Cell and Molecular Biology ch. 1 pt 1 Flashcards
Atoms
Made up of neutrons (in nucleus), protons + (in nucleus), and electrons -
Molecules
Groups of 2 or more atoms held together by chemical bonds due to electron interactions
Electronegativity
Ability of an atom to attract electrons
Ionic Bonds
Involve the transfer of electrons from one atom to another where both atoms have different electronegativities
Example: Na + Cl –> Na+ (loses e-) Cl- (gains e-)
Covalent Bonds
Electrons are shared between atoms of similar electronegativities
Which bonds can be single, double, or triple bonds?
Covalent bonds
Which bonds can be polar or nonpolar?
Covalent bonds
What is the difference between polar and nonpolar bonds?
- Nonpolar: equal sharing of electrons between two atoms of similar electronegativity
- Polar: unequal sharing of electrons between two atoms of different electronegativities; results in a dipole
Ex. O-H in water is polar covalent
What are hydrogen bonds and what type of bonds are they?
iii. A weak bond between a hydrogen attached to a highly EN atom, and a negatively charged atom on another molecule (F,O,N)
Ex. O-H in water where H reacts with O on a different water molecule
Properties of Water (5)
- Excellent solvent
- High heat capacity
- Ice floats
- Cohesion/ surface tension
- Adhesion
Addition: What is heat of vaporization?
Amt of heat needed to turn 1g of a liquid into a vapor, without a rise in the temp. of the liquid.
Excellent solvent details
The dipoles break up charged ionic molecules - easy to dissolve substances
High heat capacity details
The degree to which a substance changes temp. in response to gain or loss of heat.
Ex. Temp. of large body of water = very stable in response to air temp. changes. Must add lots of energy to warm up this water - also explains water’s high heat of vaporization
Ice floats details
Water expands as it freezes and becomes less dense - explained by H-bonds becoming rigid and forming a crystal that keeps the molecules separated
Cohesion/ surface tension details
Water is attracted to like substances due to H-bonds. Strong cohesion b/w H2O molecules produce a high surface tension that allows for phenomena like water bugs walking on water.
Adhesion details
Water is also attracted to unlike substances
Ex. Wet finger to flip pages - capillary action describes the ability of a liquid to flow without external forces (e.g. against gravity)
What are organic molecules made up of?
Carbon atoms
Monomers (1 unit) form what which are what? Two answers.
Monomers form macromolecules which are polymers (series of repeating monomers).
Functional Groups
Clusters of atoms that give organic molecules their key properties
Ex. OH, COOH, NH2, Phosphate, Carbonyl, Aldehyde, Ketone, CH3
FG OH facts
name - you know this. Polar and hydrophilic
FG COOH facts
Carboxyl. Polar, hydrophilic, weak acid
FG NH2 facts
Amino. Polar, hydrophilic, weak base
FG PO4^3-facts
Phosphate, polar, hydrophilic, acid
FG C double O facts
Carbonyl, polar and hydrophilic
FG CH3 facts
name - you know this. Nonpolar and hydrophobic
What are carbohydrates?
Sugars, starches, and fibers
As well as starch, glycogen, cellulose, and chitin
Carbo.: Monosaccharides
A single sugar molecule (e.g. glucose and fructose)
- Alpha or beta based on the position of the OH on the anomeric carbon (OH down - alpha; OH up - beta)
Anomeric Carbon
C derived from carbonyl carbon (ketone or aldehyde FG) of the open-chain form of the carbo. molecule and is a stereocenter (an atom with 3+ diff. attachments, interchanging of these attachments leads to another stereoisomer).
Carbo.: Disaccharide
Two sugar molecules joined by a glycosidic linkage (O bonds the two sugars) (e.g. sucrose - glucose + fructose, lactose - glucose + galactose, maltose - glucose + glucose)
Carbo.: Polysaccharide
Series of connected monosaccharides; polymer. Bonds form via dehydration synthesis and breakdown vis hydrolysis.
Starch
A polymer of alpha-glucose molecules; store energy in plant cells
Glycogen
A polymer of alpha-glucose molecules; store energy in animal cells (differ in polymer branching from starch)
Cellulose
A polymer of beta-glucose; structural molecules for walls of plant cells and wood
Chitin
A polymer similar to cellulose, except each beta-glucose group has a nitrogen-containing group (n-acetylglucosamine) attached to the ring.
- A structural molecule in fungal cells as well as insect exoskeletons.
Lipids
Hydrophobic molecules that function in insulation and energy storage
- Triglycerides
- Phospholipids
- Steroids
- Lipid Derivatives/Structures
- Cell Membrane Fluidity
What do lipids make up?
Structural components of cholesterol and phospholipids in membranes
What do lipids participate in?
Endocrine signaling
Lipids: Triglycerides
Also called triacylglycerols
- Structures consisting of 3 fatty acid chains attached to a glycerol backbone (3 Cs attached to an OH each)
i. Saturated: contain no double bonds and have straight chains which stack densely and form fat plaques - BAD
Ex. Steric acid
ii. Unsaturated: contain double bonds causing kinks in chains that stack less densely - can be cis or trans (regarding H’s on C-C double bond)
Ex. Oleic acid
Lipids: Phospholipids
Also called diacylglycerols
- Two fatty acids and a phosphate group (+R) attached to a glycerol backbone
- Hydrophilic head; hydrophobic tails - saturated and unsaturated triglycerides (fatty acids)
Lipids: Steroids
Three 6-membered rings and one 5-membered ring; include hormones and cholesterol
Lipid Derivatives/ Structures
i. Phospholipids
ii. Waxes
iii. Steroids
iv. Carotenoids
v. Porphyrins
vi. Adipocytes
vii. Glycolipids
viii. Lipoproteins
Lipid Derivative: Waxes
Esters of fatty acids and monohydroxylic alcohols, used as a protective coating on the skin (e.g., lanolin) and exoskeletons
Lipid Derivative: Carotenoids
Fatty acid carbon chains with conjugated double bonds (think of dienes) and 5-/6-membered carbon rings at each end.
- Includes pigments that produce colors in plants and animals - THINK ABT CARROTS BEING ORANGE.
What are subgroups of carotenoids?
carotenes and xanthophylls
Lipid Derivative: Porphyrins
Also called tetrapyrroles
- 4 joined pyrrole rings that often complex with a metal (e.g. porphyrin heme complexes with Fe in hemoglobin; chlorophyll with Mg)
Lipid Derivative: Adipocytes
Specialized fat cells
a. White fat cells - triglycerides with a thin layer of cytoplasm around it
b. Brown fat cells - lots of cytoplasm, lipid droplets scattered throughout, and lots of mitochondria
Lipid Derivative: Glycolipids
Similar to phospholipids but have a carbohydrate group instead of phosphate
Lipid Derivative: Lipoproteins
Lipids transported through blood via lipoproteins - lipid cores surrounded by phospholipids and apolipoproteins - bc lipids are insoluble
Lipids: Cell membrane fluidity
Cell membranes are capable of changing membrane fatty acid composition in order to maintain fluidity
i. In cold weather
- Cell membranes are more rigid so cholesterol and mono&polyunsaturated fatty acids are incorporated into the membrane.
ii. In warm weather
- Cell membranes are more fluid and flexible so cholesterol added to restrict movement to avoid collapse. The fatty acid tails are saturated so they become straight and pack tightly.
https://www.khanacademy.org/test-prep/mcat/cells/cell-membrane-overview/v/cell-membrane-fluidity
Proteins
Polymers of amino acids joined by peptide bonds
Amino group attached to alpha C (attached to H and R group side chain) attached to carboxyl group
Proteins
Polymers of amino acids joined by peptide bonds
Amino group attached to alpha C (attached to H and R group side chain) attached to carboxyl group
What range of function are proteins NOT involved in?
Structure, storage, insulation, transport, defense (antibodies), enzymes
Storage proteins
Casein in milk, ovalbumin in egg whites, zein in corn seeds
Transport proteins
Hemoglobin carries oxygen, cytochromes carry electrons
Proteins: Enzymes
Catalyze forward and reverse rxns
i. Efficiency is determined by substrate and enzyme concentration, temp., pH, and presence/absence of any inhibitors
ii. Amylase catalyzes rxns that break the alpha-glycosidic bonds in starch
Do enzymes change the spontaneity of reactions?
No
Enzymes are almost always considered to be proteins but what can also sometimes act as an enzyme?
RNA (e.g. ribozymes)
Proteins: Cofactors
Non-protein molecules that assist enzymes; cofactor + enzyme = holoenzyme
- When not combined, it is called apoenzyme/apoprotein
i. Organic cofactor = coenzyme (e.g. vitamins)
- Inorganic cofactors - metal ions like Fe2+ and Mg2+
ii. Cofactor covalently bound to enzyme = prosthetic group
Protein Classification
- Simple - amino acids only
- Conjugated - simple + non-protein
Simple proteins
a. Albumins and Globulins - functional proteins that act as carriers or enzymes
b. Scleroprotein - fibrous proteins with structural function (e.g. collagen)
Conjugated proteins
a. Lipoprotein - protein bound to lipid
b. Mucoprotein - PB to carbohydrate
c. Chromoprotein - PB to pigmented molecule
d. Metalloprotein - P complexed around metal ion
e. Nucleoprotein - contains histone or protamine, bound to nucleic acid
Protein Structure
- Primary
- Secondary
- Tertiary
- Quaternary
Proteins: Primary Structure
Sequence of amino acids connected by peptide bonds
Proteins: Secondary Structure
3D shape resulting from H-bonding b/w amino and carboxyl groups of adjacent amino acids (alpha helix or beta sheet)
- Causes amino acids to fold into a repeating pattern
Proteins: Tertiary Structure
3D structure that forms primarily due to non-covalent interactions b/w amino acid R groups (subunit interaction) (side chain interactions)
i. Non-covalent interactions include H-bonds, ionic bonds, hydrophobic effect (R groups push away from water), and Van Der Waals forces
ii. Includes disulfide bonds (strong type of covalent bond b/w cysteines)
Van Der Waals forces
Weak, short-range electrostatic attractive forces b/w uncharged molecules, arising from the interaction of permanent or transient electric dipole moments.
- Intermolecular
- LDF, dipole-dipole, H-bonding
Proteins: Quaternary Structure
3D shape of a protein that is a grouping of two or more separate peptide chains
Do all proteins have a primary, secondary, tertiary, and quaternary structure?
No. All proteins have primary. Most have secondary. Larger may have tertiary or quaternary.
Protein Categories
- Globular - somewhat water soluble, mostly dominated by tertiary structure
- Fibrous/Structural - not water soluble, mostly dominated by secondary structure, made of long polymers
- Membrane - includes proteins that function as membrane pumps, channels, or receptors
Functions of globular proteins
Enzymatic, hormonal, inter and intracellular storage and transport, osmotic regulation, and immune response
Functions of Fibrous/Structural proteins
Maintain and add strength to cellular and matrix structure (e.g. collagen or keratin)
What is protein denaturation?
Protein is reversed back with the removal of the denaturing agent
When does protein denaturation occur?
When proteins are taken out of their ideal temp., pH range, or solvent
Is protein denaturation reversible?
Usually irreversible but it can be reversed with the removal of the denaturing agent
What does protein denaturation imply?
All of the info. needed for a protein to assume its native state (its folded, functional form) is encoded in its primary structure.
What is the difference between protein denaturation and digestion?
Digestion eliminates all protein structure, including the primary structure
Nucleic Acids
The overall term for DNA and RNA
- Essential to all forms of life and function to encode, express, and store genetic info.
- Nucleotides
- Nitrogenous base
- DNA vs RNA
Nucleotides
Monomers that make up nucleic acids and consist of a nitrogenous base, a 5-C sugar, and a phosphate group
Nitrogenous base
Nitrogen-containing compound that makes up a nucleotide, and can vary based on whether you have DNA or RNA (polymers of nucleotides)
i. In DNA, adenine, thymine, cytosine, guanine (A,T,C,G)
- A and T pair via 2 H bonds
- C and G pair via 3 H bonds
ii. In RNA, adenine, uracil, cytosine, guanine
- A and U pair via 2 H bonds
iii. Can be purines or pyrimidines
a. Pyri - CTU 1 ring
b. Puri - AG 2 rings
DNA - deoxyribonucleic acid
Also contains a deoxyribose sugar and two antiparallel strands of a double helix
RNA - ribonucleic acid
Ribose sugar and usually single stranded
Cell Theory
i. All living organisms are composed of one or more cells
ii. The cell is the basic unit of structure, function, and organization in all organisms
iii. All cells come from preexisting, living cells
iv. Cells carry hereditary information
RNA World Hypothesis
- Self-replicating RNA molecules were precursors to current life (based on DNA, RNA, and proteins)
- RNA stores genetic info. like DNA and catalyzes chemical rxns, like an enzyme, - leads to belief that RNA played role in evolution of cellular life
i. Receives extra support from fact that RNA is unstable due to its extra OH group that makes it more likely to participate in chemical rxns
Central Dogma of Genetics
Info. must travel from DNA –> RNA –> proteins
Bio. info. cannot travel backwards from protein
Stereomicroscope (light)
Uses visible light to view the surface of a sample. Can view living samples but has low light resolution compared to a compound microscope
Compound microscope (light)
Uses visible light to view a thin section of a sample. Can view some living samples (single cell layer) but may require staining for good visibility
Phase contrast microscope
Uses light phases and contrast for a detailed observation of living organisms, including internal structures if thin. Has good resolution and contrast but not ideal for thick samples and produces a “halo effect” around perimeter of samples
Confocal laser scanning microscope and fluorescence
Used to observe thin slices while keeping a sample in tact
View chromosomes during mitosis
Can observe specific parts of a cell using fluorescent tagging but can cause artifacts
Can confocal laser scanning microscopes be used without fluorescence?
Yes in which laser light is used to scan a dyed specimen and display the image digitally
Scanning electron microscope (SEM)
Can view surface of 3D objects with high resolution but can’t use on living samples (preparation is extensive as sample needs to be dried and coated; is costly)
Cryo SEM
Sample is not dehydrated so you can observe samples in their more “natural form” but can’t use on living samples because samples must be frozen which can cause artifacts
Transmission electron microscope (TEM)
Can observe very thin cross-sections in high detail, and can observe internal structures with very high resolution but cannot be used on living samples (sample preparation extensive and technique costly)
Electron tomography
Technique used to build up a 3D model of sample using TEM data. Can look at objects in 3D and see objects relative to one another but cannot be used on living samples (sample preparation extensive and technique costly)
