fork movement so that
each new DNA fragment can be polymerized in the 5’-to-3’-directon.
- The resultng small DNA pieces, called Okazaki fragments, are later joined together to form a contnuous new
strand. The DNA strand that is made discontnuously in this way is called the lagging strand, and the other
the leading strand
- Mutatons are avoided because DNA polymerase has two special qualites that greatly increase the accuracy
of DNA replicaton.
- First, the enzyme carefully monitors the base-pairing between each incoming nucleotde and the template
strand. Only when the match is correct does DNA polymerase catalyze the nucleotde-additon reacton.
- Second, when DNA polymerase makes a rare mistake and adds the wrong nucleotde, it can correct the error
through an actvity called proofreading. Proofreading takes place at the same tme as DNA synthesis. Before
the enzyme adds the next nucleotde to a growing DNA strand, it checks whether the previously adds
nucleotde is correctly base-paired to the template strand. If so, the polymerase adds the next nucleotde, if
not, the polymerase clips of the mispaired nucleotde and tries again
- This proofreading mechanism explains why DNA polymerases synthesize DNA only in 5’-to-3’-directon,
despite the need that this imposes for a cumberstone backsttching mechanism at the replicaton fork. A
hypothetcal DNA polymerase that synthesized in 3’-to-5’-directon would be unable to proofread: if it
removed an incorrectly paired nucleotde, the polymerase would create a chemical dead end.
- When a new DNA strand is started, a short length of RNA, about 0 nucleotdes long, is base-paired to the
template strand and provides a base-paired to the template strand and provides a base paired 3’end as a
startng point for DNA polymerase. It thus serves as a primer for DNA synthesis, and the enzyme that
synthesizes the RNA primes is known as primase
- Primase is an example of RNA polymerase, an enzyme that synthesizes RNA using DNA as a template. For the
leading strand, an RNA primer is needed only to start replicaton at a replicaton origin, once a replicaton
fork has been established, the DNA polymerase is contnuously presented with a base-paired 3’ end as it
tracks along the template strand.
- But on the lagging strand, where DNA synthesis is discontnuous, new primers are needed to keep
polymerizaton going. The movement of the replicaton fork contnually exposes unpaired bases on the
lagging strand template, and new RNA primers are laid down at intervals along the newly exposed, single
stranded stretch. DNA polymerase adds a deoxyribonucleotde to the 3’end of each primer to start a new
Okazaki fragment, and it will contnue to elongate this fragment untl it turns into the next RNA primer
- To produce a contnuous new DNA strand from the many separate pieces of nucleic acid made on the lagging
strand, three additonal enzymes are needed. These act quickly to remove the RNA primer, replace it with
DNA, and join the DNA fragments together. Thus, a nuclease degrades the RNA primer, a DNA polymerase
called a repair polymerase then replaces this RNA with DNA, and the enzyme DNA ligase joins the 5’
phosphate end of one DNA fragment to the adjacent 3’-hydroxyl end of the next.
- Primase can begin new polynucleotde chains, but this actvity is possible because the enzyme does not
proofread its work. As a result, primers frequently contain mistakes.
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