Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Cell and Molecular Biology > Chapter 1-4 > Flashcards

Chapter 1-4 Flashcards

You may prefer our related Brainscape-certified flashcards:
AP® Biology flashcards Biology 101 flashcards
1
Q

Cell Theory

A

Cell, made of cells
All cells come from preexisting cells(reproduction)
Smallest unit of life is a cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

General Characteristics of Life

A

Reproduce
Made of cells
Metabolize, homeostasis
Growth
Adapt
Respond to Environment
Use energy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Central Dogma of molecular Biology

A

Genetic information flows in one direction
DNA transcribed RNA translation Protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Genotype vs. Phenotype

A

Genotype is genetic makeup of en organism ie DNA
Phenotype is physical trait that an organism develops as a result of its genotype

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Form/Shape and Function

A

Form is the Shape and Function to help it move

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Similarities between Prokaryotes and Eukaryotes

A

Cell Membrane
DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Differences between Prokaryotes and Eukaryotes

A

Prokaryote
Single cell
No Nucleus
Cell wall
No membrane-bound organelles
Reproduction is binary fission
Can be photosynthetic
Eukaryote
Multi cell
Nucleus
Membrane-bound organelles
Endomembrane system(mitochondria, chloroplast, Golgi apparatus, etc)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Organelles of Eukaryotes and Function

A

mitochondria: Generate energy to power cell
chloroplasts: Convert light energy to chemical energy
the endoplasmic reticulum: Produce Proteins
the Golgi apparatus: Transport proteins
lysosomes: Digestive system

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Endosymbiotic theory

A

Organelles inside eukaryotes evolved(came from) free living prokaryotes
Ex: Mitochondria, chloroplasts
Double membrane
Unique DNA—->protein
Binary fission reproduction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Cytoskelton

A

Support the shape of the cell
Manages the organization of the cell
Causes movement
Filament
Thin Filaments(actin)
Intermediate filaments
Thick Filaments(Microtubules)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Atomic Structure

A

The atom consists of three component parts: Protons, Neutrons, and Electrons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Octet Rule

A

The outer orbital wants to be full- if not its gonna try to by either losing electrons or gaining electrons
Stability
Outer is full you are stable
Octet rule → drive true bonding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Chemical Bonds Ionic, Covalent, Non-covalent

A

Ionic: One atom donates an electron and another atom will
accept them

Covalent: Sharing electrons
Equally or unequally sharing

Non-covalent: temporary/weak bonds
Hydrogen bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

The structure and Properties of water

A

Can be weak acid or base
Hydronium ion

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Acid and Bases

A

Acid
lower on pH scale
Lots of free floating hydrogen ions in solution
Releases hydrogen ions into the solution
Bases
higher on pH scale
Barely any free floating ions in solution
Accepts hydrogen ions and takes them out of solution
Amount of free hydrogen ions in solution

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

pH and Buffers

A

pH: acidic is 1 and basic is 14 water is 7
Buffers: Resist change in acid or base

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Condensation reaction

A

endothermic reactions, anabolic reactions)condensation
O+O → O-O

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Hydrolysis Reaction

A

Releases energy(catabolic reactions, exothermic reactions)hydrolysis
O-O → O+O

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Basic Organic Building Blocks of Life

A

Cells and Amino acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Catabolism

A

Breaking down
Exothermic
Release energy
Release heat energy heat higher entropy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Anabolism

A

Covalent or nonpolar bonds
Consumes Energy
Endothermic
Captures free energy from catabolism

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

1st law of thermodynamics

A

Conversion of energy from one form to another
Potential energy=stored energy(in a bond)
Kinetic energy=released/useful energy(broken bond)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

2nd law of thermodynamics

A

Entropy increases(increasing disorder/chaos)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Oxidation Reaction

A

(OIL) which loses the electron essentially coupling them together

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Reduction Reaction

A

Reduction(RIG) is gaining an electron from oxidation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Properties of Enzymes

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Gibbs Free Energy

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Diffusion

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Osmosis

A

Movement of water
Towards an area of high concentration of matter

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Activated Carriers

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Compare, with examples, some ways in which cells may vary in appearance and function.

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

• Explain how the relationship between DNA, RNA, and protein—as laid out in the central dogma—
makes the self-replication of living cells possible

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Explain how differentiated cell types can vary widely in form and function despite having the same
genome sequence.

A

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)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

List the three tenets of cell theory and explain their ramifications for the study of cell biology

A

-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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Describe the structural differences between prokaryotes and eukaryotes.

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

State the function of the nucleus and describe its structural features.

A

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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Explain how the structure of the mitochondrion supports its function

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Endosymbiosis Theory: Describe the ancestral cell that likely engulfed the aerobic bacteria that gave
rise to mitochondria and explain why this event is thought to have preceded the acquisition of
chloroplasts. Outline the evolution of mitochondria and chloroplasts and cite the evidence for these
origins

A

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.”

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Compare the function of lysosomes and peroxisomes

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Compare the structure, location, and function of the endoplasmic reticulum and Golgi apparatus.

A

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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

Outline the role that transport vesicles play in the cell

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

Relate the location of the cytosol with respect to the cell’s membrane-enclosed organelles.

A

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)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

List the three major filaments of the cytoskeleton and contrast the roles they have in animal cells.

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

Distinguish between elements, atoms, ions, isotopes, molecules, and salts

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

State the location, charge, and relative size of protons, neutrons, and electrons and their numbers in
an atom of carbon, hydrogen, oxygen, and nitrogen

A

Protons: nucleus, +1
Neutrons: nucleus, neutral
Electrons: orbits, -1

Carbon: 6 protons
Hydrogen: 1
Oxygen: 8
Nitrogen: 7

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

State the number of covalent bonds that can be formed by atoms of hydrogen, oxygen, nitrogen,
and carbon

A

4, 3, 2, 1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

Identify what determines the polarity of a chemical bond and summarize the consequences of this
property for the solubility and hydrophobicity of a molecule or salt, as well as its ability to act as an
acid or base.

A

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.

48
Q

Recall the characteristics of a hydrophilic molecule.

A

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

49
Q

Recall the characteristics of a hydrophobic molecule

A

Non-polar, hate water

50
Q

Distinguish between acids and bases and demonstrate how they cooperate to maintain the pH of
cells.

A

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.

51
Q

Differentiate between covalent and ionic bonds in terms of their electronic configuration, strength
and stability, and their role in biological systems.

A

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

52
Q

Contrast hydrogen bonds, electrostatic attractions, van der Waal’s attractions, and the hydrophobic
force in terms of how and when they form and the role they play in cells

A

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

53
Q

Illustrate how the processes of condensation and hydrolysis are central to the synthesis and
breakdown of the large organic molecules of the cell from sets of smaller organic building blocks.

A

free hydroxyls can combine in condensation to link

hydrolysis can break this bond and return the free hydroxyl

(for sugar)

54
Q

Relate the different roles that sugars can play in the cell.

A

source of energy and structural support
link with glycosidic bonds

55
Q

Summarize why the amphipathic nature of phospholipids is crucial for cells

A

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.

56
Q

Predict how the saturation of fatty acid tails affects the fluidity of cell membranes.

A

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.

57
Q

Identify the features that all amino acids have in common.

A

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.

58
Q

Summarize what makes amino acids chemically unique and their chemical properties.

A

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)

59
Q

Contrast RNA and DNA and evaluate why these nucleic acids play different roles in cells.

A

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

60
Q

Relate how the repetitive polymerization of monomers into polymers can yield macromolecules with
diverse properties and functions.

A

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

61
Q

Explain how weak, noncovalent bonds can lead to strong and specific associations between
macromolecules or between an enzyme and its substrate.

A

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.

62
Q

Relate anabolic, catabolic, and metabolic reactions.

A

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.

63
Q

What is Entropy and how does the cells ordered composition still follow the 2nd law of
thermodynamics?

A

All energy transfers result in a loss of usable energy

64
Q

State how living systems can generate and maintain order without violating the second law of
thermodynamics.

A

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

65
Q

Summarize how living systems take advantage of the first law of thermodynamics.

A

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

66
Q

Express why sunlight provides the ultimate source of energy for nearly all living things.

A

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

67
Q

Differentiate between oxidation and reduction in terms of the movement of electrons, protons, and
oxygen atoms.

A

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).

68
Q

Explain oxidation and reduction reactions. How are they coupled to each other?

A

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

69
Q

Make sure you are able to distinguish between a molecule that has been reduced or oxidized.

A

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

70
Q

What is an enzyme and how does it effect a chemical reaction? What are the properties of an
enzyme? What is the Vmax and KM of an enzyme’s activity and how are they determined?

A

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

71
Q

Explain free-energy and free energy change? How does this determine where a reaction will be
spontaneous or not?

A

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

72
Q

Articulate how enzymes increase the speed of a chemical reaction

A

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

73
Q

Relate how the free-energy change of a reaction determines its energetic favorability.

A

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

74
Q

Summarize how substrate concentration affects an enzyme’s activity.

A

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

75
Q

Describe how noncovalent interactions allow enzymes to interact with specific substrates.

A

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

76
Q

Explain why substrates for different enzymes can coexist in the same compartment.

A

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

77
Q

Illustrate how enzymes affect the equilibrium point of chemical reactions.

A

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.

78
Q

Review how activated carriers link catabolic and anabolic reactions.

A

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)

79
Q

Relate how the energy of ATP hydrolysis can be harnessed to drive an energetically unfavorable
condensation reaction.

A

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

80
Q

Delineate the role played by NADPH in oxidation–reduction reactions.

A

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

81
Q

State why the oxidation of NADPH is energetically favorable.

A

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).

82
Q

Relate the structures of NADH and NADPH and their different roles within cells.

A

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

83
Q

Name 3 activated carriers and state the role each plays in a cell.

A

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

84
Q

Assess the structural similarities possessed by the activated carriers that transfer chemical groups
during biosynthetic reactions.

A

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

85
Q

Evaluate the energetic favorability of condensation and hydrolysis reactions and state which type of
reaction generally requires linkage to ATP hydrolysis to occur.

A

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

86
Q

Outline how ATP hydrolysis provides the energy needed for highly unfavorable reactions, such as
the biosynthesis of nucleic acids.

A

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)

87
Q

Explain the difference between diffusion and osmosis

A

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.

88
Q

The structure of Proteins

A

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

89
Q

Side chain Properties

A

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

90
Q

levels of protein Folding

A

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

91
Q

Functions of Proteins

A

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

92
Q

Proteins can be controlled

A

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

93
Q

Feedback Inhabition

A

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

94
Q

Explain how a protein is organized

A

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

95
Q

What are the three types of noncovalent bonds that help a protein fold

A

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

96
Q

How do amino acids determine the structure and function of a protein?

A

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

97
Q

What does it mean when a protein is denatured?

A

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

98
Q

There are 20 amino acids. Make sure you are familiar with their properties: are they polar, non-polar,
hydrophobic, hydrophilic, reactive or non-reactive.

A

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

99
Q

How do disulfide bonds help protein folding?

A

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

100
Q

How are enzymes controlled? Explain Phosphorylation, feedback inhibition, ATP, GTP, and
allosteric enzymes in this context.

A

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
101
Q

Explain how noncovalent interactions—including electrostatic attractions, hydrogen bonds, van der
Waals attractions, and hydrophobic forces—influence the shape of a folded protein and how the
polypeptide backbone and amino acid side chains participate in these interactions.

A

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.

102
Q

Compare how covalent crosslinks and noncovalent bonds help to establish protein structure.

A

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.

103
Q

Describe the relationship between free energy and protein conformation

A

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

104
Q

Explain how chaperone proteins guide the folding of a polypeptide chain—and why some proteins
can fold without chaperone assistance

A

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.

105
Q

Contrast the hydrogen bonding patterns that give rise to alpha helices with those that produce beta
sheets.

A

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)

106
Q

Describe the role that protein domains play within a protein’s three-dimensional structure

A

Different domains associate with different functions.

107
Q

Define a protein’s primary, secondary, tertiary, and quaternary structures.

A

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.

108
Q

Explain the role that unstructured sequences play in protein function and how amino acid changes
in these regions may affect these functions.

A

Continually bend and flex due to thermal buffering

Function: interact with other domains, undergo post-translational modifications, link domains, signaling

109
Q

Explain how binding sites allow the assembly of multi-subunit proteins and multiprotein complexes

A

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.

110
Q

Summarize the roles that noncovalent interactions and exact protein conformation play in allowing
proteins to recognize and bind specifically to their ligands.

A

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

111
Q

Describe how enzymes can reduce the activation energy needed to catalyze chemical reactions.

A

Enzymes lower the activation energy for reactions.

112
Q

Explain how and why different forms of feedback control might be used to regulate enzyme activity

A

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.

113
Q

Explain how the binding of a ligand at a regulatory site can alter the activity of a protein or enzyme.

A

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.

114
Q

Explain how chemical modification such as phosphorylation can influence a protein’s location and
interactions.

A

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.

115
Q

Contrast how protein activity is regulated by phosphorylation or by the binding of nucleotides such
as GTP or ATP.

A

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.

116
Q

Explain how the hydrolysis of ATP or GTP can produce the directional movement of motor
proteins or coordinate the activity of large protein machines.

A

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)

117
Q

Describe how scaffold proteins aid in the assembly of protein complexes.

A

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.

Cell and Molecular Biology (1 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions