How do biological molecules come together? 8/24 - ANSWER Bonding:
Hydrogen bonding (polar bonds due to differences in electronegativity)
Covalent bonding (can be either polar or nonpolar, strongest type of bond)
covalent bonds - ANSWER Bonds are created by sharing electrons with other
atoms. (the strongest type of bond)
hydrogen bonds - ANSWER attractive forces in which a hydrogen covalently
bonded to a very electronegative atom is also weakly bonded to an unshared
electron pair of another electronegative atom (best example is H2O or water)
Hydrophobic interactions - ANSWER a type of weak chemical interaction
caused when molecules that do not mix with water coalesce to exclude water
commonly found in phospholipid bilayer in the cell membrane to keep non-
water soluble items out of the cell
How do macromolecules such as proteins, polysaccharides, and nucleic acids
each form specific 3D structures? 8/26 - ANSWER covalent bonds and non-
covalent bonds that are formed through synthesis (really dehydration synthesis),
and they are dissembled through hydrolysis/depolymerize/degrade
non-covalent bonds - ANSWER 1. hydrophobic interactions
2. hydrogen bonds
3. ionic interactions (electrostatic interactions between positively and negatively
charged ions)
4. ionic bond (donation/acceptance of electrons as bond)
polysaccharide structure - ANSWER -polymer of monosaccharides joined by
synthesis and the formation of water
-glycogen is an important storage molecule due to extensive branching with free
ends for hydrolysis (to be broken down and used for energy)
-both alpha and beta rings are formed
,polysaccharide function - ANSWER energy storage (glycogen and starch) and
structural support (cellulose in plants)
lipid structure - ANSWER composed of 3 fatty acids and 1 glycerol molecule
(called triglyceride/triacylglycerol for this reason that are joined by an ester
linkage)
hydrophobic (phospholipids are found in cell membranes due to
polarized/unpolarized ends)
can also be a carbon skeleton with fused rings (steroids)
lipid function - ANSWER fats --> long term, compact energy storage
phospholipids --> cell membrane regulation due to hydrophilic/hydrophobic
ends
steroids --> formed from cholesterol for hormones (especially vertebrae sex
hormones)
protein structure (6 things) - ANSWER a. Long chains of amino acids
b. Joined to each other by peptide bonds
c. Structure of each protein dictated by DNA of a gene
d. can be formed into secondary structures through hydrogen bonds which allow
them to fold onto each other (often dictated by protein's specific function, ex.
store hemoglobin)
e. each group has an amino group (-NH2) and a carboxyl group/acid (-COOH),
both of which are polar
f. side chain dictates the type of amino acid is formed
Amino Acid into Protein Synthesis - ANSWER the N-terminus side is put
together first while the C-terminus is at the end
nucleic acid structure - ANSWER -Chain of nucleotides that consists of a
pentose (deoxyribose or ribose), a phosphate group, and a nitrogenous base
(either pyrimidine - TCU, or purine - AG)
-two types: DNA (double-helix with AT/GC) and RNA (single-helix with
AU/GC)
-phosphate that links sugar with phosphodiester linkages make up the sugar-
phosphate backbone
,ATP function - ANSWER -transfer of energy by breaking and synthesizing a
third phosphate group onto ADP (adenine diphosphate)
-main method to convert energy from food/light energy to usable energy for the
cell
-yields energy when catabolizes (exergonic) before anabolizes (endergonic) and
builds back up
-acts as an immediate source of energy that powers cellular work
exergonic-endergonic reaction coupling - ANSWER -exergonic reactions
proceed with net release of free energy (ATP --> ADP)
-endergonic reactions absorb free energy from its surroundings (ADP --> ATP)
-cells use the exergonic process to drive the endergonic one
How are proteins folded into native shapes inside cells? 8/28 - ANSWER 1.
polypeptides are formed from mRNA in the site of ribosomes
2. as the polypeptides are formed, the hydrophobic amino acids collapse
3. the protein HSP 70 Chaperone (powered by ATP hydrolysis) tries to hold the
nonpolar regions from deforming for a little bit while they are being made (if
this process works successfully, then go to step 6, if not then go to step 4
[70ish% are incorrect] )
4. ubiquitin (UBI) ligase recognizes it and puts a tag -UBI- on the polypeptide
5. ubiquitin (UBI) will covalently bond with the unfolded amino acids before a
proteasome breaks down the polypeptide into smaller chunks which are then
used for the immune system
6. either an alpha helix (helix-shaped) or beta sheet (sheet-shaped) is formed
based on the permissiveness of side chains (whether or not they got in the way)
Chaperones - protein folding in cells - ANSWER proteins which help regulate
the folding process for proteins, leading them to be in the correct functional
state for that particular protein's function
HSP 70 helps with folding
Protein turnover in cells via ubiquitin-proteasome system - ANSWER for
proteins that did not fold correctly (even after the HSP 70 Chaperone tried to fix
it), then the ubiquitin-ligase enzyme tags the faulty protein by covalently
bonding ubiquitin with the faulty protein
Then the proteasome processes the tagged faulty protein and breaks it up into
smaller polypeptides/amino acid chains to be used by the immune system
, How do enzymes catalyze chemical reactions and how is enzyme activity
regulated? Textbook answer 8/31 - ANSWER enzymes help speed up
chemical reactions by helping to break up ATP into ADP and P_i and also
lower the necessary activation energy to start the reaction
enzyme activity is regulated through allosteric regulation (protein's function at
one site is affected by binding of regulatory molecule to a separate site) and
inhibition (disallowing the units to bind to the active sites by binding to them
instead)
How do enzymes catalyze chemical reactions and how is enzyme activity
regulated? Lecture answer 8/31 - ANSWER Non-covalent modification
-change the shape of the enzyme through noncovalent interactions of ligand or
another protein with enzyme (allosteric regulation)
-protein-protein interaction where the neighboring enzyme binds to the primary
enzyme to change the shape of active site
Covalent modification
-protein phosphorylation (phosphate group either attached or not attached to the
protein which changes shape of enzyme)
enzyme structure-function - ANSWER HSP-70 is the example
-N-terminal domain (ATPase domain) and C-terminal domain (binding
polypeptide)
-active site helps ATP --> ADP conversion through squeezing it and hydrolysis
by changing its shape (induced fit)
-when the HSP 70 protein spits out the P_i before the ADP, the shape and
function of the protein allows certain binding/releasing to occur
-when ATP is in, loose binding of polypeptide
-when ADP is in, tight binding of polypeptide
--> very mechanical type process
enzyme regulation by allostery or covalent modification - ANSWER
regulatory molecules that change the enzyme's shape and somehow affecting the
regulatory site, through covalent bonding --> can be either directly (allosteric
activation/inhibition) or indirect (cooperativity) or halt the ATP process
(feedback inhibition)
Hydrogen bonding (polar bonds due to differences in electronegativity)
Covalent bonding (can be either polar or nonpolar, strongest type of bond)
covalent bonds - ANSWER Bonds are created by sharing electrons with other
atoms. (the strongest type of bond)
hydrogen bonds - ANSWER attractive forces in which a hydrogen covalently
bonded to a very electronegative atom is also weakly bonded to an unshared
electron pair of another electronegative atom (best example is H2O or water)
Hydrophobic interactions - ANSWER a type of weak chemical interaction
caused when molecules that do not mix with water coalesce to exclude water
commonly found in phospholipid bilayer in the cell membrane to keep non-
water soluble items out of the cell
How do macromolecules such as proteins, polysaccharides, and nucleic acids
each form specific 3D structures? 8/26 - ANSWER covalent bonds and non-
covalent bonds that are formed through synthesis (really dehydration synthesis),
and they are dissembled through hydrolysis/depolymerize/degrade
non-covalent bonds - ANSWER 1. hydrophobic interactions
2. hydrogen bonds
3. ionic interactions (electrostatic interactions between positively and negatively
charged ions)
4. ionic bond (donation/acceptance of electrons as bond)
polysaccharide structure - ANSWER -polymer of monosaccharides joined by
synthesis and the formation of water
-glycogen is an important storage molecule due to extensive branching with free
ends for hydrolysis (to be broken down and used for energy)
-both alpha and beta rings are formed
,polysaccharide function - ANSWER energy storage (glycogen and starch) and
structural support (cellulose in plants)
lipid structure - ANSWER composed of 3 fatty acids and 1 glycerol molecule
(called triglyceride/triacylglycerol for this reason that are joined by an ester
linkage)
hydrophobic (phospholipids are found in cell membranes due to
polarized/unpolarized ends)
can also be a carbon skeleton with fused rings (steroids)
lipid function - ANSWER fats --> long term, compact energy storage
phospholipids --> cell membrane regulation due to hydrophilic/hydrophobic
ends
steroids --> formed from cholesterol for hormones (especially vertebrae sex
hormones)
protein structure (6 things) - ANSWER a. Long chains of amino acids
b. Joined to each other by peptide bonds
c. Structure of each protein dictated by DNA of a gene
d. can be formed into secondary structures through hydrogen bonds which allow
them to fold onto each other (often dictated by protein's specific function, ex.
store hemoglobin)
e. each group has an amino group (-NH2) and a carboxyl group/acid (-COOH),
both of which are polar
f. side chain dictates the type of amino acid is formed
Amino Acid into Protein Synthesis - ANSWER the N-terminus side is put
together first while the C-terminus is at the end
nucleic acid structure - ANSWER -Chain of nucleotides that consists of a
pentose (deoxyribose or ribose), a phosphate group, and a nitrogenous base
(either pyrimidine - TCU, or purine - AG)
-two types: DNA (double-helix with AT/GC) and RNA (single-helix with
AU/GC)
-phosphate that links sugar with phosphodiester linkages make up the sugar-
phosphate backbone
,ATP function - ANSWER -transfer of energy by breaking and synthesizing a
third phosphate group onto ADP (adenine diphosphate)
-main method to convert energy from food/light energy to usable energy for the
cell
-yields energy when catabolizes (exergonic) before anabolizes (endergonic) and
builds back up
-acts as an immediate source of energy that powers cellular work
exergonic-endergonic reaction coupling - ANSWER -exergonic reactions
proceed with net release of free energy (ATP --> ADP)
-endergonic reactions absorb free energy from its surroundings (ADP --> ATP)
-cells use the exergonic process to drive the endergonic one
How are proteins folded into native shapes inside cells? 8/28 - ANSWER 1.
polypeptides are formed from mRNA in the site of ribosomes
2. as the polypeptides are formed, the hydrophobic amino acids collapse
3. the protein HSP 70 Chaperone (powered by ATP hydrolysis) tries to hold the
nonpolar regions from deforming for a little bit while they are being made (if
this process works successfully, then go to step 6, if not then go to step 4
[70ish% are incorrect] )
4. ubiquitin (UBI) ligase recognizes it and puts a tag -UBI- on the polypeptide
5. ubiquitin (UBI) will covalently bond with the unfolded amino acids before a
proteasome breaks down the polypeptide into smaller chunks which are then
used for the immune system
6. either an alpha helix (helix-shaped) or beta sheet (sheet-shaped) is formed
based on the permissiveness of side chains (whether or not they got in the way)
Chaperones - protein folding in cells - ANSWER proteins which help regulate
the folding process for proteins, leading them to be in the correct functional
state for that particular protein's function
HSP 70 helps with folding
Protein turnover in cells via ubiquitin-proteasome system - ANSWER for
proteins that did not fold correctly (even after the HSP 70 Chaperone tried to fix
it), then the ubiquitin-ligase enzyme tags the faulty protein by covalently
bonding ubiquitin with the faulty protein
Then the proteasome processes the tagged faulty protein and breaks it up into
smaller polypeptides/amino acid chains to be used by the immune system
, How do enzymes catalyze chemical reactions and how is enzyme activity
regulated? Textbook answer 8/31 - ANSWER enzymes help speed up
chemical reactions by helping to break up ATP into ADP and P_i and also
lower the necessary activation energy to start the reaction
enzyme activity is regulated through allosteric regulation (protein's function at
one site is affected by binding of regulatory molecule to a separate site) and
inhibition (disallowing the units to bind to the active sites by binding to them
instead)
How do enzymes catalyze chemical reactions and how is enzyme activity
regulated? Lecture answer 8/31 - ANSWER Non-covalent modification
-change the shape of the enzyme through noncovalent interactions of ligand or
another protein with enzyme (allosteric regulation)
-protein-protein interaction where the neighboring enzyme binds to the primary
enzyme to change the shape of active site
Covalent modification
-protein phosphorylation (phosphate group either attached or not attached to the
protein which changes shape of enzyme)
enzyme structure-function - ANSWER HSP-70 is the example
-N-terminal domain (ATPase domain) and C-terminal domain (binding
polypeptide)
-active site helps ATP --> ADP conversion through squeezing it and hydrolysis
by changing its shape (induced fit)
-when the HSP 70 protein spits out the P_i before the ADP, the shape and
function of the protein allows certain binding/releasing to occur
-when ATP is in, loose binding of polypeptide
-when ADP is in, tight binding of polypeptide
--> very mechanical type process
enzyme regulation by allostery or covalent modification - ANSWER
regulatory molecules that change the enzyme's shape and somehow affecting the
regulatory site, through covalent bonding --> can be either directly (allosteric
activation/inhibition) or indirect (cooperativity) or halt the ATP process
(feedback inhibition)
