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biochemistry 1


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Noura Al shalan


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[Front]


what are the 8 characteristics of living organisms?
[Back]


cell composition, order, stimuli response, homeostasis, reproduction ,dynamic metabolism, heredity, evolution.

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biochemistry 1 - Details

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What does biochemistry study?
Physical and chemical processes in living organisms.
What's the difference between chemical and physical processes?
Chemical processes change the chemical composition and physical processes do not change chemical processes.
What are the 8 characteristics of living organisms?
Cell composition, order, stimuli response, homeostasis, reproduction ,dynamic metabolism, heredity, evolution.
What are the biochemical unit of life?
Macromolecules, molecules, atoms
What is abiogenesis?
The natural process of origin of life , how it arose from nonliving molecules (probiotic)
State atmospheric & hydrothermal theories ?
Atmospheric (sun+lightning) and hydrothermal (vents on ocean floor with no sunlight ) transform prebiotic molecules too biomolecules.
What is the double origin theory?
Coding system (RNA) and enzyme catalyst originated separately protocell then combined .
What directionality does nucleic acid start with?
5' to 3' and with DNA(strands are anti-parallel regarding direction)
What does the nucleotide monomer consist of ?
1-phosphate group, 2- pentos sugar (ribose or deoxyribose ) ,3- nutritious base
What's the difference between DNA and RNA?
RNA has ribose sugar and DNA has deoxyribose sugar which lacks an oxygen atom.
What base pairs are complementing regarding DNA and RNA and the bonds between them?
DNA (T-A (2 hydrogen bonds),C-G (3 hydrogen bonds)) RNA(A-U,C-G)
What are the nucleotides that are Pyramidines and purines?
Pure as gold , purines (A-G) with double rings / Pyramidines (U-C-T) only one ring.
The DNA and RNA difference regarding functions?
DNA( hereditary unit) RNA (hereditary unit , catalytic functions(ribozymes))
What are protein monomers? do they have directionality?
Amino acids that have N-terminals (amino group) and C-terminals (carboxyl group) ends
How are proteins differentiated from each other? and what do they all have in common?
Their R group differentiates them , they all have (central carbon, central hydrogen, amino group, carboxyl group)
What are the 4 different structures of proteins? explain?
Primary ( order of amino acids), secondary ( a-helices and B-sheets), tertiary (3D shape) , and quaternary (multiple amino acid chains)
What do enzymes do ? what are their parts ? what is their role in the rate of reactions?
They catalyze reactions (speed up) parts (substrate, active site) they become the enzyme substrate complex. enzymes decrease activation energy thus increasing the rate of a reaction.
What carbohydrates consist of and what is their general formula?
(carbon, hydrogen , and oxygen) the formula is C(n)H(2n)O(n)
What are monosaccharides? example?
They are the subunits of carbs that have several hydroxyl groups (OH) EX: glucose
Polysaccharide Examples 5 and their functions ?
Starch ( energy storage in plants ) glycogen (energy storage in plants) cellulose ( plant cell wall) peptidoglycan (bacterial cell wall) chitin ( hard shells of animals)
What do lipids include? are they hydrophobic or hydrophilic ?
They are hydrophobic molecules they include phospholipids( cell membranes) fats ( long term energy storage in animals) oils (long time energy storage in plants) steroids ( sex hormones , cholesterols ) waxes ( protection and prevention)
What are phospholipids and what are their parts ?
Phospholipids are amphipathic containing a hydrophilic head (polar) and hydrophobic tale (non-polar)
What are cell membranes?
They are a phospholipid bilayer that is semi-permiable that allow only non-polar small molecules to enter without needing energy.
What is taxonomy ?what are the 8 classifications ?
Is a science branch that clarifies, identify and name organisms . the parts are (domain , kingdom, phylum, class, order , family, genus, species)
What are the tree types of domains?
Archea (prokaryote), eukarya (multicellular), bacteria(prokaryote)
What is the endomembrane system functions ?
Secreting , modifying , transporting
The nucleus (nuclear envelope) function ?
Stores and protects DNA, controls nuclear transport
Rough endoplasmic reticulum (ER) function?
Studded with ribosomes ,modifies and help proteins fold
Smooth endoplasmic reticulum (ER) function?
Detoxifies the cell, makes carb /lipids
The golgi apparatus function ?
Modifies proteins/ lipids to ship to final location.
Vesicles ( lysomes ) function?
Membrane bubbles that digest or breakdown and recycle chemicals using enzymes.
What are the ribosomes in procaryotes and eukaryotes with their subunits?
Eukaryotes 80s (60s and 40s) , procaryotes 70s (50s and 30s)
What is the composition of the cytoskeleton?
Actin at the peripheral , intermediate filaments all over the cell , microtubules aids in nuclear division.
What is the endosymbiotic theory?
That the mitochondria and chloroplast( cyanobacteria) once lived as independent aerobic bacteria that went into an aerobic host and lived with a symbiotic relationship .
What is the mitochondria function and structure?
Produce ATP via oxidative energy metabolism , (transforming clucose into ATP releasing water and CO2) and it has a inner and outer membrane .
What is the chloroplast function?
Transforming solar energy into chemical energy ( phototroph )by photosynthesis by transforming CO2 and water with sunlight into glucose.
What is the central dogma ?
Transcription (DNA to RNA) and translation (mRNA to proteins) its unidirectional DNA to RNA is reversible but RNA to proteins is not .
RNA directionality ?
5' to 3' aligned on DNA template
What are functional groups ?
Molecules abundant biomolecules and are usually reactive
What does each biomolecule contain (functional group)?
Amino acids (amino group, carboxyl), carb (hydroxyl group , ether) ,lipids (methyl groups), nucleotide (phosphatediether)
What as the essential/abundant element of life (most mass, ions)
Most of the mass ( C,H,N,P,S,O) ions (Na,Ca,Cl,Mg,K)
What are the two types of chemical bonds?
Intra-molecular bond ( the bonds inside a molecule) inter-molecular bond (bonds between different molecules)
What's the difference between ionic bonds and covalent bonds?
The ionic bond is when electrons are lost or gain my opposite charged atoms, covalent bonds is when electrons are shared between atoms.
State the 3 intermolecular bonds?
Hydrogen bonds (when hydrogen bonds with NOF), dipole-dipole (the shift of electrons to the atom that's more electronegative), van der waals ( forces that exist between all molecules)
What's the difference between configuration and conformation?
Configuration is the fixed 3D arrangement (can only be changed if bonds are broken ) , conformation potential fixable 3D arrangement.
What is entropy?
Its a property of thermodynamics that measures of randomness of a system
What's an open system?
Is when the system exchanges mass and energy with its surroundings
Does entropy ever increase?
Entropy can decrease locally but universal entropy always increases.
Does entropy increase with more or less molecules?
More molecules increase entropy and when states change from atoms close to each other the further apart entropy increases .
What is gibbs free energy ?
Its energy in a system that is able to do work.
Gibs energy general formula?
Change G= change H(enthalpy) -T(K) change S(entropy)
What is the second law of thermodynamics?
That 100% energy conversion is impossible because thermal energy is always lost, increasing universal entropy.
What are exergonic ,endergonic and endothermic , exothermic reactions?
Exergonic reactions (release energy ) -G and endergonic reactions (absorb energy) +G. endothermic reactions absorb energy as heat and exothermic reactions release energy as heat.
What does the stability ,order and local entropy of a reaction depend on?
The more energy it has the less stable it is , the order increases with more energy and local energy increases when energy is released.
What the characteristics of a reaction at equilibrium?
1- forward and backward reactions have the same rate, 2- change G =0,3- its at its most stable, the ration or concentration of reactants and products is constant.
How does Keq react towards temp ? what if the temp is not mentioned?
Keq changes when temp changes, if the temp is not mentioned we assume its 25C or 298 kelvin.
How does Keq relate to the favoring products or reactants?
Keq=1 (at equilibrium) Keq<1 (favors products) Keq>1 ( favors reactants)
What the difference between Keq or Q?
K at equilibrium and Q not at equilibrium
How to know the direction Q and Keq?
When Q<Keq (left to right, forward) when Q>Keq (right left, backward) Q=Keq equilibrium.
What is the formula for standard conditions (change G)?
Change G(standard) =-RTln(Keq) R=8.315j/molxK
What's the difference between autotrophs and heterotrophs?
Autotrophs prepare their own food by photosynthesis , while heterotrophs can't make their own food so they depend on autotrophs.
What are chemoautotrophs and chemoheterotrophs?
Chemoautotrophs use inorganic compounds to synthesis energy using CO2, and chemoheterotroph use organic compounds to synthesis energy.
What are photoautotrophs and photoheterotrophs?
Photoautotrophs uses light as an energy souse and obtains inorganic carbon CO2. photoheterotrophs uses light as an energy souse and obtained organic compounds from other organisms.
What are closed systems , open systems and isolated system?
An open system exchanges energy and matter with surroundings, a closed system exchanges energy and but not matter with surroundings, an isolated system does not exchange energy nor matter with surroundings.
How do endothermic reactions become exergonic ?
Only at temperatures T yielding an entropic contribution T⋅ΔRS>ΔRH
What's a genome and proteome?
A genome is a complete set of genetic material in an organism, and a proteome is the complete set of proteins in an organism .
What's the reason for stereo specificity ?
Because each stereoisomeric reactants, behaves in its own specific way and reacts differently.
What are the benefits of drawbacks of mutations?
The benefits are that you will not get diseases such as (cancer , diabetes and asthma). and their benifits is that they will get get new capabilities that will aid them in survival.
What's the endosymbiotic theory?
Its that the mitochondria and chloroplast were once independent aerobic living organisms (bacteria) that were engulfed by an anaerobic host cell. this is suggest ed because they have genetic material , and their ribosomes are 70s like that of bacteria.
What are homologs , orthologs , and paralogs?
They are gene homologs (similar genes) , paralogs are from (same species) , oethologs are from (different species)
What's the theory of biogenesis ? and what is it missing?
Is the theory that living things come from other living things by reproduction, he did that by boiling meat broth that then fogged up and then maggots or bacteria grew on the meat proving his theory right. but it did not explain how the first living organisms arose.
What's oparin,ury theory experiment? what are coacervates ?
This experiment abiotic formation of organic compounds through chemical under primitive atmospheric conditions, that eventually transformed into biological macromolecules. a coacervates is a fluid phase that is rich in macromolecules , its like a synthetic polymer .
Why is the activation barrier important in enzymatic driven reactions?
Because activation energy constitutes a barrier for the reaction progress limiting and Enzymes reduce activation energy increasing the rate of reaction.
What is anabolism and catabolism ?
Anabolism creates molecules by using energy, Catabolism breaks down complex molecules and releases energy.
What is the difference between enantiomers and diastereomers ?
Enantiomers contain chiral centers that are non-superimposable & mirror images. Diastereomers contain chiral centers are non-superimposable but are NOT mirror images.
What are anomers?
Anomers are cyclic monosaccharides that are epimers, differing from each other in the configuration of C-1 .
What are cis-trans isomers ?
Cis isomers are when both atoms are at the same side of the double bond and trans is when they are at opposite sides.
What are geometric isomers?
Geometric isomers are two or more compounds which contain the same number and types of atoms, the same connectivity but with different spatial arrangements of the atoms.
Between which atoms in a peptide bonds rotate to form φ and ψ angles, or form peptide bond?
-ϕ (phi): angle around the a-carbon—amide nitrogen bond (1.46A) -ѱ (psi): angle around the a-carbon—carbonyl carbon bond (1.53A) In a fully extended polypeptide, both ѱ and ϕ are 180°
Why peptide bonds can't rotate?
Theoretically ϕ and ѱ angles could take any value, yet some angles of rotation around the Cα are not sterically possible. they all reside in a single plane,Because of the partial double bond between the α carbon and the amine nitrogen, no rotation is possible around that bond.
What contracts effect the stability of a a-helix?
-Not all polypeptide sequences adopt a-helical structures -Small hydrophobic residues such as Ala and Leu are strong helix formers -Pro acts as a helix breaker because the rotation around the N-Ca bond is impossible -Gly acts as a helix breaker because the tiny R-group supports other conformations -Attractive or repulsive interactions between side chains 3–4 amino acids apart will affect formation.
What are the Amino acids that form β-turns?
Proline in position 2 or glycine in position 3 are common in B-turns.
What's the structure of β-turns?
Most peptide bonds not involving proline are in the trans configuration (>99.95%).For peptide bonds involving proline, about 6% are in the cis configuration they include proline.
What are the forces that stabilize α-helix and β-sheets?
- a-helix are stabilized by hydrogen bonds between nearby residues. - B-sheets are stabilized by hydrogen bonds between adjacent segments that may not be nearby.
What are the forces that stabilize tertiary and quaternary structures?
Tertiary structure is stabilized by Stabilized by numerous weak interactions between amino acid. -Largely hydrophobic and polar interactions, also hydrogen bonds and Van der Waals forces. - Can be stabilized by disulfide bonds -Quaternary structure is held together by noncovalent bonds between complementary surface hydrophobic and hydrophilic regions of polypeptide.
What are the major classes of proteins based on their tertiary structure?
-Fibrous proteins provide support, shape, and external protection (Insoluble ,hydrophobic amino acids ) Ex: a-Keratin,Silk,Collagen. -Globular proteins enzymes and regulatory proteins (Water- soluble) Ex: plasma proteins and the immunoglobulin, Enzymes.
What's the definition of “motif”?
Motif (fold) is a recognizable pattern that involves two or more elements of secondary structure and connections between them.
What's the definition of “domain”?
Domain is a part of protein that independently stable or can move as a single entity with respect to the rest of the protein.
Why some proteins (or parts of proteins) are intrinsically disordered?
They Contain protein segments that Disordered regions less-defined structure. (Lys, Arg, Glu, and Pro). -they can conform to many different proteins, facilitating interaction with numerous different partner proteins. -They lack a hydrophobic core, and instead are characterized by high densities of charged amino acid residues, -Structural disorder and high charge density can facilitate the function of some proteins.
What are nucleotide; nucleoside; nucleobase ?
Nucleotide = – Nitrogeneous base – Pentose – Phosphate • Nucleoside = – Nitrogeneous base – Pentose • Nucleobase = – Nitrogeneous base
What are Functions of Nucleotide ?
– Energy for metabolism (ATP) – Enzyme cofactors (NAD+) – Signal transduction (cAMP)
What's Chargaff's rules?
1) the nucleotide composition of DNA varies among species. In other words, the same nucleotides do not repeat in the same order, as proposed by Levene. 2) almost all DNA--no matter what organism or tissue type it comes from--maintains certain properties, even as its composition varies. In particular, the amount of adenine (A) is usually similar to the amount of thymine (T), and the amount of guanine (G) usually approximates the amount of cytosine (C). In other words, the total amount of purines (A + G) and the total amount of pyrimidines (C + T) are usually nearly equal. (This second major conclusion is now known as "Chargaff's rule.")
What are Palindromes and what structures they form?
Palindromic DNA (or RNA) sequences can form alternative structures with intrastrand base pairing. they form : -hairpin : which is when only a single DNA (or RNA) strand is involved. -cruciform: when both strands of a duplex DNA are involved.
Why the experiment of Avery, MacLeod, and McCarty significant?
Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III. which demonstrated that hereditary units, or genes, are composed of DNA, and that DNA as the "transforming principle".
What type of chemical bonds determine the most of the stability of the helix in double-stranded B-form DNA?
The B form is the most stable structure for a random-sequence DNA molecule under physiological conditions its Antiparallel. Multitude of hydrogen and hydrophobic bonds between the polynucleotide strands provide stability