Exam 1 Flashcards
(167 cards)
1
Q
What is the Central Dogma
A
DNA to mRNA to Protein
2
Q
Common Characteristics of Cells
A
1) Central Dogma
2) Cells are self-replicating
3
Q
Name and type of building blocks for DNA
A
Nucleotides A- T and G-C
4
Q
Name and type of building blocks of mRNA
A
Nucleotides A-U and G-C
5
Q
What are the building blocks of proteins
A
Amino acids
6
Q
What is the process called when you go from DNA to mRNA
A
Transcription
7
Q
What is the process called when you go from mRNA to Protein
A
Translation
8
Q
What is cell theory?
A
all living cells are formed by growth and division of living cells
9
Q
What is a gene?
A
The portion of DNA (Chromosomes) that codes for one functional protein
10
Q
What is the genome?
A
Is the full set of all the genes to produce proteins
11
Q
What function do genes serve in the cell?
A
They provide instruction for form, function, and behavior of cells by coding protein products
12
Q
What does gene expression mean?
A
When a gene is transcribed and translated
13
Q
Describe what differential gene expression is.
A
all cells contain the entire genome but only specific genes are expressed to produce the specific protein that the cell needs to perform its function
14
Q
What use did Light microscopy have?
A
Good for defining nucleus, cell boundary, and cytoplasm
15
Q
What limitations did light microscopy have?
A
-Required very thin sections
-not capable of visualizing the smallest cell structures
16
Q
What is the use of Electron Microscopy
A
Beams of electrons are used to visualize very small cellular structures
17
Q
Transmission Electron Microscopy (TEM)
A
-Electrons transmitted through thin sections of a specimen
-Good for internal structure
18
Q
Scanning Electron Microscopy (SEM)
A
-Electrons scattered off the surface of the sample
Ability to determine the surface of structures and details
19
Q
The Tree of Life Has Which Domains?
A
Bacteria, Archaea, Eukaryotes
20
Q
What are the Differences and similarities between Prokaryotes and Eukaryotes?
A
Pro
-no nucleus
-no organelles
-Bacteria and Archaea
Euk
-Nucleus
-Organelles
-Plants, Animals, Fungi, and Protists
Shared
-Plasma Membrane (PM)
-Macromolecules
21
Q
All cells are descendants of?
A
A common prokaryotic ancestral cell
22
Q
Describe Charectisritcs of Prokaryotes.
A
-Variety of shapes (eg. spherical, rod, spiral)
-Often have a cell wall outside of PM (tough and protective coat)
-No nucleus single internal compartment with DNA and cytoplasm
-quick replication (20mins)
-often single cellular
-present in almost all habitats with varied biochemistry
-Some prok are photosynthetic others need an organic source for energy and production of energy
23
Q
List of Organelles of Eukaryotic Cells.
A
Mitochondria
Golgi Apparatus
Endoplasmic reticulum (soft and rough)
lysosomes
ribosomes
peroxisomes nucleus
chloroplast
24
Q
Function of Mitochondria.
A
production of ATP via aerobic respiration
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Function of Golgi Apparatus.
sorts new proteins
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Function of Soft ER.
synthesizes lipids, hormones, and some proteins
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Function of Rough ER.
Protein Processing
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Function of Lysosomes.
Breaks down unwanted material
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Function of Peroxisomes.
Detoxify
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Function of Nucleus.
Genome/DNA resides (transcription)
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Function of Ribosomes.
mRNA->Protein (translation)
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Endocytosis
invagination of PM, forming a vesicle and pinching off to bring substances into the cell
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Exocytosis
the phospholipids in the wall of the vesicle fuse with the phospholipid of the PM open up and content is released to the extracellular fluid
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Cytosol
gel-like fluid in which organelles are suspended ( water with dissolved proteins) eg. enzymes that carry out biological rxn -> glycolytic enzymes
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Cytoplasm
cytosol and organelles beside the nucleus
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Cytoskeleton
a network of protein filaments( actin , mircrotublues , intermiediate)
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actin filaments
microfilaments (smallest) involved in cell movement
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microtubules
composed of tubulin subunits( largest)
-structure for cellular extension
-organizing chromosomes during cell division (spindle apparatus)
-important in vesicle trafficking
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Intermediate filaments
Intermediate in size and are involved in the strengthening of cellular structures ( eg. keratin in nails)
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What are some model organisms?
Escherichia Coli( E.coli)- Prokaytoic cells that serve as bacterial species
Saccharomyces cerevisiae: Brewers yeast Eukaryotic cell
Plants: Arabidopsis
Animals: C.Elegans, Drosophila, mice, tilapia
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Why do we use model organisms?
reproduce quickly, genetic manipulation, unicellular/multicellular, and transparent species.
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atomic number
refers to the number of protons an atom has in its nucleus
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atomic weight
is equal to the number of protons + neutrons ( each weighs about 1 amu)
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neutral atom
equal number of protons and neutrons
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isotopes
are atoms of the same element ( same atomic number, same protons) with different numbers of neutrons
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Why do atoms bond with each other ?
atoms are most stable when the outermost shell contains full electrons. atoms will bond with other atoms to achieve stability
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Covalent bonds
two atoms share a pair of elctrons
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polar covalent bonds
Sharing of a pair of electrons unequally between 2 atoms
eg. O bonded with H and N bonded with H
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In aqueous solutions which type of bond is the strongest by order?
Covalent bonds
Ionic Bonds
Hydrogen Bonds
Van Der Waals
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Ions
an atom that completely gained or lost electrons
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Cations
(+) eg Na+ lost and electron
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anions
(-) eg Cl- gained an electron
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Ionic bond
form when a cation is attracted to an anion (+-)
eg. Na+Cl-(Strong bond in a vacuum but weaker in water)
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Hydrogen Bond
When 2 polar molecules ( or different regions of the same molecule) are attracted to each other: a hydrogen bond forms between (+) of one molecule and (-) ( relatively weak)
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Hydrophilic
a substance that is ionic, polar covalent bonds "charged"
they love water.
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Hydrophobic
a substance that tends to be non-charged, molecules with nonpolar covalent bonds don't interact with water. ( eg. long chains or hydrocarbons due to similar electronegativity)
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Van der Waals forces
they're nonspecific interactions resulting from the distribution of electrons
- they occur in all types of molecules including nonpolar molecules and are relatively weak.
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Acids
Substances that release protons when dissolved in water
H+= Proton
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pH scale range
1-14
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Pure water pH level
7
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Why is it important to maintain constant pH in biological molecules?
Molecules are sensitive to change in pH ( structure and function)
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What are organic compounds?
Molecules that contain carbon except CO2
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What is a functional group?
common arrangements of atoms
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mono-
one eg. monomer
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di-
dimer eg. dimer
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oligo-
A few eg. oligomer
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poly-
many eg. polymer
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Monomer of protein
amino acids
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Monomer of carbohydrates
monosaccharides ( simple sugars)
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Monomer of Lipids
possible " faty acids+glycerol"
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Monomer of nucleotides
Nucleotide ( ATGCU)
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What is a Carbohydrate?
A molecule that gives Energy and Structure is usually composed of
( CH2O) they tend to form a ring structure.
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What is an isomer?
Same chemical formula but different structures eg. glucose and fructose.
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Disaccharides
2 monosaccharides reacting to come together
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Anabolic Reaction
a reaction that makes larger molecules composed of smaller molecules
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Catabolic Reaction
breaking down bigger molecules into smaller ones
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What is a condensation/dehydration reaction
Water is removed during the reaction ( H from one monosaccharide and OH from the second Monosaccharide)
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What type of bond is formed between monosaccharides?
glycoside linkage
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Types of Disaccharides.
Maltose: Glucose + Glucose
Lactose: Galactose + Glucose
Sucrose: Glucose + Fructose
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Types of polysaccharides of Glucose.
Cellulose
glycogen
starch
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Cellulose
Structure of plant cell wall
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Glycogen
Energy storage polymer, found in muscles and liver of animals
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Starch
Energy storage polymer in plants.
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What is a lipid?
"fats" water-insoluble molecules
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Fatty acid
the common component of lipids that is made up of hydrocarbons with carboxyl groups at the end
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Saturated Fatty acids
only single bonds between all C's in the chain therefore max hydrogen and carbon bonds.
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Unsaturated Fatty acids
at least 1 double bond between adjacent C's in the chain, double bonds cause a bend in the chain and can disrupt van der Walls forces ( contributes to fluidity)
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Glycerol- Triglycerol/triglyceride
Glycerol with 3 fatty acids ( neutral fats) is very good for energy storage and exists in animal fats and plant fats
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Phospholipids
glycerol with 2 fatty acids and a phosphate group linked to another hydrophilic / charged group
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amphipathic
has both charged ( hydrophilic) regions and uncharged (hydrophobic) regions
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What is the main use for Phospholipids
They serve as the cell membrane and their ability to act a a bilayer creates those walls.
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Chololestorol
steroid, polysoprenoids
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Glycolipid
monosaccharide linked to a lipid
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Amino acid
the monomer of proteins composed of 20 different a.a that are present in a cellular context
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What is a.a that are acid ( charged)
aspartic acid
glutamic acid
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What is a.a that is basic ( charged)
lysine
arginine
histidine
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What is a.a that is polar ( uncharged)
asparagine
glutamine
serine
threonine
tyrosine
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What is a.a that is nonpolar ( uncharged)
alanine
Valine
leucine
isoleucine
proline
phenylalanine
methionine
tryptophan
glycine
cysteine
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What group of amino acids are hydrophilic?
Charged: Acid and Basic
Uncharged Polar
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What group of amino acids are hydrophobic
nonpolar/uncharged side chains
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peptide bond
forms between adjacent a.a through a condensation synthesis reaction. happens between C of the COOH group of a.a and the N of the amino group of the next a.a
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polypeptide/peptide
shorter chain of amino acid( less than 50 a.a)
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protein
larger chain of a.a folded into its functional protein
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What are the ends of a protein called
N ( amino terminus)
C ( Carboxly terminus)
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Nucleotides
monomers of nucleic acids, DNA, and RNA
-they also can be used for energy and cell signaling
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What is the general structure of a nucleotide?
Phosphate, Sugar, Base
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What sugar is involved in nucleotides?
5 C's ribose(RNA) and deoxyribose(DNA) .
the difference lies in the 2' carbon lacking an OH
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What are the two types of bases in nucleotides?
Pyrimidines
Purines
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Pyrimidines
One six-membered ring
Uracil (U, RNA only)
Cytosine (C, Both)
Thymine (T, DNA only)
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Purines
5-membered ring fused to the 6-membered ring
Adenine ( A, Both)
Guanine ( G, Both)
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What is the role of the Phosphate group in nucleotides?
-nucleotides used to produce chains of DNA or RNA have one phosphate
-nucleotides used for other purposes may have 2 or 3 phosphates
eg. AMP, ADP, ATP, GMP, GTP
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What characteristic allows proteins to carry out their job?
each protein has a special 3-D conformation
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What leads to protein folding? In tertiary structures
it is due to noncovalent interactions between atoms of the backbone as well as side chains (eg. H-bonds, Other electrostatic interactions, van der Walls)
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What role do hydrophobic forces play in determining shape?
nonpolar side chains tend to cluster in the interior of a protein
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What type of fold conformation due proteins take and what determines that shape?
Lowest Energy, and specific amino acids in the polypeptide chain.
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Primary Structure of Proteins
refers to the order of amino acids in the polypeptide chain
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Chaperon Proteins ( Chaperoins)
heat shock proteins (HSP), help other proteins fold into the proper configuration
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Proteins come in a variety of shapes and sizes such as?
size of 50-2000
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common folding patterns
alpha helix
Beta sheets
(secondary structure)
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What interactions lead to secondary structure?
occur between the N-H and C=O in backbone
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alpha helix
polypeptide turns around itself-> forms a rigid cylinder
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what bonds form in alpha helix?
H-bond is made with the H of amino group and O of carboxyl of 4th a.a down the chain
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Beta sheets (pleated)
hydrogen bonds forming between the amino and carboxyl groups of different a.a in segments of the polypeptide chain that lie side by side
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What directions do beta sheets face?
can have parallel and antiparallel configurations.
125
Tertiary Structure
The Full 3-D conformation formed by the entire polypeptide folding and looping Often involves side chain-to-side chain interactions (noncovalent and hydrophobic)
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Quaternary structure
if a protein exists and functions as a complex of more than one polypeptide chain ( subunits) how those subunits fit together is the quaternary structure.
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Domain
A region of a polypeptide with a specific function ( folded into a compact and stable structure)
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Subunit
separate polypeptide chain that comes together and binds with another polypeptide subunit to form a fully functional protein.
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What are the characteristics of proteins with multiple subunits?
-specific binding of subunits together ( quaternary structure)
-subunits can be the same or different
-The number of subunits can vary
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Protein Structure can be stabilized by?
disulfide bonds formed between nonadjacent cysteine residues
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True or False proteins have regions and domains that are highly conserved.
True
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Proteins are broken down into families, Give some examples.
serine protease
kinase
phosphates
^(all enzymes)
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serine protease
cleave peptide bonds of proteins
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kinase
phosphorylate other proteins
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phosphatases
dephosphorylate other proteins
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Protein Function
all proteins work by binding to another molecule ( binding is specific)
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Ligand
any substance that is specifically bound to a protein
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Given the protein name the Ligand
Enzyme
Antibodies
Receptor
substrate
antigen
Chemical Signal: Nuerotransmiter or hormone
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Binding site
the region/domain that associates with a ligand ( usually consisting of a cavity composed of specific a.a)
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antibodies
The immune system produces Immunoglobin in response to foreign pathogens( viruses, bacteria, etc.).
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What do antibodies bind to?
antigens ( target molecules on the pathogen)
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What are the 4 subunits of the antibody
2 heavy chains
2 light chains
hypervariable domain (bind the antigen)
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What allows for variation of antibodies?
Humans can make billions of different antibodies because of the hypervariable domain.
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How does an antigen neutralize antigens?
mechanism like aggragetaion of antigens
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Enzyme
biological catalyst
reduces the activation energy to increase the role of biochemical reactions
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Describe the process of enzymes doing work.
-Enzymes bind to one or more substrate molecules and form the enzyme-substrate complex
(reaction occurs)
-Enzyme -Product Complex
( product dissociates)
Enzyme and Product
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What happens to the enzyme at the end of the reaction?
The Enzyme is not consumed so it's ready to bind to more substrates
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Rate of reaction
(conversion of substrate to product)
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affinity
how tightly an enzyme interacts with its substrate
150
what role do noncovalent interactions play between substrate and enzyme
more -> higher affinity
less -> lower affinity
151
Describe how to set up an experimental design to measure the reaction rate and affinity of enzyme-substrate interactions.
-a known and constant amount of enzyme is added to each of a series of test tubes.
-the same amount of enzyme in each tube
-add to the tubes known and increasing concentrations 0->uM
-after this measure the rate of the reaction ( either substrate consumption or product formation)
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Michaels Menton plot
the plot of the rate of reaction vs substrate concentration
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Km
-Michaels constant
-Relative measure of affinity
-substrate concentration at 1/2 Vmax
-the lower the Km higher the affinity
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line weaver Burk plot
reciprocal of each side of the equation
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What does b represent in Burks plot
y-intercept = 1/Vmax
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what does the m represent in the Burks's plot
slope= (Km/Vmax)
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Co-factors/Co-enzymes
additional helper ions for molecules that facilitate enzymatic reactions
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enzyme modulation
enzymes can be inhibited or activated
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allosteric enzymes
regulatory molecules bind to sites on the enzyme other than the active site that modulates activity
160
In what ways do cells control protein function?
-Regulating gene expression
-Controlling catalytic activity
-Controlling degradation
-Formation of Protein complex
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Regulation of gene expression for protein control.
upregulating and downregulating levels of protein via regulation of gene expression
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Regulating catalytic activity
-other molecules often regulate enzymes
-feedback, allosteric, phosphorylation, kinases.
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feedback inhibitor
an enzyme acting early in a pathway is inhibited by a product produced later in the pathway.
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What types of interactions are occuring with allosteric molecules?
often noncovalent interactions
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What types of interactions are occuring with phosphorylates and kinases?
covalent interactions
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Controlling degradation involves?
tagging a protein with ubiquitin( small peptide) flags it for destruction
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Formation of protein complexes
-To complete a complicated task assemblages of more than 1 protein often rely on a timed sequence of ATP or GTP hydrolysis
-scaffolding proteins help protein complexes assemblage
