Chapter 1-4 Flashcards

Question

Reduction Reaction

Answer 1

Reduction(RIG) is gaining an electron from oxidation

Answer 2

Proteins Catalyst that speeds up reaction process Can turn molecule to fit Can change shape to fit molecule Bind to both reactants to bring closer together Pacman figure(enzyme) its mouth is where it binds its substrate(s) called the active site Anything that has shape to fit into pac man mouth can substrate to fit or change shape Enzymes shape never changes Can fit multiple substrates as long as it fits

Answer 3

Energy released from covalent bond or high energy electron Some released to do work or heat Energy released to do work is free energy called negative delta G( -ΔG) -10 Δ G + +9 Δ G = -1Δ G Cannot do -10 Δ G + 10 Δ G =0 Δ G no entropy

Answer 4

Movement of matter(particles) from high concentration of matter towards and area of low concentration of matter

Answer 5

Movement of water Towards an area of high concentration of matter

Answer 6

Small organic molecules that contain one or more energy-rich covalent bonds

Answer 7

Size: bacterial cell is a few micrometers in length, frog egg is a millimeter in length Shape: neuron, Paramecium, plant (squat surrounded by a rigid box of cellulose and wax), fission vs. budding yeast (rod/spherical), macrophage Chemical requirements: oxygen/no oxygen, carbon dioxide, water, sunlight -Some cells are specialized to produce hormones, starch, fat, latex, or pigments. -Muscle cells use ATP -Modified muscle cells in the electric eel generate electricity

Answer 8

DNA replicates then is translated into RNA which is the _______ in to proteins that then assist in DNA replication so the cell cycles to support self replication DNA --> RNA --> proteins

Answer 9

Varied characteristics stem from the way that individual cells use their genetic instructions. Different cells express different genes - use genes to produce some RNAs and proteins and not others, depending on their internal state and on cues from surroundings (signals from other organisms)

Answer 10

-all living cells are formed by the growth and division of existing cells -the cell is the basic unit of life -all living organisms are made of cells To understand cells, we must know their history.

Answer 11

eukaryotic cells have a membrane-bound nucleus and prokaryotic cells do not

Answer 12

Structure: Nucleus is situated in the cytoplasm of the cell. Usually, it is round but many different shaped nuclei can be seen in some cells. It is surrounded by two porous membranes called nuclear membranes which remain continuous with the Endoplasmic Reticulum. Within the nuclear membrane is present a liquid substance called nucleoplasm. Nucleoplasm contains two types of chromatin material: Heterochromatin and Euchromatin. Chromatin fibres are thin thread-like structures composed of DNA and proteins. These fibres condense to form short thick chromosomes during cell division and become visible. DNA molecules transfer hereditary information from one generation to the next. Function: Nucleus is one of the most important components of the cell. It controls the various metabolic activities of the cell. Therefore, it is called the control centre of the cell. If the nucleus is removed, the cell ultimately dies. It controls cell division. It is involved in transmission of hereditary characters from parents to off springs.

Answer 13

The folding of the inner membrane increases the surface area inside the organelle

Answer 14

suggests that mitochondria are descended from specialized bacteria (probably purple nonsulfur bacteria) that somehow survived endocytosis by another species of prokaryote or some other cell type, and became incorporated into the cytoplasm. The ancestral eukaryote consumed aerobic bacteria that evolved into mitochondria. In a second endosymbiotic event, the early eukaryote consumed photosynthetic bacteria that evolved into chloroplasts."

Answer 15

Lysosomes are responsible for the digestion of cells while peroxisomes are responsible for the protection of cells against hydrogen peroxide.

Answer 16

Golgi bodies are an arrangement of few fluid-filled dishes whereas Endoplasmic reticulum is a network of tubules and vesicles. Golgi apparatus sorts, modifies, and delivers the components in a cell, whereas Endoplasmic reticulum is much a structurally aiding organelle for metabolic activities. The structure of Endoplasmic reticulum is expanded inside the cell much more than the Golgi apparatus. Lysosomes are formed at the Golgi complex while the enzymes in lysosomes are synthesized at Rough Endoplasmic reticulum.

Answer 17

help move materials, such as proteins and other molecules, from one part of a cell to another

Answer 18

the cytosol is surrounded by the cell membrane and is part of the cytoplasm, which also comprises the mitochondria, plastids, and other organelles (but not their internal fluids and structures)

Answer 19

actin filaments, microtubules, and intermediate filaments animals: provide mechanical structure and motility

Answer 20

Element: substances that cannot be broken down or interconverted by chemical means Atom: the smallest particle of an element that still retains its distinctive chemical properties Ion: an atom carrying an electrical charge, either positive or negative Isotope: different number of neutrons but the same number of protons; physically distinguishable but chemically identical Molecule: atoms linked together in a group Salts: ions held together solely by ionic bonds

Answer 21

Protons: nucleus, +1 Neutrons: nucleus, neutral Electrons: orbits, -1 Carbon: 6 protons Hydrogen: 1 Oxygen: 8 Nitrogen: 7

Answer 22

4, 3, 2, 1

Answer 23

A polar structure is one in which the positive charge is concentrated toward one atom in the molecule and the negative charge is concentrated toward another atom. The tendency of an atom to attract electrons is electronegativity. Polar molecules are more soluble in polar solvents, like water. Nonpolar molecules are not soluble in water and are hydrophobic. Electronegativity increases the acidity but decreases the basicity.

Answer 24

A hydrophilic molecule is water-loving, polar, and can form hydrogen bonds.

Answer 25

Non-polar, hate water

Answer 26

Acid: release protons when dissolved in water Base: accept protons when dissolved in water Because an OH- ion combines with a proton to form a water molecule, an increase in the OH- concentration forces a decrease in the H+ concentration. Buffers are mixtures of weak acids and bases that will adjust proton concentrations around pH 7 by releasing protons and taking them up whenever the pH changes.

Answer 27

Covalent: share electrons (cloud of negative charge is densest between the two positively charged nuclei), very strong, shorter bond length, very stable and takes more energy to break, connects monomers to form polymers Ionic: electrons are donated by one atom to another, weaker than covalent but stronger than other noncovalent interactions, forms interaction between polymers

Answer 28

Hydrogen bonds: much weaker than covalent, forms when a positively charged H atom held in one molecule by a polar covalent linkage comes close to a negatively charged atom, help molecules fold and compose the properties of water (cohesion/adhesion) Electrostatic attractions: strongest when atoms involved are fully charged but weak attractions can form between molecules that contain polar covalent bonds, water weakens these interactions van der Waal's attractions: nonspecific interactions form from fluctuations in the distribution of electrons in every atom, which can generate a transient attraction when atoms are in close proximity

Answer 29

free hydroxyls can combine in condensation to link hydrolysis can break this bond and return the free hydroxyl (for sugar)

Answer 30

source of energy and structural support link with glycosidic bonds

Answer 31

The lipid end (fatty acid) of fatty acid is non-polar (hydrophobic), and the phosphate attached alcohol serves as a polar head. In the cell membrane structure, the outer and inner layers are exposed with these polar ends, and the middle part contains the lipid layer. Thus, the hydrophobic lipid layer is sandwiched between two hydrophilic phosphate layers, so it is also called a phospholipid bilayer (PLP- phosphate-lipid-phosphate). Thus, phospholipids' amphipathic nature (both polar and nonpolar) provides the nature of selectivity to the cell membrane. So that the polar drugs must be modified to cross the cell membrane because they cannot cross the cell membrane in the polarized state, similarly, the lipophilic molecules can readily cross the cell membrane.

Answer 32

As you can see above, saturated fatty acids tails are arranged in a way that maximizes interactions between the tails. These interactions decrease bilayer fluidity.

Answer 33

the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom.

Answer 34

Side chains!!! Acidic: aspartic acid (Asp, D), glutamic acid (Glu, E) Basic: lysine (Lys, K), arginine (Arg, R), histidine (His, H) Uncharged Polar: asparagine (Asn, N), glutamine (Gln, Q), serine (Ser, S), threonine (Thr, T), tyrosine (Tyr, Y) Nonpolar: alanine (Ala, A), valine (Val, V), leucine (Leu, L), isoleucine (Ile, I), proline (Pro, P), phenylalanine (Phe, F), methionine (Met, M), tryptophan (Trp, W), glycine (Gly, G), cysteine (Cys, C)

Answer 35

DNA does not have hydroxyl at the 2ʹ position of the ribose carbon ring, its replaced by hydrogen DNA, with its more stable, hydrogen-bonded helices, acts as a long-term repository for hereditary information RNA is usually a more transient carrier of molecular instructions

Answer 36

By varying the sequence of subunits, the cell can make an enormous diversity of polymeric molecules.

Answer 37

They can add up to create a strong attraction between two molecules when the molecules fit together very closely. This provides great specificity in the binding of a macromolecule to other small and large molecules because the multipoint contacts required for strong binding make it possible for a macromolecule to select just one of the many thousands of different molecules present inside a cell.

Answer 38

A cell's metabolism refers to the combination of chemical reactions that take place within it. Catabolic reactions break down complex chemicals into simpler ones and are associated with energy release. Anabolic processes build complex molecules out of simpler ones and require energy.

Answer 39

All energy transfers result in a loss of usable energy

Answer 40

Biological order is made possible by the release of heat energy from cells. Decreasing the cell's entropy, inc. extracellular entropy.

Answer 41

Living systems use different forms of energy that interconvertible, but the total amount of energy remains the same.

Answer 42

The energy source of sunlight is use by plants, which are eaten by species who use that energy.

Answer 43

oxidation: means the addition of oxygen atoms to a molecule. when electrons are transferred from one atom to another. Oxidation, in this sense, refers to the removal of electrons from an atom reduction: opposite, addition of electrons to an atom in cell proton + electron picked up -----> reduction(hydrogenation).

Answer 44

electrons have unique exchanging property which drives the chemical processes to perform both reactions as a coupled reaction.

Answer 45

When substance comes into contact with oxygen while reduced it gains a hydrogen

Answer 46

Allosteric Two forms/shapes One is on or active shape Open pacman without substrate One is off or inactive state Pacman with closed mouth Something binds to enzyme and changes its shape Small molecule binds outside of active site putting pressure on shape of enzyme to kind of close up When not there its opens to natural state of on/active 100 substrates and 50 enzymes Goes down to 30 substrates Enzyme still affected, but reaction will be less quick because less there Have something bind to substrate so no longer can bind to enzyme Put a blocker in the active site

Answer 47

Energy released from covalent bond or high energy electron Some released to do work or heat Energy released to do work is free energy called negative delta G( -ΔG) -10 Δ G + +9 Δ G = -1Δ G Cannot do -10 Δ G + 10 Δ G =0 Δ G no entropy

Answer 48

lowering activation energy, does dis by bindin to substrate n holds them in a way that greatly reduces the activation energy needed to facilitate a specific chemical interaction between them

Answer 49

favorable rxns downhill meaning neg in delta g Energetically favorable reactions, by definition, are those that create disorder by decreasing the free energy of the system to which they belong; in other words, they have a negative ΔG

Answer 50

an increase in substrate concentration leads to an increase in the rate of an enzyme-catalyzed reaction

Answer 51

when the enzyme and substrate are well matched, they form many weak interactions, which keep them held together long enough for a covalent bond in the substrate molecule to be formed or broken

Answer 52

When two colliding molecules have poorly matching surfaces, few noncovalent bonds are formed and they disassociate quickly

Answer 53

As is true of any catalyst, enzymes do not alter the equilibrium point of the reaction. This means that the enzyme accelerates the forward and reverse reaction by precisely the same factor.

Answer 54

These molecules diffuse rapidly and carry their bond energy from the sites of energy generation to the sites where energy is used for bio- synthesis take energy from energetically fav rxn (catabolism) and use it for unfav rxn (anabolism)

Answer 55

energy from ATP hydrolysis is first used to convert B-OH to a higher-energy intermediate compound, which then reacts directly with A-H to give A-B. The simplest mechanism involves the transfer of a phosphate from ATP to B-OH to make B-O-PO3

Answer 56

It can give up its hydride ion (oxidation) to drive a reduction reaction and it can gain (reduction) a hydride ion as a oxidizing agent

Answer 57

the oxidized form of NADPH is more stable than the reduced form. FEEDBACK: NADPH carries two high-energy electrons. Losing these electrons in an oxidation reaction is energetically favorable because the oxidized form, NADP+, is more stable than the reduced form (NADPH).

Answer 58

The different structures allow the two carriers to be substrates to different sets of enzymes. and deliver electrons to different molec.

Answer 59

NADH: help form ATP and move electrons in the ETC NADPH: ATP: energy acetyl CoA;

Answer 60

transferable group only makes up small portion large organic portion, w/ nucleotide, that serves as handle

Answer 61

Condensation is energetically unfavorable while hydrolysis is favorable, condensation requires linkage to atp hydrolysis

Answer 62

Nucleic acids require coupling to rxn with large neg delta g ATP hydrolyzed to AMP having a large enough G to overcome unfavorability of rxn of linking nucleic acids together (polynucleotides)

Answer 63

Osmosis is the movement of water molecules through the cell. Diffusion is the movement of molecules, such as oxygen, in and out of a cell.

Answer 64

Come in different shapes, size, and chemical properties Charge Hydrophobicity Chains of Amino Acids Side chain which is either hydrophobic(non-polar, no charge) or hydrophilic(polar) Side chains that determine how protein will eventually fold Non-polar hydrophobic side chains rush together to get away from water The chain will get bunched up because hydrophobic bunch together and hydrophilic are on outside touching water Protein folds because of its side chains Non-covalent bonds can form once folded

Answer 65

Side chain which is either hydrophobic(non-polar, no charge) or hydrophilic(polar) Side chains that determine how protein will eventually fold Non-polar hydrophobic side chains rush together to get away from water The chain will get bunched up because hydrophobic bunch together and hydrophilic are on outside touching water Protein folds because of its side chains Non-covalent bonds can form once folded

Answer 66

Primary Structure: unique sequence of amino acids -determined by inherited genetic information -like the order of the letters in a word -dictates secondary and tertiary structure Secondary Structure: the coils and folds of the polypeptide chains that result from hydrogen bonding between backbone constituents -alpha helix and beta pleated sheets (held together through hydrogen bonds) -only has hydrogen bonding Tertiary Structure: -overall shape of a polypeptide that results from bonding between the side chains (R groups) of various amino acids -hydrophobic interactions contributes to this structure -conformation is reinforced and held by covalent bonds called disulfide bridges -contains all types of bonding -final configuration for most proteins Quaternary Structure: -aggregation of two or more polypeptide chains into one functional macromolecule EX: hemoglobin

Answer 67

Structural Support. Movement. Signal Transduction. Binding. Molecule transport across membranes. Catalysis.

Answer 68

localization of the gene product and/or the species it interacts with, by the covalent or non-covalent binding of effector molecules, and by the amount and lifetime of the active protein

Answer 69

Non-competitive inhibition Add non-competitive inhibitor that turns off the enzyme by binding something to enzyme to make opening small Negative Feedback A to B to C but B has x, y, z. When b hits c it turns off x, y, z After a while concentration gets low so it starts again Positive Feedback Inhibition Instead of blocking makes more and more Cells keep feedback to self positively forcing to stay on Interactions lead to stabilize and keep on or destabilize and turn off

Answer 70

the primary structure of a protein is read and written from the amino-terminal (N) to the carboxyl-terminal (C) end. Each amino acid is connected to the next by a peptide bond

Answer 71

1) electrostatic attractions (attractions between positive and negative charges) 2) hydrogen bonds 3) van der Waals attraction

Answer 72

The amino acid sequence (primary structure) will determine the 3-D structure of the protein.

Answer 73

when its normal shape gets deformed because some of the hydrogen bonds are broken

Answer 74

https://quizlet.com/462255484/20-essential-amino-acids-and-properties-flash-cards/

Answer 75

impose distance and angle constraints between the Cβ and Sγ atoms of the joined cysteine residues, thus destabilizing the unfolded state by reducing its entropy

Answer 76

Substrate and product concentration: MM enzymes Allosteric Enzymes Feed forward and feedback mechanisms - Enzyme concentration: synthesis/degradation - Inhibitors: reversible and irreversible - Isozymes (isoenzymes) - closely related variants of the same enzyme - Proteolytic cleavage: activate zymogens - Covalent Modification: post-translation modifications like phosphorylation, glycosylation

Answer 77

Stability of each shape is determined by the combined strength of larger numbers of non-covalent bonds. An important factor for governing the fold of any protein is the distribution of its polar and non-polar amino acids.

Answer 78

Covalent crosslinks stabilize and maintain the structure. They can tie two amino acids together or combine many polypeptides. They do not change the proteins confirmation.

Answer 79

The final folded structure is adopted by the polypeptide chain is determined by energetic considerations A protein generally folds into the shape in which Free Energy is minimized The folding process is energetically favorable as it releases heat and increases disorder of the universe

Answer 80

Some chaperone proteins bind to partly folded chains and help them to fold along the most energetically favorable pathway. Others form "isolation chambers" in which single polypeptide chains can fold without the risk of forming aggregates in the crowded conditions of the cytoplasm. The 3D shape is still specified by its amino acid sequence - chaperones just make the process more efficient and stable. Function of chaperones requires ATP binding and hydrolysis.

Answer 81

a-helices - form from H bonds every 4 a.a. - C=O of one a.a. binds with the N-H of another a.a. B-sheets - form from H bonds of a.a. segments that are side by side - parallel = all segments face same direction (N-C) - antiparallel = segments alternate (N-C, C-N, N-C)

Answer 82

Different domains associate with different functions.

Answer 83

The simplest way to see it: primary is merely a sequence of amino acids, one dimension, like a line; secondary is a folding of this line, two dimensions like on a sheet of paper, planar; tertiary is a folding in three dimensions, like a ball, for example, there are so called globular proteins; quaternary is next level of structural complexity when two or more three-dimensional proteins join together to make something more functional.

Answer 84

Continually bend and flex due to thermal buffering Function: interact with other domains, undergo post-translational modifications, link domains, signaling

Answer 85

Binding site: any region on a proteins surface that interacts with another molecule through non-covalent bonds. The tight binding of two folded polypeptides create a larger protein.

Answer 86

The specific confirmations and receptors allow for the proteins to recognize their specific and correct bindning spot.

Answer 87

Enzymes lower the activation energy for reactions.

Answer 88

Negative inhibition: enzyme acting early in a reaction pathway is inhibited by a late product of that pathway. whenever large quantities of the final product begin to accumulate, the product binds to an earlier enzyme and slows down its catalytic action, limiting further entry of substrates into that reaction pathway used cuz many branch points where different enzymes compete for the same substrate. The system is so complex that elaborate controls are required to regulate when and how rapidly each reaction occurs.

Answer 89

binding of a ligand to the regulatory site causes a shift in the protein's structure from one folded shape to a slightly different folded shape, which alters the binding of a ligand to a second site.

Answer 90

The addition and removal of phosphate groups from specific proteins often occur in response to signals that specify some changes in a cell's state. Protein phosphorylation 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. Phosphorylation can either STIMULATE protein activity or INHIBIT it, depending upon the protein involved and the site of phosphorylation. Phosphorylation can create docking sites where other proteins can bind, thus promoting the assembly of proteins into larger complexes.

Answer 91

During phosphorylation, a phosphate group is enzymatically transferred from ATP to the protein. Binding of nucleotides such as GTP or ATP, hydrolyze GTP/ATP to GDP/ADP to release a phosphate and flips the conformation to inactive. The active conformation is regained by dissociation of the GDP, followed by the binding of a fresh molecule of GTP.

Answer 92

Movement of motor proteins: undergo a series of conformational changes; to make irreversible/unidirectional, one of the conformational changes is coupled to the hydrolysis of an ATP molecule that is tightly bound to the protein (lots of free energy released which makes the step irreversible) Large protein machines: the hydrolysis of bound nucleoside triphosphates drives an ordered series of conformational changes in some of the individual protein subunits, enabling the ensemble of proteins to move coordinately (linked processes are more efficient than the sequential use of individual tools)

Answer 93

The unstructured regions of the scaffold act as FLEXIBLE TETHERS and enhance the rate of formation of the function complex by promoting RAPID, RANDOM collision of the proteins bound to the scaffold.

Chapter 1-4 Flashcards

(117 cards)