Midterm 1 Flashcards
Cell
The basic microscopic unit of all living beings; cell produces energy and uses it to build all the substances necessary for its life.
Organ
a fully differentiated structural and functional unit in an animal that is specialized for some particular function
The Nine properties of Cells
1.Cells are highly complex and organized
2.Have and express genetic code
3.Cells can reproduce
4.Cells acquire and utilize energy
5.Cells carry out a variety of chemical reactions
6.Cells engage in mechanical activities
7.Cells are able to respond to stimuli
8.Cells are capable of self-regulation
9.Cells evolve
catabolism
the break down of complex molecules
anabolism
set of metabolic pathways that construct molecules from smaller units.
Metabolism
sum total of chemical reactions in cells
How do cells transport materials around the cell
Motor proteins like actin fillaments or kinesin protein
Commonalities from eukaryotes and prokaryotes
1.an identical genetic language
2.a common set of metabolic pathways
3.many common structural features
Scale of a cell
10^-6 to 10^-9
What limits cell size
1)Surface area to volume ratio
2)Rate of diffusion
3)Sufficient space to perform reactions
Diffusion
unassisted motion that relies on concentration gradient
Active transport
specialized machinery can move molecules/vesicles along the cytoskeleton from one place to another
Requirements to be a model organisim
1)Relatively simple organisms
2)Fast generation time
3)Large numbers of offspring
4)Easy to manipulate in the lab
5)Inexpensive to breed
Hypothesis
statement consistent with most of the data, may take the form of a model (an explanation that appears to account for the data); must be testable
Theory
a hypothesis that has been extensively tested by many investigators, using different approaches, widely accepted
Law
a theory that has been tested and confirmed over a long period of time with virtually no doubt of its validity
Virus
An infectious agent that can only replicate inside of a living cell.
Provirus
A virus genome that has been incorporated into the genome of its host.
Virion
A complete viral particle, which includes the genome, capsid and in some cases an envelope
Viriod
An infectious agent that is composed solely of RNA (i.e., no coat proteins)
Prion
A infectious protein that can transmit its folded shape to other native folded proteins.
3 requirements of viral RNA
*for replication
*for packaging and delivery
*for modification of host cell
3 tenants of cell theory
1.All organisms are composed or one or more cells
2.The cell is the structural unit of life
3.Cells can arise only by division from a pre-existing cell
Hydrogen bonds
Weak attractive interaction between an electronegative atom and a hydrogen atom that is covalently linked to a second electronegative atom
Hydrophobic effects
Not a bond or attraction. These interactions are based on the desire of hydrophobic molecule to not interact with water.
Van der Waals Forces
Weak attractive forces between uncharged molecules that are very close to each other.
4 main elements of life
H,N,O,C
The four types of macromolecules
1)Proteins
2)Nucleic Acids
3)Lipids
4)Carbohydrates
Main functions of carbohydrates
1)Energy
2)Structural component of cell walls
3)Structural components of DNA and RNA
4)Used in protein signalling glycoprotiens
General Formula of a carbohydrate
Cn(H2O)n
Ketose
monosaccharide containing one ketone group per molecule.
Aldose
a monosaccharide (a simple sugar) with a carbon backbone chain with a carbonyl group on the endmost carbon atom, making it an aldehyde, and hydroxyl groups connected to all the other carbon atoms.
Requirements for carbohydrate formation
Carbon chain of 5 or longer
Anomeric carbon
the carbon derived from the carbonyl carbon (the ketone or aldehyde functional group) of the open-chain form of the carbohydrate molecule and is a stereocenter
Alpha bond
formed when both carbons have the same stereochemistry
α‐pyranose
when the OH group of the first carbon projects below the plane of the ring
β‐pyranose
when the hydroxyl OH of the first carbon projects upward from the plane of the ring
Beta Bond
formed by covalent bonding between the oxygen of the C1 (Carbon number 1) of one glucose ring and the C4 (carbon number 4) of the other connecting ring. The beta-1,4-glycosidic bond has the hydroxyl group pointing up.
Polysaccharides
Long chains of polymers of sugar and sugar derivitice that do not store information
Main functions of poly saccharides
1)Storage or energy in glycogen and starch
2)Structural support in cellulose
3)Signalling using oligosaccharides
Starch
Storage of energy in plants that form less organized chains with two different carbohydrates Amylose and Amylose pectin
Glycogen
Storage of energy in animals, they are a monomer that forms highly complex long branches capable of forming coils
Different types of structural polysaccarides
1)Cellulose
2)chitin
3)GAGS which fill inter cellular space
How does alpha bond vs Beta bond affect structure
Alpha bonds are capable of forming coils where beta bonds form rigid rods
Glycomics
systematic characterization of all of the carbohydrate components of a cell or tissue
(including those attached to proteins or lipids)
O-linked
oligosaccharide in a glycosidic bond with a serine or threonine hydroxyl
N-linked
oligosaccharide in a glycosidic bond to the amide nitrogen of an Asparagine residue
Nucleic acid composition
1)5 carbon sugar
2)Phosphate group
3)N-containing aromatic bases
Purines
Guanine and Adenine
Pyrimidines
Cytosine,Thymine,Uracil
Difference between G-C and A-T bonds
G-c forms 3 bonds where as A-T forms only 2 bonds
Which way is dna built?
5’ to 3’
Different types of noncoding RNA
snRNA-Regulate molecules
MiRNA-Regulate gene expression
tRNA-Builds protiens
rRNA-Scaffodling for ribosomes
incRNA-Act as protiens
Six types of Lipids
1)Fatty acid, Saturated or Unsaturated
2)Triglycerols
3)Phospholipids
4)Steroids
5)Glycolipids
6)Terpenes
What is this
Fatty acid
Saturated vs unsaturated Fatty acid
saturated fatty acids have no double bonds are are straight chains of CH bonds where as unsaturated has a double bond causing a kink in the chain
Fatty Acid
a long unbranched hydrocarbon chain with a carboxyl group at one end they influence cell and tissue metabolism, function, and responsiveness to hormonal and other signals
Trans fat vs Cis Fat
Normal fatty acid is in the cis conformation where both ends of the double bond are on the same side where as trans fats have the substituent on either side of the double bond
Hydrogenation
a chemical process by which hydrogens are added to mono-unsaturated or poly-unsaturated fats to reduce the number of double bonds
Why do unsaturated stick together better than saturated ones
Unstaurated fats have a kink in them at their double bonds reducing van der whal interactions
Triacylglycerols
also known as triglycerides, consist of a glycerol molecule with three fatty acids attached to it
What is this
Triacylgerols
Glycerol
a three-carbon alcohol with a hydroxyl group on each carbon
Tail portion of a triacylglycerol
Fatty acids are linked to glycerol, one at a time, by esterbonds formed by the removal of water
Function of Triaclglycerols
Energy storage and insulation of the body
Phospholipids
they have two ends with different properties: one end contains a phosphate group (hydrophilic); the other end has fatty acid tails (hydrophobic
What is this
Phospholipid
Describe the anatomy of a phospholipid
A phospholipid molecule has two fatty acid chains attached to a glycerol backbone = diacylglycerol and The third hydroxyl of glycerol is bonded to a phosphate group, which is bonded to a small polar group like choline.
Steroids
are derivatives of a four-ringed hydrocarbon skeleton that act as signalling throughout the body
Terpenes
are synthesized from the five-carbon compound isoprene and are sometimes called isoprenoids important mediators of ecological interactions. For example, they play a role in plant defense against herbivory, disease resistance, attraction of mutualists such as pollinators, as well as potentially plant-plant communication.
What is MW or molecular weight for amino acids and proteins measure in
Dalton, one twelfth the mass of Carbon-12
What are all amino acids composed of
1.carboxyl group
2.amino group
3.single carbon atom,the α‐carbon
4. unique side chain,called an R group
Which way is a protein synthesized
N terminus to C terminus
Purpose of charged amino acids
Capable of forming ionic bonds
Purpose of polar amino acids
Found on the surfaces of proteins and are involved in H bonding
Purpose of Non-polar amino acids
Buried inside the core of proteins and allow for hydrophobic interactions and vanderwhal interactions
Conformation vs Configuration
Conformation is the 3-d shape a protein will assume when folded where as configuration is what the molecular composition of a protein is
Primary structure
Amino acid residues within a protein
Secondary structure
Alpha helices, Beta sheets, turns and loops that are generated from the interactions between the poly peptide backbone (CO and NH groups)
Number of amino acids per alpha helix turn
3.6
Alpha Helix constrains
1.Electrostatic repulsion (or attraction) between successive amino acid residues with charged R groups
2.Bulkiness of adjacent R groups
3.Interactions between R groups spaced three (or four) residues apart
4.“Helix forming” amino acids include: Leucine (L), Methionine (M), Glutamate (E)
5.“Helix breakers” include Proline (P) and Glycine (G) residues
Beta sheet forming amino acids
Isoleucine (I), Valine (V) and Phenylalanine (F)
What does this depict
Anti-parallel beta sheets
What does this depict
Parallel Beta sheets
Motifs
Certain combinations of secondary structures are common among many different proteins Structural motifs often perform common functions in different proteins
Tertiary structure
3-D shape of a protein stabilized by covalent and noncovalent bonds between the side chains of the protein
X‐ray crystallography
Provides higher resolution structures for larger proteins, but is limited by the ability to get any given protein to form pure crystals
Nuclear magnetic resonance (NMR) spectroscopy
provides information about dynamic changes in structure, and can rapidly reveal drug binding sites, but is difficult to use on larger proteins
Interactions that hold a tertiary structure together
1.Hydrogen Bonds
2.Ionic Bonds
3.Van Der Waals Interactions
4.Hydrophobic Interactions
5.Disulfide Bridges (between Cysteine residues)
Domain
is a discrete locally folded unit (i.e., as substructure) of the overall tertiary structure, usually with a specific function
Homodimer
a protein composed of two identical subunits
Heterodimer
a protein composed of two non-identical subunits
Monomeric
Proteins that consist of a single polypeptide
multimeric proteins
consist of two or more polypeptides
native conformation
stable three-dimensional structure for a particular polypeptide
Fibrous Proteins
Have extensive regions of secondary structure, giving them a highly ordered, repetitive structure, these are typically found outside of the cell like hair,keratin,collegen
Globular Proteins
Different segments of a polypeptide chain (or multiple polypeptide chains) fold back on each other generating a compact structure.Each type has its own unique tertiary structure, which provides structural diversity necessary for proteins to carry out a wide array of biological functions
Self Assembly
The primary sequence of amino acids contained all of the information required for the formation of the polypeptide’s 3D conformation
How do proteins determine their native state?
They likely explore a range of conformations, then funnel down to the most energetically favourable state.
Molecular chaperone
bind to short stretches of hydrophobic amino acids that are exposed in non-native proteins to facilitate proper folding
How do prions damage the body
Prions are misfolded protiens that when in contact with other native proteins causes them to reconfigure into a prion. These prions aggregate forming plaques in the body
