CH2. Chemical bonds and Molecular Bonds In Biology Flashcards
What is the essence of the formation of macromolecules?
Bonds
Covalent Bonds
- give an example
- how are these bonds formed?
- why do atoms engage in covalent bonds?
- H2
- e- are shared
- Atoms engage in covalent bonds to make up for the # of missing e-. The fist shell wants 2e- and the other shells want 8e-
Why does bond length matter if the atoms become too close?
- If they are brought too close, the positive charges of the nuclei will create opposing forces
- If they are too far, it would not be close enough for the e- to be shared and orbit around the two nuclei.
The two atoms that are coming together must stay at the defined distance (bond length)
What determines the size of the atom?
The # of protons
What determines the # of e-
Protons
For a molecule of water to be formed, how many e- need to be shared?
For a molecule of water to be formed, 2e- need to be shared.
(The electrons need to be shared by the 2 H atoms - which contain 1 e- in their individual orbits - and the one oxygen atom - w/ 6e- in its orbit.
How many e- are shared between 2 water molecules making an H-bond?
NO e- are shared btwn 2 water molecules making an H-bond. There is NO sharing of e- in H-bonds
Which is stronger: H-bonds or covalent bonds?
H-bonds are weaker than a covalent bond, but they are strong when they are all together in nature and they can affect the structure (e.g. DNA strands are held together by covalent bonds)
Define strength (in terms of bond strength)
Strength = the energy required to break a bond
usually expressed in units of either kilocalories per mole (kcal/ mole) or kilojoules per mole (kj/mole)
What mainly drives interactions btwn molecules in the cell
H-bonds (electrostatic interactions)
What are hydrophobic interactions and why are they important?
Hydrophobic interactions are when hydrophobes (usually no polar substances) come together
—> …comparable to 2 drops of olive oil in a glass of water, they will tend to come together
—> In water, covalent bonds are stronger than non-covalent bonds
What is the function of covalent bonds in biomolecules?
F: forms the backbone of the molecule
What is the function of electrostatic interactions/hydrogen bonds in a biomolecule?
F: to form the structure of a molecule; also allows molecule-molecule interactions
What is the function of the backbone?
The backbone does NOT contribute to the final shape/structure
It means having all the elements aligned to make the shape
Why are covalent bonds formed/broken?
Why are H-bonds formed/broken?
- Covalent bonds are made (or broken) thanks to the help of specialized proteins (NOT spontaneous)
- H-bonds are made (or broken) w/out the help of specialized proteins
DNA
- function?
- made up of what?
F: stores the genetic information/instructions of the cell
Made up of “sugar phosphate(phosphate+sugar) + (letter) base”
→ nucleotide
Nucleotide
Why is their orientations important
Nucleotide= made of a base, a sugar and a phosphate group.
This orientations is essential to the formation of the double-strand DNA later on
What does each DNA strand represent?
What are the strands made of?
Each DNA strand represents the backbone.
It is made out of nucleotides
How is each DNA strand held together?
How is the backbone’s parts held together?
Each strand represents the backbone and is made of nucleotides bonded together.
The strands are held together by H-bonds. The backbone is held together covalent bonds.
What type of bonds link nucleotides together? How is this mechanism driven?
Covalent phosphodiester bonds to link nucleotides forming the single strand DNA (and RNA). Specialized proteins (DNA polymerase) drive this mechanism by making covalent bonds btwn nucleotides.
Why would the double strand of DNA need to open?
DNA replication
What is responsible for the shape and function each cell type will have?
Proteins are responsible for the shape and function each cell type will have.
What types of molecules do proteins attach to?
Proteins blend w/ water, but could, in some case, also attach to lipids.
- Proteins can bind to basically anything (SHAPE IS ESSENTIAL TO ALLOW PROTEIN FUCTION)
Why is it important that proteins have a 3D shape?
This is necessary for protein interactions
- This is important b/c proteins don’t work alone. They need to interact w/ other molecules to do things
What do amino acids do in proteins?
Amino acids and bonds define the shape and function of the proteins
Why is the coronavirus able to affect us?
The shape of the coronavirus allows it to affect us; it makes contact w/ the transmembrane ACE-2 receptor
- There are no proteins in the skin that recognize the COVID-19 spike protein. The ACE-2 receptor accumulates in the respiratory system
What does the shape of the protein affect in regards w/ other molecules
Thee shape of a protein defines the interacton(s) it will be able to make with other molecules
What is one important function of proteins in a synaptic vesicle?
There are many proteins that are able to facilitate a neuron’s job.
What type of bond joins amino acids together?
Proteins are made when covalent bonds are formed btwn the COOH group of the preceding amino acid and a NH2 group (called peptide bonds) of the following one along the chain. (during the process, one molecule of water is released)
All proteins have the same direction…H2N…COOH (They all have an unbound H2N and, eventually, end at COOH)
- We have as many peptide bonds as are we have amino acids
What are the building blocks of amino acids?
- amino group [H2N]
- carbonyl group [COOH]
- side chain [R]
What is responsible for the shape and function of each protein?
(a) Non-covalent chemical bonds within the protein itself also determine the shape of a protein
(b) The type of protein folding (e.g. alpha helix, beta sheet)
(c) The chemistry of the side chain determines the protein
Why do hydrophobic interactions happen in proteins?
- hydrophobic interaction happen b/c of hydrophobic side-chains
- these usually form the core of a protein (this is like drops of olive oil wanting to group together in water)
Why are electrons depicted as a continuous cloud?
What does the shading of the cloud depict?
Electrons depicted as a continuous cloud b/c there’s no way of predicting where they would be in a particular instant
The shading of the cloud depicts the probability that electrons will be found there
What is the range of diameters for e- clouds?
The density of shading of the cloud is an indication of the probability that electrons will be found there. The diameter of the electron cloud ranges from about 0.1 nm (for hydrogen) to about 0.4 nm (for atoms of high atomic number). The nucleus is very much smaller: about 5 x 1CT 6 nm for carbon, for example.
What do the black lines in this diagram represent?
The concentric black circles represent in a highly schematic form the “orbits” (that is, the different distributions) of the electrons.
What is the smallest partical that still retains its distinctive chemical properties?
The smallest particle of an element that still retains its distinctive chemical properties is an atom. The characteristics of substances other than pure elements—including the materials from which living cells are made—depend on which atoms they contain and the way these atoms are linked together in groups to form molecules.
What “value” of an atom dictates chemical behavior
atomic number
The electric charge carried by each proton is exactly equal and opposite to the charge carried by a single electron. Because the whole atom is electrically neutral, the number of negatively charged electrons surrounding the nucleus is equal to the number of positively charged protons that the nucleus contains; thus the number of electrons in an atom also equals the atomic number.
Why can isotopes exist?
Neutrons have essentially the same mass as protons. They contribute to the structural stability of the nucleus—if there are too many or too few, the nucleus may disintegrate by radioactive decay—but they do not alter the chemical properties of the atom. Thus an element can exist in several physically distinguishable but chemically identical forms, called isotopes, each having a different number of neutrons but the same number of protons.
Multiple isotopes of almost all the elements occur naturally,
What allows archaeologists to estimate the age of organic material?
Carbon 14 undergoes radioactive decay at a slow but steady rate, which allows archaeologists to estimate the age of organic material.
What is atomic weight? Molecular weight?
The atomic weight of an atom, or the molecular weight of a molecule, is its mass relative to that of a hydrogen atom.
What is the mass of an atom/molecule measured in?
Daltons
1 Dalton = 1 amu = approximate mass of one H atom
How much does a proton/neutron weigh?
1/6x10^23 grams
How much does one carbon atom weigh?
6x10^23 molecules
This if called Avogadro’s number
What is a mole quantitiatively?
What is a mole conceptually?
A mole is X grams of a substance, where X is the molecular weight of the substance. A mole will contain 6 x 10 23 molecules of the substance.
The concept of mole is used widely in chemistry as a way to represent the number of molecules that are available to participate in chemical reactions.
1 mole of carbon weighs 12 g 1 mole of glucose weighs 180 g 1 mole of sodium chloride weighs 58 g
A one molar solution has a concentration of 1 mole of the substance in 1 liter of solution. A 1 M solution of glucose, for example, contains 180 g/l, and a one millimolar (1 mM) solution contains 180 mg/I.
The standard abbreviation for gram is g; the abbreviation for liter is L.
When is the arrangement of electrons most stable?
The arrangement of electrons in an atom is most stable when all the electrons are in the most tightly bound states that are possible for them— that is, when they occupy the innermost shells, closest to the nucleus.
True or false: All of the elements commonly found in living organisms have outermost shells that are not completely filled with electrons
True: An element’s chemical reactivity depends on how its outermost electron shell is filled. All of the elements commonly found in living organisms have outermost shells that are not completely filled with electrons and can thus participate in chemical reactions with other atoms.
Why do we see a recurrence of elements of similar properties in the areas of the periodic table?
Because the state of the outer electron shell determines the chemical properties of an element, when the elements are listed in order of their atomic number we see a periodic recurrence of elements with similar properties: an element with, say, an incomplete second shell containing one electron will behave in much the same way as an element that has filled its second shell and has an incomplete third shell containing one electron.
What type of bonds is a molecule held together by?
A molecule is a cluster of atoms held together by covalent bonds, in which electrons are shared rather than transferred between atoms. The shared electrons complete the outer shells of the interacting atoms.
What are polar covalent bonds?
Covalent bonds in which the electrons are shared unequally in this way are known as polar covalent bonds.
Is it true that covalent bonds are always much stronger than ionic bonds?
When water is present, covalent bonds are much stronger than ionic bonds. In ionic bonds, electrons are transferred rather than shared, as we now discuss
Why are ionic bonds normally formed?
Ionic bonds are usually formed between atoms that can attain a completely filled outer shell most easily by donating electrons to—or accepting electrons from—another atom, rather than by sharing them.
For example, we see that a sodium (Na) atom can achieve a filled outer shell by giving up the single electron in its third shell. By contrast, a chlorine (Cl) atom can complete its outer shell by gaining just one electron. Consequently, if a Na atom encounters a Cl atom, an electron can jump from the Na to the Cl, leaving both atoms with filled outer shells. The offspring of this marriage between sodium, a soft and intensely reactive metal, and chlorine, a toxic green gas, is table salt (NaCl).
What are “salts”?
These are ions held together by ionic bonds
What, if anything, is wrong with the following statement: “When NaCl is dissolved in water, the water molecules closest to the ions will tend to preferentially orient themselves so that their oxygen atoms face the sodium ions and face away from the chloride ions”? Explain your answer.
The statement is correct. The hydrogen – oxygen bond in water molecules is polar, so that the oxygen atom carries a more negative charge than the hydrogen atoms. These partial negative charges are attracted to the positively charged sodium ions but are repelled from the negatively charged chloride ions.
What types of bonds help to bring molecules together in cells?
noncovalent bonds
What are electrostatic attractions? What makes them stronger?
Attraction caused by a complementary set of charges
The ionic bonds that hold together the Na + and Cl - ions in a salt crystal are a form of noncovalent bond called an electrostatic attraction. Electrostatic attractions are strongest when the atoms involved are fully charged, as are Na + and Cl - . But a weaker electrostatic attraction also occurs between molecules that contain polar covalent bonds
How are these proteins binding in the image?
noncovalent, electrostatic interactions
A large molecule, such as a protein, can bind to another protein through complementary charges on the surface of each molecule. In the aqueous environment of a cell, the many individual electrostatic attractions shown would help the two proteins stay bound to each other.
Why (because of what force) is water a liquid at room temperature and not a gas?
It is because of these interlocking hydrogen bonds that water at room temperature is a liquid—with a high boiling point and high surface tension—and not a gas. Without hydrogen bonds, life as we know it could not exist.
When do H-bonds form?
In general, a hydrogen bond can form whenever a positively charged H atom held in one molecule by a polar covalent linkage comes close to a negatively charged atom— typically an oxygen or a nitrogen—belonging to another molecule
Give examples of hydrophilic molecules:
A large proportion of the molecules in the aqueous environment of a cell fall into this category, including sugars, DNA, RNA, and a majority of proteins.
What are the three main properties of hydrophobic molecules?
Hydrophobic (“water-fearing”) molecules are:
(1) uncharged and
(2) form few or no hydrogen bonds, and they
(3) do not dissolve in water.
Why is it important that lipids don’t dissolve in water?
Because lipids do not dissolve in water, they can form the thin membrane barriers that keep the aqueous interior of the cell separate from the surrounding aqueous environment
True or false: the reason protons are not constantly exchanged between molecules is because of the stability of the water molecule
False: Protons move continuously from one water molecule to another in aqueous solutions.
(A) The reaction that takes place when a molecule of acetic acid dissolves in water. At pH 7, nearly all of the acetic acid molecules are present as acetate ions.
(B) Water molecules are continually exchanging protons with each other to form hydronium and hydroxyl ions. These ions in turn rapidly recombine to form water molecules.
A. Are there any H 3 0 + ions present in pure water at neutral pH (i.e., at pH = 7.0)? If so, how are they formed?
B. If they exist, what is the ratio of H 3 0 + ions to H 2 O molecules at neutral pH? (Hint: the molecular weight of water is 18, and 1 liter of water weighs 1 kg.)
A. Yes. Hydronium (H3O+) ions are formed when water dissociates into protons and hydroxyl ions, with each proton forming a hydronium ion by attaching to a water molecule (2H2O—> H20 + H+ + OH- –> H3O+ + OH-). At neutral pH, the amounts of H3O+ ions and OH- ions are equal in the absence of an acid that provides more H3O+ ions or a base that provides more OH- ions. We know that the pH at neutrality is 7.0, hence the H+ concentration is 10-7 M. The concentration of H+ is equivalent to the concentration of H3O+.
B. We need to know the concentration of water molecules in order to compute the ratio of H3O+ ions to H2O molecules. Water has a molecular weight of 18 (i.e., 18 g/mole), and 1 liter weighs 1 kilogram. The concentration of water is thus 55.6 M (=1000(g/l)/(18 g/mole)), and the ratio of H3O+ ions to H2O molecules is 1.8x10^-9 (=10^-7/55.6): at neutral pH, for example, just two water molecules in a billion are dissociated.
What keeps the interior of the cell close to neutral?
Buffers
True or false: Water is an inorganic molecule
True. The small and large carbon compounds made by cells are called organic molecules. By contrast, all other molecules, including water, are said to be inorganic.
What are the 4 main families of small organic molecules in cells?
Sugars, fatty acids, amino acids, and nucleotides are the four main families of small organic molecules in cells.
They form the monomeric building blocks, or subunits, for larger organic molecules, including most of the macromolecules and other molecular assemblies of the cell. Some, like the sugars and the fatty acids, are also energy sources.
Where are small organic molecules mainly found? What are their two main roles?
(1) They are usually found free in solution in the cytosol and have many different roles.
Many have more than one role in the cell—acting, for example, as both a potential subunit for a macromolecule and as an energy source. The small organic molecules are much less abundant than the organic macromolecules
In ball and stick models, what atom corresponds to black? White? Red? Blue?
C = black
H = white
O = red
N = blue
What type of model is this?
(doesn’t have a specific name) A structural formula in which the atoms are shown as chemical symbols, linked together by solid lines representing the covalent bonds. The thickened lines are used to indicate the plane of the sugar ring and to show that the -H and -OH groups are not in the same plane as the ring.
What type of model is this?
Another kind of structural formula that shows the three- dimensional structure of glucose in the so-called “chair configuration.”
What type of model is this?
A ball-and-stick model in which the three-dimensional arrangement of the atoms in space is indicated.
What type of model is this?
A space-filling model, which, as well as depicting the three-dimensional arrangement of the atoms, also gives some idea of their relative sizes and of the surface contours of the molecule
monosaccharides
- two other names
- general formula
- does the general formula fully define the molecule?
- alternative forms?
- sugars; carbohydrates
- general formula (CH20)n(n is usually 3, 4, 5, or 6)
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No, there can be isomers; glucose can be converted into mannose or galactose)
- Yes, there can be optical isomers; Each of these sugars, moreover, can exist in either of two forms, called the D-form (rotates plane-polarized light to the right) and the L-form (rotates plane-polarized light to the left), which are mirror images of each other
optical isomers
mirror images of isomers; enantiomers
- different molecules “handedness”
- same formula
- non-superimposable mirror images
- the L-isomer if preferred in the body b/c there is an overabundance of L-receptors
monosaccarides
- linked together by what type of bonds? What are these bonds called?
- atomically describe the formation of one of these bonds
- atomically describe the breaking of one of these bonds
- covalent bonds; glycosidic bonds
- The way sugars are linked together illustrates some common features of biochemical bond formation. A bond is formed between an -OH group on one sugar and an -OH group on another by a condensation reaction, in which a molecule of water is expelled as the bond is formed.
- The bonds created by all of these condensation reactions can be broken by the reverse process of hydrolysis, in which a molecule of water is consumed
What is the most abundant organic molecule on earth?
The most abundant organic molecule on Earth—the cellulose that forms plant cell walls—is a polysaccharide of glucose.
Chitin
- F:
- made of what?
- F: extraordinarily abundant organic substance, the chitin of insect exoskeletons and fungal cell walls, is also a polysaccharide
- in this case, a linear polymer of a sugar derivative called N-acetylglucosamine
saturated vs. unsaturated fats
saturated = no double bonds; solid @ room temp; saturated fats are found in meat and dairy products
unsaturated = double bonds; bent tails; plant oils, such as corn oil, contain unsaturated fatty acids, which may be monounsaturated (containing one double bond) or polyunsaturated (containing multiple double bonds); this is why plant oils are liquid at room temperature; The double bonds create kinks in the hydrocarbon tails, interfering with their ability to pack together,
phospholipids
- structure + function
- 2 hydrophobic fatty acid tails; 1 hydrophilic head that contains a phosphate group (negatively charged)
With their two hydrophobic fatty acid tails and a hydrophilic, phosphate-containing head, phospholipids are strongly amphipathic. This characteristic amphipathic composition and shape gives them different physical and chemical properties from triacylglycerols, which are predominantly hydrophobic.
What determines the nature of each amino acid?
Side chains determine the nature of each amino acid.
The side chains come together to help the initial steps of the folding process; THEY DO NOT DETERMINE THE FINAL STRUCTURE
The H-bonds happen every __ amino acids.
The H-bonds happen every 4 amino acids
Describe the bond(s) for the situations below
- backbone to backbone
- backbone to side chain
- side chain to side chain
***see image
***see image
The higher number of chances to be folded into something is when we haven’t started folding anything
As the paper is folded, the number of possibilities to fold it in different ways are reduced…In protein folding, it is the number of folding possibility.
- The higher the number of folding possibility, the less stable the protein will be; The amount of free energy is highest when the protein is unfolded and will decrease when it folds
- In nature, proteins will fold so that they can reach their own lowest level of free energy to remain stable (“stable” doesn’t mean it can’t be modified).
- (the image is called the “folding funnel”)
structure of an amino acid
All amino acids have an amino group, a carboxyl group, and a side chain (R) attached to their a-carbon atom. In the cell, where the pH is close to 7, free amino acids exist in their ionized form; but, when they are incorporated into a polypeptide chain, the charges on their amino and carboxyl groups disappear.
The amino acid shown is alanine, one of the simplest amino acids, which has a methyl group (CH 3 ) as its side chain.
(don’t answer): amino acid info
Twenty types of amino acids are commonly found in proteins, each with a different side chain attached to the a-carbon atom. The same 20 amino acids are found in all proteins, whether they hail from bacteria, plants, or animals. How this precise set of 20 amino acids came to be chosen is one of the mysteries surrounding the evolution of life; there is no obvious chemical reason why other amino acids could not have served just as well. But once the selection had been locked into place, it could not be changed, as too much chemistry had evolved to exploit it. Switching the types of amino acids used by cells would require a living creature to retool its entire metabolism to cope with the new building blocks.
Like sugars, all amino acids (except glycine) exist as optical isomers in d- and L-forms. But only L-forms are ever found in proteins (although D-amino acids occur as part of bacterial cell walls and in some antibiotics, and D-serine is used as a signal molecule in the brain). The origin of this exclusive use of L-amino acids to make proteins is another evolutionary mystery.
The four amino acids shown are linked together by three peptide bonds, one of which is highlighted in yellow. One of the amino acids, glutamic acid, is shaded in gray. The amino acid side chains are shown in red. The two ends of a polypeptide chain are chemically distinct. One end, the N-terminus, is capped by an amino group, and the other, the C-terminus, ends in a carboxyl group.
The sequence of amino acids in a protein is abbreviated using either a three-letter or a one-letter code, and the sequence is always read from the N-terminus
***refer to image
C. If we change the conformation, we change the interaction
Why is the free energy fluctuating in the image?
there can be thermal changes or collisions in the cell
What would happen if chaperones were not present?
Folding is a continuous mechanism; if chaperones are not present, there would be loss of correct folding
What types of interactions happen between ligands and proteins?
Electrostatic interactions (weak interactions); NOT covalent
What is responsible for releasing?
beta and gama secretase are responsible for releasing the B-amyloid plaque into the APP molecule
How does the B-amyoid make the aggregate?
Each of the stretches of B-amyloid turns into a beta sheet from an alpha helix (caused by hydrophobic interactions).
An aggregate refers to the beta street structure here?
What is it that makes the B-amyloid form the plaque?
The intrinsic nature of the B-amyloid causes it to form H–bonds w/ one another; this gives the system rigidity, so it’s hard to disassemble
aggregates still have free energy, even though they are rigid
What does this image show?
As an aggregate is formed, the system of the aggregate reaches a stability that makes it more difficult to change the structure again
What is a 5-reel?
A larger aggregate of many molecules in a beta sheet
What two problems can misfolding cause?
(1) an alpha helix might turn into a beta sheet structure (has rigidity) (2) A change in function (makes it inactive)
When we see Alzheimer’s under a microscope, what are we actually seeing?
Protofibrils
T or F: misfolding only affects the brain
diseases associated to misfolding are not specific to brain diseases; they can also affect the heart and the kidneys; this can lead to loss of the organ’s function
What do alpha synuclein cause?
found in the pulmanergic nuerons; problem w/ Parkingson’s disease
What does protein tau cause?
Many neurodegenerative diseases caused by alpha helixes that turn into beta sheets
What is prion’s disease?
Mad cow disease
What is phosphorylation?
the addition of a phosphate group to a protein to turn its functions off
What happened w/ Rosaline Franklin?
She had trouble pronouncing her own name and discovered how the nucleotides are organized.
By using beams and an x-ray, she was able to see the diffraction patterns of the DNA on the film
What carbon is the phosphate group bound to in a nucleotide?
Phosphate group: bound to the 5th carbon of the sugar; this is important b/c it determines how nucleotides come together
Are H–bonds formed randomly in DNA?
What nucleotide bond is favored?
No, H–bonds are always btwn an adenine w/ a guanine and a cytosine w/ the thymine
A-T is easier to pull apart than C-G
How many chromosomes are needed to make life possible?
46
23 chromosomes from mom; 23 from dad
What is the purpose of genes?
Provides the information to generate proteins
What does this tell us?
Not all DNA is used to store information
Some is for structuring of the DNA and some is for packaging of the DNA
The two strands are not identical (different information may be stored in each strand; they can be used to store different types of genetic information)
What are the covalent bonds that hold the backbone together called?
phosphate de-ester bonds
What are chromosomes attached to in a cell?
They are located in a cell’s nucleus and they are attached to the nuclear membrane
For most of the life of chromosomes, is it usually compacted or dispersed?
For most of the life of the cell, the DNA found in the nucleus is slightly dispersed
How can we fit chromosomes in the nucleus?
What are two reasons why this is important?
What two things does it enable the cell to do?
The DNA wraps around itself and proteins in beads
- It allows the long DNA molecule to fit into a small place like the nucleus
- Organization also allows accessibility to DNA
- This enables the correct copying of DNA
- To use the genetic information stored to express proteins
What is DNA wrapped around?
nucleosomes (forms of proteins that are wrapped in disks)
**know the Hs (histomes)
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It can be wrapped differently
But when we look @ thee unwrapped ones, we aree looking at individual nucleosomes.
The space btwn the nucleeosomes changes
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This sits inside the nucleosomes, making the distance btwn them shorter
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histomes make the nucleosomes
nucleosomes are made of 4 different kinds of histomes (representeed by two molecules of eact; for a total of 8 molecules)
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A tail is a part of the protein that does not directly react w/ everything
They are what allows the DNA to become accessable
DNA is a negatively charged molecule b/c of the phosphate groups. Histomes are positive, so they are attracted to DNA. This is how it unwrapps the DNA to make it more or less accessible
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What are these small beads
a chromosome
a pair is called “chromatids”
What are nucleosomes and what do we call the DNA that is wrapped around the nucleosomes?
?
chromatin
The filament of DNA (147 nucleotides) wraps around twice
- this means that each nucleosome has a defined size (the size depends on the protein content of the nucleosome itself)
If we have a positively charged tail, will it be more or less attracted to the nucleosome?
It will be more attracted to the nucleosome and make the DNA less accessible
What do acetylation groups do?
Acetylation occurs on the positively charged amino acids
The acetylation group covers the positive charge (like putting a HAT on the positive charge)
This is like tranfering an acetyl group.
Whenever we have an acetylation, we are putting a hat on something with a positive charge. This results in loosening up the DNA from the nucleosome
What is HDACs
Histones DeAcetylation
These remove the acetyl hat“HAT”
Why is the ability to pass modifications from one nucleosomes to the next important
This leads to the generation of DNA that will carry the same modifications (until it hits a barrier DNA sequence)
What does ATP chromatin do?
ATP chromatin remodeling complexes (formed my many molecules of protein together that can bind to nucleosomes and DNA) require energy
They condense and decondense
Generally, how does DNA change in the cell cycle?
How is this cycle able to happen
- DNA changes in terms of structure and amount in the cell cycle.
- The DNA generation carries 1 chromosome from maternal inheritance and 1 chromosome from paternal inheritance
- Modifications need to be made on the DNA
Speak about the relevant charges on a histone
The histones carry a positive charge
Arginines and lysines
Acetylation puts a HAT (histone acetyl transferase) on the positive group → uncoiling of DNA (opens structure)
The protein that removes this HAT is HDACs (Histone DeAcetylase) → tight coiling of DNA
How does chromatin remodeling complexes lead to the creation of chromatin fiber?
chromatin remodeling complexes unwrap the DNA from the chromosome to make chromatin fiber
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Descibe T and C
There are specific areas along the sequence that have a specific function
- telomeres = prevent damage and cutting of the chromosome (there are no genes here, so this usually remains super compacted)
- centromere = is employed during cell division (there are no genes here, so this usually remains super compacted)
What is special about these regions of the DNA
remains super compacted
Telomeres protect the ends of chromosomes from proteins (the mechanisms could randomly start breaking down the ends of the chromosomes)
What do we need to do first to copy DNA
We need to separate these two strands by breaking the hydrogen bonds between the C-G and T-A
- the 1st step is denaturation
Why do we say each strand of DNA has the fist nucleotide of the sequence
B/c DNA synthesis always occurs from the 5’ to the 3’ direction
nucleotides are added to thee 3’ end of the last nucleotide of the already-existing growing strand
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Why are replication origin important?
Whenever we replicate DNA in the test tube, what is one way to denature the DNA?
- @ 90 degrees celsius
- gets rid of the hydrogen bonds
- we can NEVER denature the entire chromosome
Does DNA replication or division occur in interphase?
DNA replication occurs in interephase
The first step of PCR?
denaturation
What are the two strands of DNA that are used for replication called?
The starting strands are called templates/parental DNA
A new strand will be synthesized/annealed
Why is DNA synthesis antiparallel?
DNA is synthesized from 5’ to 3’
What nucleotides need to be at the replication origin domains
Replication origin domains are the regions that enter denaturation first.
AT nucleotides need to be at the replication origin domains b/c they make 2 Hydrogen bonds
What does this figure tell us?
The figure tells us that synthesis starts as soon as thee replication origin domain is opened
Considering how long chromosomes are, how is this mechanism occurring?
We use replication forks (one that opens on the left and one that opens on the right)
What does this show?
The opening of the replication origins using forks; the forks will eventually meet one another while going down the DNA
What direction does the used template strand go in during replication?
Synthesis occurs ONLY in the 5’-to-3’ direction.
This means that the used TEMPLATE DNA strand will be in the 3’-to-5’ direction.
How can we copy two strands that are opening in the same direction and running antiparallel, using an enzyme (the fork) that only runs in one direction?
This is the lagging strand that slows down the synthesis of the DNA
The lagging strand synthesizes in pieces; the antiparallel strand becomes available to copy one piece at a time; the first fragment available will be in the middle of the opening; all the Okazaki fragments will, eventually form the “lagging DNA strand”
Synthesis follows the direction of the opening of the fork.
This means that DNA is synthesized on both template strands AS the template strands separate.
What are Okazaki fragments?
The Lagging strand is synthesized one little piece at the time!! Each little piece is called Okazaki Fragment. They will be later bound together.
