AP Bio Unit 1- combined doc sets
genomics
- analyzing large sets of genes or analyzing another genome of completely different species to analyze genome
Which of the following statements about the formation of polypeptides from amino acids is true? A. A bond forms between the carboxyl functional group of one amino acid and the amino functional group of the other amino acid. B. A bond can form between any carbon and nitrogen atom in the two amino acids being joined. C. Polypeptides form by condensation or hydrolysis reactions. D. The reaction occurs through the addition of a water molecule to the amino acids.
A. A bond forms between the carboxyl functional group of one amino acid and the amino functional group of the other amino acid. Using dehydration; The carboxyl group is one one and and meets up with the amino functional group, use dehydration to extend the peptide bond
Which of the following best describes cis-trans isomers? a. They differ in their spatial arrangement around inflexible double bonds. b. They are long chains of hydrogen and carbon atoms. c. They are mirror images of each other. d. They have the same number of atoms of the same elements but different structures. e. They differ in the arrangement of covalent bonds and in covalent partners.
A. a. They differ in their spatial arrangement around inflexible double bonds. tricky thing here is spatial arrangement around inflexible double bonds notes just says 'have the same covalent arrangements but differ in spatial arrangement' Cis-trans isomers maintain the same covalent partnerships, but the atoms may be arranged differently.
Which of the following statements concerning unsaturated fats is true? A. They have double bonds in the carbon chains of their fatty acids. B. They have fewer fatty acid molecules per fat molecule. C. They generally solidify at room temperature. D. They are more common in animals than in plants. E. They contain more hydrogen than do saturated fats having the same number of carbon atoms.
A.They have double bonds in the carbon chains of their fatty acids. pg 73
Which molecule is a nucleotide? a.The amino acid glycine b. Deoxyribose c. ATP
ATP A nucleotide consists of three parts: a nitrogenous base, a pentose sugar, and one or more phosphate groups. ATP consists of a nitrogenous base (adenine), a pentose sugar, and three phosphate groups. deoxyribose would be the sugar part and amino acid glycine would be a nitrogenous base
pairing of nitrogenous bases DNA / RNA
DNA - A always pairs with T - G always pairs with C RNA -A always pairs with U , as the T is not present - G always pairs with C
Sucrose is formed when glucose is joined to fructose by a(n) _____.
Glycosidic linkages join simple sugars to form polysaccharides.
If reaction doesnt need energy to start (exergonic)
How do you know if a reaction is spontaneous?
The structural level of a protein least affected by a disruption in hydrogen bonding is the_________
Primary level.
Which levels of the protein structure may be stabilized by covalent bonds?
Primary, tertiary and quaternary levels of protein structure The primary structure of a protein is the specific linear sequence of amino acids forming the protein. The amino acids are joined by *covalent peptide bonds*. Tertiary structure, producing the unique structure of a protein, is stabilized by interactions among the R groups on each amino acid in the protein. Tertiary structure may be stabilized by covalent bonds, called *disulfide bridges*, that form between the sulfhydryl groups (SH) of two cysteine monomers. Tertiary structure may also be stabilized by weaker interactions, including hydrogen bonds between polar and/or charged areas, ionic bonds between charged R groups, and hydrophobic interactions and van der Waals interactions among hydrophobic R groups. Many globular proteins are made up of several polypeptide chains called subunits stuck to each other by a variety of attractive forces but rarely by covalent bonds. Protein chemists describe this as quaternary structure.
The molecular formula for glucose is C6H12O6. What would be the molecular formula for a polymer made by linking ten glucose molecules together by dehydration reactions?
Remember this linking involved the process of dehydration meaning it expels water for each linkage ( 9 in this case) 10 x C6H12O6 - 9x H2O =C60H102O51
3 kinds of cellular work done by ATP
Shuttle renewable and nonrenewable ENERGY, provide ENERGY for cellular functions, provide ENERGY for catabolic reactions
What is denaturation ?
When a protein for any reason unravels and loses its native shape - this can happen if physical and chemical conditions of the proteins environment. If the pH, salt concentration temp or other aspects of its environment are altered the weak chemical bonds and interactions of within a protein may be destroyed.
Sugars are molecules that have __________ C:H:O and are called __________.
a 1:2:1 ratio ; carbohydrates
enzymes
a catalytic protein, speeds up metabolic reactions by lowering activation energy, very specific, reusable, unchanged by reaction
catalyst
a chemical agent that speeds up chemical reactions without being consumed by the reaction
What is a nucleotide?
a nucleotide in general is composed of three parts: a five carbon sugar , a nitrogen containing ( nitrogenous) base, and one or more phosphate groups.
what is a nucleic acid?
a polymer made of monomers called nucleotides, it is technically called a polynucleotide as well - there are two types - DNA and RNA, these enable living organisms to reproduce their couplex components from one generation to the next -DNA provides its own directions for replication -DNA also directs RNA sytnetis and through RNA controls protein synthesis through a process called gene expression
endergonic reaction
a reaction that absorbs free energy from its surroundings, non-spontaneous, positive free energy
exergonic reaction
a reaction with a net release of free energy, negative free energy, spontaneous
metabolic pathway
a sequence of chemical reactions undergone by a compound in a living organism, start with substrate end with product
DNA
a type of nucleic acid, the genetic material that organisms inherit from their parents -each chromosome contains one long DNA molecules -the DNA does not do all the work rather tells the proteins what to do
Alpha helix
a type of structuring of proteins in the secondary phase of protein structuring. a delicate coil held together by hydrogen bonding between every fourth amino acid.
beta pleated sheets
a type of strutting of proteins developed in the secondary phase of protein structuring. two or more segments of the polypeptide chain lying side by side called beta strands) are connected by hydrogen bonds between the two parallel segments of the polypeptide backbone. = these structures can make the core of many globular proteins. ex spider silk, the pleated sheets can give the silk an extra tough quality.
What structural difference accounts for the functional differences between starch and cellulose? a. Starch and cellulose differ in the glycosidic linkages between their glucose monomers. b. Starch is a polymer of glucose, whereas cellulose is a polymer of fructose. c. Starch can be digested by animal enzymes, whereas cellulose cannot.
a. starch and cellulose differ in the glycosidic linkages between their glucose monomers. Both starch and cellulose are glucose polymers, but the glycosidic linkages in these two polymers differ. Glucose can have two slightly different ring structures. When glucose forms a ring, the hydroxyl group attached to the number 1 carbon is positioned either below (alpha) or above (beta) the plane of the ring. In starch, all the glucose monomers are in the alpha configuration. In cellulose, all the glucose monomers are in the beta configuration. As a result, every other glucose monomer is "upside down" with respect to its neighbors. The differing glycosidic linkages in starch and cellulose give the two molecules distinct three-dimensional shapes, leading to key functional differences.
Denature
above a certain temp activity declines, protein unwinds
negative feedback inhibition
accumulation of end product slows the process that produces that amount -stop production
Lock and Key
active site on enzyme fits substrate exactly
ATP
adenosine triphosphate, composed of ribose (5 carbon sugar), adenine (nitrogenous base), and 3 phosphate groups. Phosphate tail can be broken through hydrolysis to produce energy, ADP, and an inorganic phosphate
The tertiary structure of a protein includes all of the following interactions except _________ bonds. -peptide -ionic -disulfide bridges -hydrophobic -hydrophillic
all are involved with the tertiary structure of a protein except peptide bonds.
secondary level of protein folding
alpha helix and beta pleated sheets , held together by hydrogen bonds only -coils and folds with the backbone of the structure built in phase one
Gene
amino acid sequence of a polypeptide is programmed by a gene. genes consist of DNA which is a nucleic acid
proteonomics
analysis or a large set of proteins, similar to genomics, the translation of proteins sequence can help learn about the DNA sequences that coded them .
cooperativity
another type of allosteric activation, binds to one active site but locks ALL active sites open, allowing products to be constantly produced
Noncompetetitive Inhibitor
bind to another part of enzyme to change shape and block substrate from producing
catabolic
breaking a complex molecule down into its simpler parts, releasing energy. ie. cellular respiration
induced fit
brings the chemical groups of the active site into positions that enhance their ability to catalyze the reaction, makes the enzyme more effective
Allosteric Regulation
can accelerate or inhibit production and enzyme activity by attaching to another part of the protein. this changes the shape of the active site which inhibits substrates from bonding and producing more products
Ways enzymes lower activation energy
can do this by having a favorable environment, straining substrate molecules, orienting substrates correctly
energy
capacity to cause change, do work
Sugars have a(n) __________ group that interacts with a _________ group that forms ring structures when the dry molecule is placed in water.
carbonyl ( -C=O) , hydroxyl ( -OH)
Gene Regulation
cell switches on or off the genes that code for specific enzymes
this protein is crucial to the folding process of of other proteins and will segregate the protein into its own hollow cylinder shielding the protein for proper folding.
chaperonins
Renature
coils it back to normal after temp gets too high and the activity decreased
What is an example of a protein that is made in the quartenary structuring of a protein and involves three identical helical polypeptides inter winded into a larger triple helix?
collagen
What is a nucleotide?
composed of three parts ; a five carbon sugar ( pentose ) , a nitrogen containing base , and one or more phosphate groups. -in a polynucleotide each nucleotide only contains one phosphate group
disulfide bridges
covalent bonds formed in the tertiary structuring, further reinforce the shape of a protein. They form where two cysteine monomers , which has sulfydryl (-SH)on their side chains are brought close together by folding of the protein. The Sulfers form an S-S bond creating the disulfide bridge
The type of bond that forms to join monomers (such as sugars and amino acids) into polymers (such as starch and proteins) is a(n) __________ bond.
covalent; Monomers are joined together by a dehydration reaction in which two molecules are covalently bonded to each other through the loss of a water molecule.
What is an amino acid ?
def; an organic molecule with both an amino group and a carboxyl group attached by an alpha carbon ( carbon side chain or r group ) the monomer of a polymer 'polypeptide ' many amino acids make up polypeptides through covalent bonds called peptide bonds. multiple peptide bonds form into a specific molecular shape called *proteins* -amino acids can be considered acidic or basic depending on their side chains
free energy
delta G, energy that can do work when temperature and pressure are constant, related to change in enthalpy(delta H), change in entropy(delta S) and temperature in Kelvin(T). delta G = delta H - T delta S
entropy
disorder, randomness
2nd law of thermodynamics
during every energy transfer, some energy is unusable and often lost, every energy transfer or transformation increases the total entropy of the universe
Feedback inhibition
end product of a pathway that continues to produce product (positive) and then turns off (negative)
positive feedback inhibition
end product speeds up production (less common)
kinetic energy
energy of motion
potential energy
energy of position
1st law of thermodynamics
energy of the universe is constant, cannot be created or destroyed, can only be transferred or transformed, conservation of energy
Carbohydrates are used in our bodies mainly for __________.
energy storage and release While carbs can be use for storage and structuring the primary use for our bodies is energy storage and release.
ways enzymes are affects
environment, pH, temp, salinity, chemicals that infuse enzyme, increase activity by increasing substrate concentration
Enzyme-Substrate Complex
enzyme and substrate
the amino acid sequence of a polypeptide is programed by a discrete unit of inheritance known as a ________
gene
hydrolysis
happens when phosphate leaves ATP to give energy to something else. This causes ATP to become ADP, produces water
phosphorylation
how ATP drives endergonic reactions, covalently bonding a phosphate with another molecule, such as as reactant
Competitive Inhibitor
inhibitor that mimics original substrate by blocking the original substrate
activation energy
initial energy needed to start a chemical reaction, free energy for activating reaction, given off by heat
the reactions of the tertiary structuring level of a protein are reactions between what parts of the molecules?
interactions between the side chains (R groups)of the various amino acids
DNA
is a double helix of two polynucleotides referred to as sugar phosphate backbone that run anti parallell ( 5-3) -these are linked up by hydrogen bonds between the nitrogenous bases which are the inside of the double helix and the the sugar phosphates are on the outside
tertiary level of protein folding
is the overall shape of a polypeptide resulting from interactions between side chains ( r groups ) of the various amino acids. -involves hydrophobic interactions ( all the non polar side chains will group up as a cluster at the core of the protein out of contact with water held together by vanderwalls interactions , meanwhile H bonds between the polar sides help stabilize the rest of the tertiary structure. -covalent bonds are also present through the disulfide bridges formed by the sulfydryl groups further reinforce the shape of the p protein. ( hydrogen bonds, vanderwalls bonds, covalent bonds )
closed system
isolated from surroundings, no energy transfer, cant work at equilibrium bc its exhausted its ability to do work. free energy at a min
heat(thermal energy)
kinetic energy associated with random movement of molecules
Do all proteins go through all four levels of protein structuring?
no, Quaternary structure results from the aggregation of two or more polypeptide subunits, and not all proteins are composed of more than one polypeptide.
cofactors
non-protein enzyme helpers ex. zinc, iron, copper
quartenary structure of a protein folding
not all make it here -must have atlas two or more polypeptide changes required -collegen is an example of a molecule that makes it to this level
open system
not isolated, energy and matter can be transferred between system and surroundings, ie. cells
nucleic acids - nucleotides - polynucleotides ( nucleic acids)
nucleic acids ( DNA /RNA) make up 1 part of the 3 part nucleotides. -nucleotides are the monomers of the polymer nucleic acids ( poly nucleotides)
Inhiibitor
one of the allosteric regulators, doesnt allow active site to work or produce, wedges closed
Activator
one of the allosteric regulators, stabilizes and keeps active site open for production, wedges open
primary level of protein folding
order of amino acids determined by inherited genetic information. this is forming the 'backbone' of the protein through its specific sequence of amino acids and side chains present -connected via peptide bonds ( covalent bonds )
coenzymes
organic enzyme helpers ex. vitamens
The lipids that form the main structural component of cell membranes are __________.
phospholipids
the reactions of the secondary structuring level of a protein are reactions between what parts of the molecules?
polypeptide backbones In the secondary structure it is important to note that the hydrogen bonds of this secondary level are bonds between the repeating constituents of the polypeptide backbone (not the amino acid side chains. - within the backbone the oxygen atoms have a partial negative charged, and the hydrogen atoms attached to the nitrogens have a partial positive charge, there fore hydrogen bonds can form between the atoms
chemical energy
potential energy available for release in a chemical reaction, energy within bonds
The four main categories of large biological molecules present in living systems are _____.
proteins, nucleic acids, carbohydrates, and lipids
Active Site
region on the enzyme where substrate binds
c terminus and n terminus involving polypeptides
side with a single carboxyl end ( c terminus ) side with a single amino ( N terminus ) - the polypeptide chain will end with one each
thermodynamics
study of energy transformations
Hydrogen and Ionic Bonds
substrate held in active site by WEAK interactions
Substrate
the REACTANT that an enzyme acts on
what ultimately determines a proteins structure?
the amino acids in the primary phase
Tertiary structure
the overall shape of a polypeptide resulting from interactions between the side chains r groups) of the various amino acids - this process involves a hydrophobic interaction, as the polypeptide folds into its function shape, amino acids with hydrophobic side chains will cluster at the core of the proteins , keeping out of contact with water, and are held together by van der walls interactions. Meanwhile hydrogen bonds between polar side chains and ionic bonds between positively and negatively charge side chains (R groups ) also help stabilize the tertiary structure.
nucleoside
the portion of a nucleotide without any phosphate group is a nucleoside ( nucleobiatch)
Which stage of protein folding involves the creation of alpha helix structures and beta pleated sheets
the secondary structure These pleats or helix structures are bonded by *hydrogen bonds*
Bioenergetics
the study of how organisms manage their energy resources
Metabolism
the totality of an organisms chemical reactions that result from interactions between molecules within the cell
coupled reactions
the use of exergonic processes to drive endergonic ones, the energy given off from the exergonic is absorbed by the endergonic
all proteins are made of some sort of combination of the ____ amino acids that are available
there are 20 different types of amino acids that make up all proteins
RNA
type of nucleic acid, eat gene along a DNA molecule directs synthesis of a type of RNA called messenger RNA -the m RNAN molecules interacts with the cells protein synthesizing machinery to direct production of a polypeptide which fold into all or part of a protein -this protein synthesis takes place in a Ribosome
anabolic
using energy to build complex molecules from simpler molecules. ie. protein synthesis
endergonic
what reaction is not spontaneous (positive G)
exergonic
what reaction is spontaneous (-G)
