Chapter 4 Proteins and Nucleic Acids Flashcards
Out of all the macromolecules proteins have the most diverse what?
Range of functions
What is the most abundant organic molecule in living systems?
Proteins
What do all proteins have in common?
They are all polymers of animo acids, and they are all arranged in a linear sequence
What are the traits of proteins?
Structural, regulatory, contractile, and protective
Where do proteins serve?
Transportation, storage, and membranes
What are the types of proteins?
Enzymes or toxins
What are the two ways proteins vary most?
Structure and function
How many proteins can a cell in a living system contain?
Thousands of uniquely functioning proteins
What are four examples of digestive enzyme proteins?
Amylase, lipase, pepsin, and trypsin
What is the function of digestive enzyme proteins?
They digest food by catalyzing nutrients into monomeric units
What are two examples of transport proteins?
Hemoglobin and albumin
What is the function of transport proteins?
To carry substances in the blood or lymph nodes throughout the body
What are three examples of structural proteins?
Actin, tubulin, and keratin
What is the function of structural proteins?
To construct different structures, like cyto skeletons found inside cells
What are two examples of hormone proteins?
Insulin and thyroxine
What is the function of hormone proteins?
To coordinate the activity of different body systems
What is an example of a defense protein?
Immunoglobulin
What is the function of defense proteins?
To protect the body from foreign pathogens
What are two examples of contractile proteins?
Actin n myosin
What is the function of defense proteins?
To effect muscle contraction
What are two examples of storage proteins?
Legume storage proteins and egg white/albumin
What is the function of storage proteins?
To provide nourishment in early development of the embryo and seedling
Denaturation Definition/Explanation
A change in temperature, pH, and/or exposure to chemicals results in a permanent change in the proteins shape which causes it to lose function; a process
What shape is hemoglobin?
Globular
What shape is collogen?
Fibrous
How is the shape of proteins maintained?
Via various different chemical bonds
Is shape critical to protein function?
Yes
What is an amino acid?
A monomer that makes up proteins
What is the fundamental structure of all animo acids?
A central carbon with an attached amino group (NH2), carboxyl group (COOH), and a variable R group/sidechain
What is another term for side chain?
R group
Where is the name animo acid derived from?
The amino group and acidic carboxyl group
How many animo acids are essential to humans?
10
What makes an amino acid essential?
The body’s inability to synthesize the amino acid on its own
What part of an amino acid is different from other animo acids?
The R group/side chain
What are the chemical natures of amino acids?
Acidic (positively charged), basic (negatively charged), polar, and non-polar
What determines the amino acids’ nature?
The nature of its R group/side chain
What are the 9 nonpolar amino acids?
Glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, and proline
What are the 6 polar amino acids?
Serine, threonine, cysteine, tyrosine, asparagine, glutamine
What are the 2 acidic/positively charged amino acids?
Aspartic acid and glutamic acid
What are the 3 basic/negatively charged amino acids?
Lysine, arginine, histidine
What is often used as an interchangeable term for protein?
polypeptide
What is a polypeptide?
A polymer of amino acids where the monomers are linked in linear chains
What is a protein
Polypeptide(s) that have a distinct shape and unique function
What determines a protein’s shape, size, and function?
The sequence and number of amino acids
What must happen before a protein can function completely?
It must have gone through protein synthesis and modification
What are the parts of a polypeptide?
A N terminal with an amino group and a C terminal with a carboxyl group
What type of bonds do amino acids use?
Covalent bonds called peptide bonds
What parts of the amino acids bond?
The carboxyl group of one to ethe amino group of another
Where are additional amino acids added?
To the C terminus (the last carbon)
What is a carbon-nitrogen backbone?
A peptide backbone that is identical for all proteins
What are the four levels of protein structure?
Primary, secondary, tertiary, and quandary
What is primary structure?
A linear sequence of amino acids in a protein
What is a disulfide-bond (S – S bond)
The only covalent bond formed during protein folding in tertiary structures
What determines the primary sequence?
The gene encoding the protein
What happens if there is a change in a protein encoding gene?
A different amino acid may result and be added on to a peptide chain possibly resulting in ailment
What is secondary structure?
A regular structure formed by proteins by hydrogen bonding between the amino acids
What are the most common secondary structures?
a-helix and b-pleated sheet
What do the a-helix and b-pleated sheet have in common?
Both are formed by hydrogen bonds between oxygen atoms in the carbonyl group and the oxygen in the amino group four acids further in the chain
What is tertiary structure?
The three-dimensional conformation of a protein formed from interactions between amino acid side chains
The tertiary structure is mostly made of interaction between what part of an amino acid?
R-group
What is the interaction between to like charged R groups
Repulsion
What is the interaction between two oppositely charged R groups?
Attraction in the form of an ionic bond
What happens when protein folding happens in a watery environment?
Hydrophobic R groups of nonpolar amino acids lay on the interior of the protein while the hydrophilic R’s of the poplar amino acids face out
What type of R groups interact using van der Waals forces?
Hydrophobic R groups
What R-groups interact in disulfide bonds?
Cysteine R-groups
What happens what a protein losses its shape
cease function
What is quandary structure?
An association of discrete polypeptide subunits in a protein
What stabilizes the structure of quandary structures?
Weak interaction between subunits
Catalyst
A substance that helps a chemical reaction take place
Enzyme
A protein that catalyzes biochemical reactions
What is an enzymes task?
To lower the amount of energy needed to perform a certain chemical reaction
How do enzymes complete their task?
They bind to substrates and hold them in a way to speed up creation or breakage of a bond
Is an enzyme an organic catalyst? And what does this mean?
Yes, it means all enzymes increase the rate of reaction
Substrate
The chemical reactants that bind to enzymes
Active site
The special place on an enzyme where the substrate binds to
What is at an enzyme’s active site?
A unique combo of amino acids that create an environment specific to certain substrates and their chemical reactions
What are enzyme’s known for?
Specificity
What happens to an enzyme when it faces extreme temperatures?
It may become less suited for binding substrates, and at high temperature it may denature
What happens when enzymes face extreme pH values?
It may denature
The ranges of what affect enzymes?
Temperature and pH
Induced Fit Definition
A dynamic fit between an enzyme and its substrate
What happens in induced fit?
Substrates interact with an enzyme causing a mild shift in the enzyme which confirms the ideal binding arrangement maximizing ability to catalyze the reaction
What always happens after a reaction occurs in an enzyme?
It returns to its original state
What is an enzyme’s hallmark property relating to the completion of a chemical reaction?
Remains unchanged by the catalyzed reaction
What are products released from an enzyme?
After, the chemical reaction is completed
Free Energy
The usable energy, or energy that is available to do work
What is another term for free energy?
Gibbs free energy (G)
What does Gibbs free energy refer to specifically?
The energy associated with a chemical reaction after entropy is accounted for
What is delta G?
The change in free energy
What is the equation that calculates delta G?
ΔG = ΔH − T ΔS
How is delta G denoted in an equation?
ΔG
What does ΔH symbolize in the delta G formula?
The total energy change of the system
What does ΔS symbolize in the delta G formula?
The amount of energy lost to entropy
What does T symbolize in the delta G formula?
Absolute temperature in Kelvin
In what units is the standard free energy change expressed when under standard pH, temperature, and pressure change?
Kilojoules per mole (kJ/mol) or kilocalories per mole (kcal/mole)
What are considered the standard conditions for free energy change?
A pH of 7 at 25 degrees Celsius under 1 atm of pressure
What is a reaction where the reactants have more free energy than the products?
Exergonic reaction
What is the reaction when the delta G equation is negative?
Exergonic
Enthalpy
The total energy of a system
What is a reaction where the product has more free energy than the reactants?
Endergonic Reaction
What is the reaction when the delta G equation is positive?
Endergonic
What reaction is referred to as a spontaneous reaction? And why?
Exergonic, because they occur without additional energy
What are two terms for a reaction that requires additional energy to occur?
Endergonic and non-spontaneous
Out of exergonic and endergonic reactions which releases energy, and which requires energy?
Exergonic releases energy and endogenic requires energy
Does a reaction be spontaneous mean that the reaction occurs immediately or Fastly?
No
What is activation energy (E(subscript)A)?
The energy necessary for a chemical reaction to occur
How much activation energy is needed in exergonic reactions?
Very little
Do enzymes affect the output of free energy?
No
Why do exergonic reactions still need energy to occur?
Due to the breakage and formation of bonds
What state must a molecule be in to break a bond?
transition state
Transition state
The high energy, unstable state of a molecule
What determines whether the products exit with higher or lower energy than the reactions?
Whether they are exergonic or endergonic
The transition state always exists what in comparison to reactants?
At a higher energy state
What is typically the source of activation energy?
Heat energy from the surroundings
What does heat energy do?
It speeds up the motion of molecules increasing collisions and moves atoms and bonds helping a molecule reach the transition state
The rate at which a chemical reaction will occur is determined by its what?
Activation energy requirements
Which reaction is slower, a high activation energy reaction or a low activation energy reaction?
The high activation energy reaction
Most of the chemical reactions found in cells require too much of what to make them efficient?
Activation Energy
Why can’t enzymes be in a 100% ideal scenario?
Cellular needs vary from cell to cell and may change in individual cells over time
What happens during competitive inhibition?
An inhibitor molecule attaches to the activation site to prevent substrate-enzyme bonding
What happens in allosteric inhibition?
An inhibitor molecule attaches to an area that is not the activation site of an enzyme, and alters the shape of the activation site preventing substrate-enzyme bonding
What is the site where something attaches to an enzyme that isn’t the activation site?
Allosteric site
What is an allosteric activator?
An activator that binds to an allosteric site and increases the compatibility of an enzyme and its substrate(s)
Do many enzymes work optimally on their own?
No
What is needed to make many enzymes work and work optimally?
A specific non-protein helper molecule
What are two types of helper molecules?
Cofactors and coenzymes
What are cofactors?
Inorganic ions that bind to enzymes to promote optimal conformation and function
What are the most common sources of coenzymes?
Dietary vitamins
Which dietary enzymes are coenzymes or precursors of coenzymes?
Vitamin A, Folic Acid, Vitamin B1, Vitamin B2, Vitamin B6 (pyridoxine), Vitamin C, Vitamin D2 (calciferol), and Vitamin E (alpha – tocopherol)
Is enzyme function partially regulated by coenzymes and cofactors?
Yes
How do eukaryote cells typically organize molecules like enzymes?
Into different organelles
How can eukaryotic cells better regulate enzymes for more efficient reactions?
Housing the enzymes for certain cellular processes and their substrates separately
How many chemicals reactions can occur in a single cell at any given time?
Thousands
How do cells simplify the regulation of reactions?
The organize reactions into pathways
What is a metabolic pathway?
A series of interconnected biochemical reactions that convert a substrate molecule(s) through a series of metabolic intermediates to produce a product
A metabolic pathway can be equated to what metaphorically?
An assembly line
What are anabolic pathways?
Pathways that make larger products from smaller substrates
What are catabolic pathways?
Pathways that make smaller products from larger substrates
Of anabolic pathways and catabolic pathways, which requires energy and which produces energy?
Anabolic pathways use energy and catabolic pathways produce energy
What is feedback inhibition?
A form of reaction regulation; it occurs when the product of a pathway inhibits the activity of the first enzyme in the pathway
What allows a cell to maintain homeostasis of a product?
Feedback inhibition
What does feedback inhibition mean what there are high levels of product and low levels of products?
High levels of products means that a pathway reduces product production and low levels of products means that a pathway increases product production
Nucleic Acid
A biological macromolecule that carries the genetic blueprint of a cell
What is the most important macromolecule for the continuation of life?
Nucleic Acids
What are the two main types of nucleic acids?
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
DNA
The nucleic acid that contains the hereditary information of a being and carries the codes to make protein
RNA
A nucleic acid involved with protein synthesis
Nucleic acid
The linear chains of monomers that make up nucleic acids
What are the components of a nucleotide?
A pentose sugar, nitrogenous base (contains nitrogen), and one or more phosphate group(s)
What are the carbons of a nucleotide’s pentose sugar called?
One prime, two prime, etc. or 1’, 2’, etc
The nucleotide’s nitrogenous base is attached to which carbon in its pentose sugar?
One prime or 1’
The nucleotide’s phosphate group(s) are attached to which carbon(s) in its pentose sugar?
Five prime or 5’
What is always attached to the 3rd carbon in a nucleotide’s pentose sugar?
hydroxyl group
What are the two pentose sugars of nucleic acids?
Deoxyribose and ribose
How are deoxyribose and ribose different?
Deoxyribose is found in DNA and lacks a hydroxyl group in its 3’ carbon (means it has a hydrogen there instead); ribose is found in RNA and has a hydroxyl group in its 3’ carbon
What are the nitrogenous bases of nucleotides?
Organic molecules containing nitrogen
Why are the nitrogenous bases of nucleotides bases?
Because they have an amino group that can bind to an extra hydrogen
What are the 4 possible nitrogenous bases of DNA?
Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)
What are the 4 possible nitrogenous bases of RNA?
Adenine (A), Guanine (G), Cytosine (C), and Uracil (U)
What are the 3 shared nitrogenous bases between DNA and RNA?
Adenine (A), Guanine (G), and Cytosine (C)
How are nitrogenous bases classified?
As either purines or pyrimidines
What makes a nitrogenous base a purine?
Having two carbon-nitrogen rings
What makes a nitrogenous base a pyrimidine?
Having a single carbon-nitrogen ring
What nitrogenous bases are purines?
Cytosine, Thymine, and Uracil
What nitrogenous bases are pyrimidines?
Adenine and Guanine
What are phosphodiester linkages/bonds?
Covalent bonds between nucleotides
What are phosphodiester linkages/bonds?
Covalent bonds between nucleotides
What is the nucleic acid directionality?
The first nucleotide has a free (unbonded) phosphate at 5’ and the last nucleotide has a free hydroxyl group at 3’
What is the structure of DNA?
Double helix
What is a double helix structure?
A structure with two linear strands of nucleotides held together with hydrogen bonds between complementary nitrogenous bases
What does complementary nitrogenous bases mean?
Each nitrogenous base only connects to one other bases
What happens in DNA replication?
Each strand of the DNA is copied resulting in two daughter DNA double helixes each with one copied strand from the parent and one synthesized strand
What form the outside of a DNA helix?
Sugar n phosphate(s)
What form the inside of the DNA helix and how are they arranged?
The nitrogenous bases form DNA interiors and are stacked like ladder rings
Are the two DNA strands antiparallel?
Yes
How is antiparallel shown in DNA?
If lined up the free phosphate would be parallel to the other strands free hydroxyl
Where is DNA in eukaryotes?
In their nucleus, chloroplasts, and mitochondria
Is DNA enclosed in a prokaryote’s nucleus?
No
In what order is DNA coded?
Order of the nucleotide in the chain
What is a gene?
A segment of DNA that code for one polypeptide chain
Do all genes code for polypeptides?
No
What besides a polypeptide may a gene code for?
RNA products
In cell DNA is found as?
Long chains of nucleotides that wrap around proteins, predominantly histones, which form chromosomes
How many genes may a chromosome hold?
Tens of thousands
What is the entire genetic content of a cell?
The cells Genome
What is the structure of RNA?
Single stranded and 3-d
What nitrogenous base connects to guanine?
Cytosine
Which nitrogenous bases connect to adenine?
Uracil in RNA and Thymine in DNA
What is the structure of RNA?
Three dimensional single strands
What are the four major types of RNA?
Messenger RNA mRNA, ribosomal RNA rRNA, transfer RNA tRNA, and microRNA miRNA
What does mRNA do?
Carries the copy of genetic code from DNA
How is RNA read?
Three sets of bases known as codons
What does a codon do?
Codes for a single amino acid in a protein
What is the information flow?
DNA – mRNA – Protein
What is transcription?
A process through which messenger RNA forms on a template of DNA
What does DNA dictate during transcription?
mRNA sequence
What is translation?
A process through which RNA directs the formation of protein
What does RNA dictate in translation?
The structure of a protein
What is the Central Dogma of Molecular Biology?
DNA contains instructions for making a protein
mRNA
Messenger RNA
tRNA
Transfer RNA
rRNA
Ribosomal RNA
mrRNA
MicroRNA
What is the function of rRNA?
What is the function of rRNA?
A major constituent of ribosomes that a mRNA bind to to make a protein
What is the function of tRNA?
Carries amino acids to the site of protein synthesis
What is the function of miRNA?
Deals in regulation of gene expression
What is adenosine triphosphate
ATP, which is the cells energy currency
What is ATP made of?
An adenine and three phosphates
How does ATP work?
The phosphates are negatively charged and trying to repel each other, when they do bond it is a weak unstable high-energy bond particularly between the last two phosphates which means that they release a lot of energy when that bond is broken
What are the products of ATP hydrolysis (bond break)?
Adenosine diphosphate (ADP) and an inorganic phosphate group (pi)
How much ATP does the body make a day?
Equivalent to the body weight
How long do you have to use ATP?
little time
How is energy released during ATP hydrolysis?
lost as heat
What is energy coupling?
A process cells use to harness the energy release in ATP hydrolysis
What type of reaction is ATP hydrolysis?
Exergonic
