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Foundational Toolkit > Biochemistry Review > Flashcards

Biochemistry Review Flashcards

1
Q

What are the things to remember regarding the basic principles of cell organization and foundations of disease?

A
  1. All animals (including human and mouse) share the same basic principles of organization
  2. Most animals have special features in their physiology
  3. Every disease has an underlying molecular reason, known or unknown
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2
Q

What are embryonic stem cells? What do they do? What current research is being done?

A

These cells are formed after fertilization from egg and sperm

They divide and differentiate in the process of embryonic development to give rise to all the organs and tissues in the body

Injecting stem cells into different damaged organs can help to repair them

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3
Q

What do fibroblasts do?

A
  1. Crawl as a monolayer to close the healing wound (have a leading edge and trailing edge)
  2. Secrete extracellular matrix that forms the connective tissue inside the body
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4
Q

What do epithelial cells do?

A
  1. Form sheets (tight spaces) that line the skin and internal organs, creating barriers between interacting environments
    - Examples include skin, digestive tract (absorptive epithelia), and respiratory system (ciliated epithelia)
  2. Specialized kinds of epithelia perform secretory functions in the endocrine glands
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5
Q

What are myocytes? Describe each type. What is their function?

A

Form muscle tissues in the body including striated muscle, smooth muscle, and cardiac muscle

  1. Striated - alternating actin and myosin filaments
  2. Smooth - singled celled, no striations, compose organs that contract on their own
  3. Cardiac - have own pacemaker, have striated fibers that can contract on their own (combination of smooth and striated muscle)
  4. Respond to nerve stimuli to produce mechanical force by contraction
  5. Are the driving force for body movement and normal functioning of many organs, including heart, blood vessels, and digestive system
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6
Q

What are the types of blood cells and their functions?

A
  1. Red blood cells (erythrocytes) are highly specialized cells that carry hemoglobin and deliver oxygen to all areas of the body
  2. White blood cells (all other types) utilize several mechanisms to protect the body against infection
  3. Platelets - help with blood clotting
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7
Q

What are the functions of neurons?

A
  1. Conduct electrical signals to each other and to effectors throughout the body
  2. Form major structures of the nervous system, including brain, spinal cord, and ganglia
  3. Ensure the coordination of all systems and information processing for an animal
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8
Q

Describe cytosol. What does it do?

A

Cytosol is aqueous but not liquid

  1. It is a viscous phase whose physical and chemical properties vary in different areas of the cell, ensuring cell polarity and compartmentalization
  2. Molecules, particles, and organelles move through the cytosol either by passive diffusion or by active cytoplasmic transport
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9
Q

Describe the plasma membrane. What does it do?

A

Membrane is liquid but not aqueous

  1. Is formed by a lipid bilayer with incorporated protein molecules
  2. Creates a fluid barrier between the aqueous cytosol and the aqueous extracellular space
  3. Regulates exchange of chemicals and macromolecules between the cell and the extracellular space
  4. Mediates cell adhesion and all types of cell-cell communication
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10
Q

What are intracellular membranes? Give two examples.

A

Divide the cell into compartments

  1. Endoplasmic reticulum (ER)
  2. Golgi apparatus
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11
Q

What is the function of the endoplasmic reticulum (ER)? What is the function of the Golgi apparatus?

A

ER - exchanges material within the cell

Golgi - exchanges material with the extracellular space

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12
Q

What is the function of the nucleus? What are its structural components?

A

To store and deliver genetic information

  1. Nuclear envelope
  2. Inside the envelope - chromatin, nucleoli, nuclear lamina (intermediate fibers)
  3. Outside the envelope - microtubules if anchored onto the nucleus, ER if connected to the nuclear membrane
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13
Q

What is the function of mitochondria?

A
  1. Mitochondria contain an outer membrane and an inner membrane that create two internal compartments
  2. The major function of mitochondria is to convert oxidation energy into ATP – the ‘fuel’ molecule for all the metabolic processes
  3. Mitochondria have their own genome and have mysterious evolutionary origin
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14
Q

What makes up the cytoskeleton?

A
  1. Microtubules
  2. Actin filaments
  3. Myosin filaments
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15
Q

What are microtubules? What do they do?

A

A highly dynamic radial network of fibers

  1. Mediate intracellular transport
  2. Coordinate global cellular events, such as polarization and division
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16
Q

What are actin filaments? What do they do?

A

Are the major component of muscle fibers

  1. Form stress fibers and cortical network of thin filaments
  2. Mediate all types of motile and contractile behavior of cells
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17
Q

What are intermediate filaments? What do they do?

A

A rigorous network of fibers that follows the microtubule cytoskeleton

  1. Assist in cell shape maintenance and provide support for anchoring intracellular structures
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18
Q

Describe the molecular composition of a cell.

A
  1. Inorganic molecules - water (70%), inorganic ions
  2. Small organic molecules - sugars, fatty acids, nucleotides, amino acids
  3. Macromolecules - proteins, nucleic acids
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19
Q

What does DNA do?

A
  1. Carries genetic information
  2. Provides the code for protein synthesis
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20
Q

What does RNA do?

A
  1. Delivers the code for protein synthesis
  2. Involved in all stages of protein synthesis
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21
Q

What are structural proteins? What do they do?

A

Are the basic components of many intracellular and extracellular structures

They provide structural support, anchoring, and spatial organization of intracellular compartments (examples: cytoskeleton, nuclear lamina, and chromatin)

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22
Q

What do regulatory proteins do?

A
  1. Facilitate biological reactions that are essential for all aspects of cell metabolism and coordinate many biological processes
  2. May participate in the reactions either structurally (by bringing the reaction components into proximity of each other) or chemically (enzymes)
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23
Q

What do proteins do?

A
  1. Enzymatic catalysis
  2. Transport
  3. Storage
  4. Motility
  5. Structure and support
  6. Immune protection
  7. Signaling
  8. Defects in protein structure and expression are features of most diseases
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24
Q

Describe the protein structures.

A
  1. primary - sequence of amino acids (amino end to carboxyl end)
  2. secondary - local folding patterns (main: beta pleated sheets (flat), alpha helices (swirl))
  3. tertiary - folding of a single polypeptide chain into a distinct shape
  4. quaternary - assembly of multiple polypeptide chains
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25
Q

What makes up the basic structural unit of a protein?

A
  1. Amino group
  2. Carboxyl group
  3. R chain (side chain)
  4. Center (a) carbon
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26
Q

What are zwitterions?

A

amino acids with both positive and negative charges due to the ionization of the amino and carboxyl groups in aqueous solution (different charge properties depending on the pH)

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27
Q

Chirality versus steroisomers

A

Because the alpha carbon has four different groups bound in tetrahedral geometry, amino acids are chiral. There are both L and D isomers (except for glycine). Proteins contain only the L-isomers. These are referred to as stereoisomers

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28
Q

What are the polar charged, polar uncharged, hydrophobic, and other amino acids?

A

Polar charged: arginine, histidine, lysine, aspartic acid, glutamic acid

Polar uncharged: threonine, serine, asparagine, glutamine

hydrophobic: alanine, isoleucine, leucine, methionine, phenylalanine, tryptophan, tyrosine, valine

other: proline, cysteine, glycine

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29
Q

What forms a peptide bond? How does one get broken?

A

Formation of the peptide bond requires energy. During protein synthesis, peptide bonds are formed with the help of enzymes on the ribosome.

Breaking the peptide bond requires H2O, and is called hydrolysis. In cells, breakage of the peptide bonds is catalyzed by proteases.

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30
Q

What are peptides? What do they do?

A

Peptides are short amino acid chains and perform important regulatory – and therapeutic - functions

  1. Peptide hormones regulate whole body functions (ex. Insulin, glucagon, angiotensin)
  2. Synthetic peptides are an important part of your therapeutic arsenal (ex. Insulin, LHRH)

Comparing to proteins - proteins are long and folded, peptides are short

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31
Q

What are the bonds important for establishing protein structures in order from strongest to weakest?

A
  1. Covalent Bonds
  2. Electrostatic Interactions
  3. Hydrophobic Bonds
  4. Water Shells and Charged Surface Residues
  5. Hydrogen Bonds
  6. Van der Waals Forces
  • A combination of these bonds creates a folded protein molecule
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32
Q

What do covalent bonds do?

A

share electrons

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33
Q

What do electrostatic or ionic bonds do?

A

have opposite charges

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34
Q

What are hydrophobic bonds?

A

non-polar amino acids staying away from water

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35
Q

What are water shells and charged surface?

A

opposite of hydrophobic bonds, as these bonds form between charged surface residues and polar water molecules, which helps stabilize and solubilize the protein

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36
Q

What is a hydrogen bond?

A

sharing of hydrogen by two partially negative atoms

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37
Q

What are Van der Waals forces? Why do they exist?

A

transient, weak electrical attraction of one atom for another
- weak but can play important role in maintaining protein’s shape

each atom has an electron cloud that can fluctuate, yielding a temporary electric dipole

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38
Q

What can result from a secondary structure?

A

can fold into motifs and domains with distinct functions - this folding happens immediately and independently

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39
Q

Describe the process of protein folding.

A

proteins use chaperones to fold

unfolded proteins can be toxic
- should be degraded in the proteosome
- if not safely degraded, they can aggregate which can cause neurodegenerative disease

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40
Q

What are prions?

A

misfolded proteins that come in contact with good proteins and cause them to misfold, which can lead to aggregation in the brain

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41
Q

What are enzymes and what role do they play in cellular and animal health?

A

they are biological catalysts that mediate virtually every biological process - they drive reactions that convert one or more substrates into one or more products
- many diseases are due to enzyme deficiencies

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42
Q

Answer the following questions regarding enzymes:

  • Do they accelerate reactions?
  • Are they consumed by the reactions they catalyze?
  • Do they change the equilibrium between reactants and products?
  • Do they change the overall free energy of a reaction?
  • Do they lower the free energy of activation?
A

YES! Between 10^5 and 10^17 times faster than it would happen normally (Negative delta G, the reaction can occur)
No
No
No (difference of energy between the reactant and the product does not change)
YES! Activation rate lower, rate higher

43
Q

What do proteases do?

A

cleave peptide bonds

44
Q

What do kinases do?

A

covalently add phosphates

45
Q

What do phosphatases do?

A

remove phosphates

46
Q

What do dehydrogenases do?

A

always involved oxidation/reduction reactions (transfer of electrons)

47
Q

What do polymerases do?

A

generate chains of nucleotides, i.e catalyze phosphodiester bonds

48
Q

How do enzymes work?

A
  1. precise orientation with the help of side groups in the active site to favor a reaction
  2. rearrangement of electrons and charges to favor a reaction
  3. induction of strain or distortion to favor a reaction
49
Q

What are coenzymes/cofactors?

A

the “helper” molecules that aid enzymatic reactions to help move or position enzymes

50
Q

Describe the Michaelis Menten equation.
V = Vmax [S] / Km + [S]

A

V = velocity of rection, which is the rate the enzyme can do things

Vmax = maximum velocity that the enzyme can do things

Km = constant, which is a measure of the binding affinity of enzyme and substrate; this is the concentration at which an enzyme achieves half max velocity

51
Q

Describe the effect that Km and affinity has on the enzyme.

A

High Km, low affinity, somewhat efficient enzyme

Low Km, high affinity, efficient faster enzyme

52
Q

Why is enzyme inhibition important to veterinarians?

A
  1. Inhibition regulates normal enzymatic activities - ex. when a cell has enough ATP, ATP can inhibit enzymes responsible for generating ATP
  2. Many drugs work by inhibiting enzymes
  3. Many toxins work by inhibiting enzymes
53
Q

What are the types of enzyme inhibition? Define each.

A
  1. Competitive - inhibitor is blocking the substrate from entering into the active site
  2. Non-competitive - substrate can bind, but inhibitor prevents reaction and decreases efficacy of an enzyme
  3. Irreversible - inhibitor binds with the enzyme by a strong bond and inhibits the enzyme activity
  4. Reversible - once inhibitor is removed, the enzyme it was inhibiting can begin working again
54
Q

Describe how aspirin works as an inhibitor and its mode of inhibition.

A

Aspirin is an irreversible inhibitor, as it binds tightly to cyclooxygenase, which prevents this enzyme from stimulating inflammation. However, COX enzymes also produce protective factors of the stomach, so by inhibiting this enzyme, we are more at risk for GI ulcers or bleeding.

55
Q

What are the functions of membranes?

A
  1. Membranes provide a barrier between the cell and its environment and between intracellular compartments
  2. Membranes allow molecules to be organized and concentrated
  3. Membranes help generate the potential energy that drives some of the most important reactions in life
    - Allows energy to flow (selective)
56
Q

What are the functions of the plasma membrane?

A
  1. To receive signals from the environment
  2. To regulate transport of molecules in and out of a cell
  3. To mediate changes in cell shape (movement) and size (expansion)
57
Q

What is the role of the membrane in eukaryotic and prokaryotic cells?

A

Eukaryotic cells are surrounded by a plasma membrane
- Have a lipid bilayer with integral transmembrane proteins as well as some proteins tethered to one leaflet or the other (either outer leaflet or inner leaflet)

Prokaryotic cells also have at least one lipid bilayer with integral proteins

58
Q

Describe the membrane in gram negative bacteria and gram positive bacteria.

A

Gram-negative bacteria (like E. coli) have two lipid membranes, separated by a peptidoglycan layer

Gram-positive bacteria (like Staph and Strep) have one lipid membrane covered with a thick peptidoglycan layer

59
Q

What do all cell membranes have?

A

all cell membranes have a lipid bilayer with incorporated or tethered protein molecules
- bilayer is “two dimensional liquid,” so molecules can float freely
- lipids are amphipathic molecules with a HYDROPHILIC HEAD and HYDROPHOBIC TAILS (most are phospholipids)

60
Q

What specifically is embedded within the animal plasma membrane?

A

Cholesterol - between phospholipid tails
NOT IN PLANTS!!!!!!

61
Q

What are transporters and ion channels?

A

transmembrane proteins that assemble to provide passage of molecules and ions into the cell
- membrane proteins can assemble to create a hydrophilic channel through the membrane that allows transport of a variety of molecules

62
Q

What are the ways that transport across membranes occurs? How does transport across membranes occur?

A
  1. High gradient to low gradient - passive transport
  2. Low gradient to high gradient - active transport

Occurs by simple translocation of a molecule via a transporter (uniport), or by coupled transport with another molecule or ion (symport, in the same direction, or antiport, in the opposite direction)

63
Q

What are the specific stimuli that can trigger an ion channel to open?

A
  1. Electrical (voltage gated) - open or close depending on charge
  2. Ligand - will only open if there is another protein
  3. Mechanical - if a cell is squished or moved
64
Q

What is the function of an ion channel? Describe how they function in the sodium potassium pump.

A

Ion channels are fast and they maintain membrane potential as well as mediate bodily functions

The ion channels maintain the membrane potential, or voltage difference across the membrane, by keeping a higher concentration of Na+ on the outside, and a higher concentration of K+ on the inside through use of ATP hydrolysis

65
Q

What is an action potential? What happens at the synapse of the neuron?

A

traveling wave of electrical excitation that is triggered by a change in membrane potential (depolarization) and propagates down the neuron at high speeds

At the synapse, calcium flows in the channel, which triggers the neurotransmitter to be released. The neurotransmitter then binds to the receptor, which causes positive ions to flow in

66
Q

In regards to vesicular transport, what is the secretory pathway versus the endocytic pathway?

A

Secretory pathway (exocytosis) : delivery to the cell exterior of the macromolecules (vesicles) produced in the cell.

Endocytic pathway (endocytosis): uptake of macromolecules (vesicles) and delivery of these molecules to lysosomes, which contain digestive enzymes.

67
Q

How does transport and exchange of vesicles occur?

A
  1. Proteins are provided by the donor compartment
  2. Vesicles bud off of the membrane, then will transport in the cytoplasm
  3. The vesicle then enters the target compartment
68
Q

How are vesicles able to be pinched off of a compartment?

A

To pinch a vesicle off the compartment, the membrane must be forced by coat proteins
- The coat proteins are removed after the vesicle is pinched off

69
Q

What are SNAREs? What is a v-SNARE?

A

SNAREs are docking proteins that must be cleaved apart using energy

v-SNARE is a vesicle SNARE
- v-SNARE looks for a t-SNARE to bind tightly to, then they fuse to a target membrane
- once fused, the SNARE is then recycled

70
Q

How are proteins transported from the ER to the Golgi apparatus?

A
  1. ER proteins are recognized by a KDEL receptor in the Golgi, and are transported via vesicle exchange
  2. Proteins enter at the cis-golgi network (curved around nucleus), where the recycling of ER proteins takes place
  3. Protein processing occurs linearly as proteins move through the Golgi stacks
  4. The trans-golgi network (near cell periphery) is the site of final protein processing, as well as sorting
71
Q

How are proteins sorted at the trans-Golgi network?

A
  1. Trafficking to lysosomes
  2. Regulated secretion
  3. Bulk flow
72
Q

What are the three pathways to degradation in lysosomes? Describe them.

A
  1. Autophagy: digesting of damaged cell organelles and diseased tissue for later recycling or repurposing
  2. Endocytosis: uptake of macromolecules and particulates by the cell, and the trafficking of these from the plasma membrane to the lysosome - how cells get their food
  3. Phagocytosis: ingestion of large particles
73
Q

Describe the process of transporting newly synthesized lysosomal hydrolases to lysosomes.

A

Lysosomal hydrolase precursor is produced and is attached to mannose, which makes its way to the trans-Golgi network where it attaches to the M6P receptor. There, it is coated and a vesicle is pinched off. The vesicle makes its way over to the late endosome and fuses. The receptor molecule unattaches and is recycled, while the lysosomal hydrolase precursor will fold properly and produce the hydrolase enzyme in the acidic environment produced by the proton pump, which will allow the early endosome to mature and become the lysosome

74
Q

What are the three major types of endocytosis?

A
  1. Phagocytosis - “cell eating;” involves the intake of solid material or food particles
  2. Pinocytosis - “cell drinking;” involves the intake of molecules dissolved in fluid
  3. Receptor-mediated endocytosis - involves the intake of molecules based upon their interaction with receptors on a cell’s surface
75
Q

What is clathrin? What are the functions?

A

Clathrin is the major coating protein for the endocytic vesicles

Functions of the coat:
1. Concentrates specific membrane proteins
2. Deforms the membrane patch and molds the forming vesicles

76
Q

What is exocytosis?

A

transport from the trans Golgi network to the cell exterior

77
Q

What is the function of the cytosol?

A

cell metabolism, protein synthesis

78
Q

What is the function of the nucleus?

A

storage and replication of genetic information, RNA synthesis

79
Q

What is the function of the endoplasmic reticulum (ER)?

A

protein synthesis and distribution, lipid synthesis

80
Q

What is the function of the Golgi apparatus?

A

protein modification, sorting, and packaging for secretion or delivery to other organelles

81
Q

What is the function of lysosomes?

A

degradation and recycling

82
Q

What is the function of endosomes?

A

sorting of materials taken up from the extracellular environment

83
Q

What is the function of the mitochondria?

A

energy metabolism

84
Q

What is the function of peroxisomes?

A

oxidation of toxic molecules

85
Q

What is the function of chloroplasts?

A

photosynthesis in plants

86
Q

What are the different types of transport that molecules do between compartments?

A
  1. Gated transport: transport through nuclear pores, opens and closes
  2. Transmembrane transport: transport across membranes
  3. Vesicular transport: transport by vesicles, one compartment infused with another
87
Q

What is protein sorting? What does it involve? Where does synthesis of the protein occur? What happens after synthesis?

A

Selective transport of proteins from the cytosol into membrane compartments (organelles).

Involves binding of sorting signals (signal sequences) on a protein with a translocator in the membrane to be crossed.

Proteins are synthesized in the cytoplasm either on the cytosol-suspended ribosomes, or on the ribosomes attached to the membranes of the endoplasmic reticulum (ER)
- ALWAYS IN THE CYTOSOL - exam question!

After synthesis, proteins get sorted and transported to their destinations in different intracellular compartments
- Signal sequences direct proteins to the correct organelle
- Proteins that need to go to a certain compartment have a signal sequence which directs them to that compartment
- Some proteins get the signal sequence before folding, while other proteins don’t get the signal sequence until it is folded

88
Q

What occurs during transmembrane transport? What receptors are present? What does the protein contain when it gets its structure?

A

transport of proteins into mitochondria
- Proteins synthesized on soluble ribosomes are targeted to mitochondria post-translationally

  1. TOMs (translocators on the outer membrane)
  2. TIMs (translocators on the inner membrane)
    - Each receptor has a unique confirmation that allows it to fit on the mitochondria

When the protein gets its structure, it contains a-helix with positively charged residues on one side and hydrophobic residues on the other side

89
Q

What type of reactions are peroxisomes involved in? What do they do?

A

oxidative reactions

  1. detoxify various toxic molecules that enter the bloodstream
  2. involved in lipid synthesis and breakdown of fatty acids
90
Q

What is the largest organelle in most eukaryotic cells?

A

Endoplasmic reticulum

91
Q

Where are proteins synthesized on the rough ER membrane targeted?

A
  1. ER
  2. Golgi
  3. Lysosomes
  4. Plasma membrane
  5. Secreted outside the cell
92
Q

Describe the process of targeting proteins to the ER.

A
  1. Binding of SRP (signal recognition particle) to the ER targeting signal of nascent peptide chains. SRP then drags the entire peptide with bound ribosomes-mRNA complex to the SRP recognition protein in the rough ER
    - SRP: recognizes protein by binding to the signal sequence
  2. SRP then comes off the nascent chain which is then fed into the translocator channel formed of many proteins
  3. After the N-terminus of the nascent peptide enters the ER channel, peptide chain elongation continues and the signal peptide is cleaved off by a specific signal peptidase. Translation continues until the entire polypeptide is synthesized and the newly synthesized polypeptide resides in the lumen of ER.
    - Special proteases cleave off the signal peptide
93
Q

What is the role of stop transfer signals in the transmembrane proteins in the ER?

A

there is a hydrophobic stretch that traps the protein in the membrane

94
Q

How are proteins sorted in the ER? Define glycosylation and o-linkage.

A
  1. Secreted or lumenal proteins are translocated, their signal peptides are cleaved, and the soluble proteins are released
  2. Integral membrane proteins remain embedded in the ER membrane. Key is a stop-transfer sequence of hydrophobic amino acids
  3. Proteins undergo specific modifications (glycosylation) in the ER as part of sorting and packaging for transport to their destination
    - Glycosylation: enzymes add sugars to the protein
    - O-linkage: linked via oxygen to the sugar
95
Q

Describe how N-linked Glycosylation is initiated in the ER.

A

A unit of 14 sugar residues is transferred to specific asparagine residues in the growing polypeptide chain, while translation is still in progress.
- The recognition sequence for addition of N-linked sugars is Asn-X-Ser/Thr.
- Liked via nitrogen to the sugar

96
Q

What is the cytoskeleton? What is it composed of? Where is it located?

A

skeleton of a cell

  1. Actin filaments
  2. Microtubules (thickest)
  3. Intermediate filaments

cytoskeletal fibers form a network in the cytoplasm

97
Q

What do actin filaments do? (3)

A
  1. Form stress fibers and cortical network of thin filaments in most cell types
  2. Are the major component of muscle fibers
  3. Mediate all types of motile and contractile behavior of cells
98
Q

What are microtubules? What do they do? (2)

A

A highly dynamic radial network of fibers

  1. Mediate intracellular transport
  2. Coordinate global cellular events, such as polarization and division
99
Q

What roles does actin have in the cell? (6)

A
  1. Cell structure - forms different structures in nonmuscle cell
  2. Cytokinesis
  3. Adhesion
  4. Contractility
  5. Cell motility (in fibroblast)
  6. Local organelle transport
100
Q

How does the actin cytoskeleton drive cell movement? (2)

A
  1. Actin filaments will polymerase and protrude the plasma membrane, then the cell will move. Contraction then allows the back of the cell to move as well
  2. When actin polymerases at the end of the membrane, the filaments pull at the cell membrane to pull it forward at the leading edge
101
Q

What is the function of myocytes? (3)

A
  1. Form muscle tissues in the body (including striated muscle, smooth muscle, and cardiac muscle)
  2. Respond to nerve stimuli to produce mechanical force by contraction
  3. Are the driving force for body movement and normal functioning of many organs, including heart, blood vessels, and digestive system
102
Q

Describe the ends of actin filaments.

A
  1. Plus end - fast growing end, barbed
  2. minus end - slow growing end, pointed
103
Q

Why is it important that actin is able to attach to the extracellular matrix?

A

It is depended on for all functions. During cancer, this mechanism is affected. Normal cells can no longer attach, so they continue to grow, leading to metastasis.

104
Q

LEFT OFF AT ACTIN DYNAMICS

A

Foundational Toolkit (7 decks)

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