Biomolecules (Topic 1) Flashcards
What do atoms share? (2)
Electrons
What are the strongest bond types? (2)
Nonpolar and polar
What are nonpolar characteristics? (2)
- They share electrons equally
- no partial charges
What are polar characteristics? (2)
- unequal electron sharing
- has partial charges
What is a solute? (4)
substance dissolved in a liquid
What is the solvent? (4)
The liquid in which solutes dissolve
What is a solution? (4)
solutes dissolved in a solvent
What does it mean to be hydrophilic? (4)
- Water loving
- polar and/or charged things
What does it mean to be hydrophobic? (4)
- water fearing
- nonpolar and/or not charged things
What does it mean to be amphipathic (amphiphilic)? (4)
- to have hydrophilic and hydrophobic ends
(not both on the same end)
What is pH? (5)
The amount of H+ in a solution
(pH = -log[H+])
Hydrogen ion is the same as what? (5)
proton
As proton concentration increases, what happens to pH? (5)
pH decreases and proton concentration increases and vice versa
What is a buffer? (5)
Something resistant to pH change
What is the primary buffer system?
What does its direction depend on? (5)
H2CO3 <–> H+ + HCO3-
- Its direction depends on pH. if pH is low, the system moves to the left
Why are they called carbohydrates? (6)
Because they are made of hydrocarbons (Cs and Hs)
What are the functions of carbohydrates? (6)
- energy structure
- storage
- cell signaling
What are the different sizes of carbohydrates? (6)
- monosaccharides
- disaccharides
- oligosaccharides
- polysaccharides
What are monosaccharides?(6)
- “one” saccharide
- examples: glucose, fructose, galactose
What are disaccharides? (6)
- Two simple sugars linked by a dehydration reaction
- ex: sucrose, lactose, maltose
What are oligosaccharides? (6)
- “few” (no distinct number) between di and poly.
What are polysaccharides? (6)
- “many” polymers of glucose
What are plant polysaccharides? (6)
Starches and cellulose
What are animal polysaccharides? (6)
glycogen
What has more calories starch or cellulose? (7)
Starch
What is the difference between starch and cellulose? (7)
- they have different orientations
- there are enzymes to break down starches but not cellulose
What is cellulose also known as? (7)
fiber
What does glycogen do and where is it found? (8)
- Glycogen exists in the body as a reservoir of available energy
- found in the liver, kidneys, and muscles
What does the hydrolysis of glycogen do? (8)
hydrolysis (breakdown by water) of glycogen from the liver and kidney, leads to release of the glucose monomers into the blood
What is glucose often called? Why? (8)
- blood sugar
- It is the major monosaccharide found in the blood.
What is a lipid? (9)
primarily hydrocarbons (sometimes O)
Are lipids polar or nonpolar? Why? (9)
- nonpolar
- they are made of C-H bonds (nonpolar covalent bonds)
What are the four subclasses of lipids? (9)
- fatty acids
- triglycerides
- phospholipids
- steroids
What are some functions of lipids? (9)
- energy storage
- insulation
- cell membranes
- hormones (communication)
What are the functions of fatty acids? (10)
- Provide energy for metabolism
- Regulate cell function
- Component of triglyceride & phospholipid
Why are they called fatty acids? (10)
Because of their carboxylic acid group
Why are they called saturated acids? (10)
because there is no room (full of H+)
Why are they called unsaturated fatty acids? (10)
Because there is room for more groups/atoms
What are the differences in bonds between saturated and unsaturated fatty acids? (10)
- saturated has all single bonds
- unsaturated has double bonds where they bend
What are triglycerides? (10)
- the majority of lipids in the body
What are triglycerides often known as? (10)
fat
What do triglycerides do? (10)
provide energy to cells
What do triglycerides consist of? (10)
glycerol (3C alcohol) + three fatty acids
Where do you find phospholipids? (11)
In the cell membrane
Are phospholipids polar or nonpolar? (11)
They are amphipathic (polar heads and nonpolar tails)
Compare and contrast triglycerides and phospholipids (11)
Similarities:
- both have glycerol (3C alcohol)
- both have fatty acids
Differences:
- phospholipids have phosphate groups and their attachments
- phospholipids have 2 fatty acids and triglycerides have three
What is different about steroids’ structure than other lipids? (11)
They have ring structures
What are examples of steroid? (11)
- cholesterol
- estrogen
- testosterone
What do steroids do? (11)
- depends on the steroid
- cholesterol regulates membrane fluidity and is the starting point of many hormones
If you put a few phospholipids in water how would they orient? (12)
- they would for a micelle
- tails attract to each other b/c they are hydrophobic (nonpolar)
If you put thousands of phospholipids in water how would they orient? (12)
- They would form a bilayer
- They have hydrophilic (polar) heads so they would face the outside toward the water
- can’t make a micelle b/c they can only be so big
What molecules are nucleic acids? (13)
- DNA
- RNA
- ATP
- GTP
What is the function of a nucleic acid? (13)
- info. storage (DNA and RNA)
- energy transfer (ATP and GTP)
What is the monomer of a nucleic acid? (13)
A nucleotide
What is the difference between deoxyribose and ribose? (13)
Deoxyribose is missing an oxygen
- ex: H vs OH
What do proteins do? (14)
- storage
- transport
- enzymes
- protection
- hormones
- contractile
- receptors
- structure
How are proteins made? (15)
DNA -> RNA -> protein
Where are proteins made? (15)
The rough endoplasmic reticulum
What are the steps for transcription? (15)
- RNA polymerase unzips DNA
- RNA is made from base pairing (A->U, G->C, T->A, C->G)
- mRNA detaches from DNA and exits nucleus
What are the steps for translation? (15)
- mRNA goes to a ribosome (made of rRNA and proteins) in the cytoplasm or ER
- codons are read by tRNAs anticodon and form peptide bonds -> peptide chains (proteins) till a stop codon is read
What does SRP stand for? (15)
signal recognition particle
Do all proteins in the rough ER start with a signal peptide? (15)
Yes, the signal peptide is what directs them to go to the rough ER in the first place
Where are proteins released after being made in the ER? (15)
either into the lumen or the membrane
If peptides work in the cytoplasm, are the ribosomes free or docked? In the membrane or lumen of ER? (16)
- free
- N/A
If peptides work embedded in the cell membrane, are the ribosomes free or docked? In the membrane or lumen of ER? (16)
- docked
- membrane
If peptides work released from the cell, are the ribosomes free or docked? In the membrane or lumen of ER? (16)
- docked
- lumen
Where do proteins start and end after exocytosis? (16)
They start inside the cell and end outside of the cell
What are the monomers of proteins? (17)
Amino acids
What is the basic structure of a protein?
What is the one group that changes? (17)
H H O
N C C
H R OH
- The R group changes depending on the protein
What are the different groups of proteins? (17)
- nonpolar (all CHs)
- polar (not all CHs)
- Ionized/charged
What is a primary structure? (18)
A sequence of amino acids
How do you get a secondary, tertiary, and quaternary structure? (19)
Fold a primary structure
What is a peptide? (20)
A chain of amino acids
What causes peptide folding? (20)
Certain interactions that depend on the R-group
- hydrogen bond = polar R
- ionic bond = charged R
- hydrophobic interactions - nonpolar R
What is a ligand? (21)
any molecule or ion that is bound to a protein
How does ligands bind? (21)
charged or other interactions
What is a binding site? (21)
the region of a protein to which a ligand binds
True or false
Proteins can have only one binding site (21)
False
What are the properties of binding sites? (22)
- specificity
- affinity
- saturation
What is needed for ligands to bind? (23)
They must complement in
- shape
- interaction
True or false
Some sites only bind one ligand while others can bind many ligands 923)
true
Which protein is more specific? One that binds to many or only one? (23)
Only one
What is affinity? (24)
The strength of a ligand-protein bond
What does the affinity of a binding site determine? (24)
How likely it is that a bound ligand will leave the protein surface and return to its unbound state.
What binding site has the highest affinity?(24)
One that has the same shape and opposite charge
What is saturation? (25)
fraction or percent of total binding sites that are bound at a given time
What does the percent saturation of a binding site depends upon? (25)
- the concentration of unbound ligand
- the affinity of the binding site for the ligand
As ligand concentration increases, what happens to saturation? (25)
Saturation increases as ligand concentration increases till saturation reaches 100% then plateaus
When does competition occur? (25)
- Between multiple ligands (for the same protein)
- Multiple proteins (for the same ligand)
What are two ways of controlling protein activity? (27)
- Regulating the number of particular proteins in the cell
- Changing protein shape which alters ligand bonding
How are the number of particular proteins in a cell regulated? (27)
- protein synthesis/degradation
- membrane -> up and down regulation (exo and endocytosis)
What process brings proteins into a membrane?
Exocystosis
What are two types of modulation? (27)
Allosteric and covalent
How many binding sites in allosteric modulation? (28)
Protein has two binding sites
What happens in allosteric modulation? (28)
a modulator binds to a regularity site and changes the shape of the functional site
Allosteric activation vs inhibition (28)
active- no modulator
Inactive- has a modulator
What is covalent modulation? (29)
When charged chemical groups bond covalently to some of the protein’s side chains.
What is the effect of covalent modulation? (29)
Changes shape of functional site
What is the most common type of covalent modulation? (29)
phosphorylation
What does covalent modulation require? (29)
Enzymes
- kinase (If ATP is involved)
- phosphatase (if ATP is not involved)
How do modulators bind in allosteric modulation? (28)
specific interactions with r groups in the binding sites
Catabolism (catabolic reactions) (30)
the breakdown of molecules (releases energy)
Metabolism (30)
the body’s chemical reactions
Anabolism (anabolic reactions) (30)
synthesis of molecules (requires energy)
What is a chemical reaction? (30)
The breaking and formation of chemical bonds
What is an enzyme? How do they work? (31)
- a protein catalyst
- lowers activation energy and makes it more likely to happen)
How many enzymes are in a typical cell? (31)
About 4000
What three major factors regulate enzyme-mediated reactions? (32)
- Substrate concentration
- enzyme concentration
- enzyme activity
What is a substrate?
the reactant in an enzyme mediated reaction
How does substrate concentration affect reaction rate? (32)
As substrate conc. increases, reaction rate increases
- eventually plateaus at saturation
How does enzyme concentration affect reaction rate? (32)
an increase in enzyme conc., increases reaction rate
- plateaus at saturation, but could plateau at a higher reaction rate if there is more enzymes
How does enzyme activity (affinity) affect reaction rate? (32)
As enzyme affinity increases, reaction rate increases
- if there is a higher affinity, saturation is reached sooner and then plateaus
What is a metabolic pathway?
a sequence of enzyme-mediated reactions
What is feedback inhibition?
When an end product of a metabolic pathway inhibits an enzyme early in the pathway
