BIOL 411 - Ch 4, 6 & 7

A site
tRNA’s recognize a codon in the _____ site of the ribosome
What is the term for the measure of the speed of molecules?
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The anaerobic process of breaking down glucose into 2, 3 carbon molecules is called:
To increase entropy as heat or light
When transforming chemical energy, some of it is used for work. Where does the remaining energy go?
Lactic acid is generated from ________ acid
The Kreb Cycle begins with ________
Transition state
Enzymes catalyze reactions by stabilizing the ________ in the reaction
Alpha helices and beta sheets
What are the two main types of secondary protein structures?
Heterotrophs; autotrophs
________ utilize pre-assembled organic molecules, while _______ do not require preassembled organic molecules
For every glucose that you start with, the Kreb cycle makes how many NADH2 molecules?
Aminoacyl tRNA synthetase
What enzyme is responsible for charging tRNAs (attaching an amino acid)?
________ proteins interact with exposed hydrophobic regions to prevent protein aggregation
Dehydration reaction
Peptide bond formation results in a loss of water. This type of synthesis reaction is a ___________
_________ is used to break large molecules into smaller molecules using water
Allosteric enzymes
Enzymes that are regulated by molecules that bind somewhere other than the active site are called ______
Primary, secondary, tertiary, quarternary
Please list the sequential levels of protein structure:
Electron carriers
What type of molecule transfers energy from the Kreb cycle to the oxidative phosphorylation process?
The products of glycolysis will undergo fermentation if ________ is not present
Reading frame
A consecutive sequence of codons following a start codon is called a:
Oak trees are categorized as:
T/F: Members of a protein family often contain the same folding domain
The ATP molecule contains:
The initiation complex would fail to form properly, and translation would not occur
Imagine that a primary RNA transcript from your favorite eukaryotic gene was processed incorrectly, such that it has no 5′ cap. What would be the result?
The unfolding of a protein by heat or chemical treatment is referred to as:
To both increase the rate of a specific reaction and decrease the amount of energy needed to reach the transition state
What is the function of an enzyme?
T/F: There is approximately the same number of protein families as there are folding domains
Some organisms obtain their energy from preexisting chemical compounds and get their carbon from the atmosphere. Which of the following terms describes these organisms?
Autotrophs typically obtain their carbon from:
A lot of potential energy
Weak covalent bonds, such as ones in carbohydrates and lipids, have:
T/F: The individual polypeptide chains in a multi-subunit protein each have their own primary, secondary, and tertiary structure
Potential; covalent
Organic molecules store _____ energy in their _____ bonds
Endergonic; a positive
The synthesis of ATP from ADP and Pi is a(n) ______ reaction with ______ Delta G
Entropy is often increased by:
Peptide bonds form between the amino acids stabilize the _______ structure of a protein
Cells make energy when they produce ATP
Which of the following statements violates the first law of thermodynamics?
In a population of organisms, beneficial and harmful random mutations are retained or eliminated through the process of:
-They change the configuration of the polypeptide in such a way as to facilitate proper folding of other regions
-They create surfaces whose shape and charge allows them to interact with other folding domains
-They create regions whose shape and charge can bind specific small molecules
Folding domains show how structure relates to function because:
The large ribosomal subunit
Binding sites for tRNA are located in:
T/F: A cooperative effect can occur in some types of multi-subunit proteins, leading to improved function of the subunits when bound to each other
No, because most amino acid sequences cannot produce functional proteins
One of your friends has decided to make it his life’s work to characterize all functional proteins, as he is convinced that all possible amino acid combinations can result in a protein. Is it possible to confirm his hypothesis in this way?
Release factor
Which one of the following types of proteins interacts directly with a stop codon?
Proteins that prevent inappropriate folding of newly synthesized proteins are called:
3′ – UCCUCCA – 5′
It is actually the 16S rRNA component of a 30S ribosomal subunit that is responsible for recognition of a Shine-Dalgarno sequence. Which one of the following sequences in the 16S rRNA would you predict is responsible for the interaction between a small subunit and mRNA?
A single mRNA can possess multiple protein coding regions
Which one of the following statements about translation in eukaryotes is incorrect?
Hydrogen bonding between the carbonyl oxygen of one peptide bond and an amide hydrogen of a nearby peptide bond
Which one of the following interactions is NOT a stabilizing force at the tertiary level of protein organization?
Glutamic acid
You are studying a protein that you call Protein X. There is an aspartic acid at a key position in Protein X that is important in the folding and stabilization of that protein. If this aspartic acid is changed to a different amino acid, which one of the following amino acid substitutions is most likely to allow the protein to fold normally?
Precursors of tRNAs bound to nucleotides, and not amino acids
Imagine that a researcher was able to travel back in time, shortly after the appearance of the first RNAs on Earth. What would she find?
Transfer of an amino acid to a ribosome
Which of the following is not a possible function of a protein-folding domain?
Hydrogen bonding
Secondary structures are stabilized by which type of interaction?
T/F: For a folding domain that forms a sort of “fist” with certain amino acid R groups buried within and other R groups facing out, the hydrophobic R groups mainly face “out” and the hydrophilic R groups mainly face “in”
Translation only
Which of the following processes occur in the cytoplasm of eukaryotic cells?
The positively charged R group of a basic amino acid could bind DNA
Which of the following statements is true regarding a basic amino acid?
Connects amino groups and carboxyl groups of adjacent amino acids
The bond that forms between amino acids:
Glycine increases the flexibility of the peptide backbone
Which of the following statements is true regarding glycine?
Proteins would be long compared to proteins today and would possess several folding domains
Imagine that a scientist is able to travel back in time to when the first proteins appeared. What would she not observe?
A change in the sequence of a gene is referred to as a(n) ______
T/F: The frequency of mutations does not necessarily decrease or increase over time
Alpha helices are coils with how many amino acids per complete turn?
The bridge between cysteines, which connects parts of a protein, is a stable but non-covalent interaction
Which of the following statements about amino acids is incorrect?
Chemical potential; kinetic; heat
You have entered a 5K race. As you finish the last 500 yards, your body has converted _____ energy to _____ energy with the loss of _____.
Imagine that you discover a microbial deep-sea organism that can derive energy from (inorganic) hydrogen gas (H2). However, this microbe can also synthesize organic compounds from carbon-containing inorganic molecules in the ocean. This microbe is a:
Imagine that you discover a carnivorous deep-sea fish that cannot utilize the carbon in carbonic acid (or any other inorganic molecule) present in seawater to form glucose (or other organic molecules). Living so far beneath the water’s surface, this fish is also incapable of harnessing energy from the sun. This fish would be considered a:
ATP is a nucleotide composed of adenine, _____, and three phosphate groups
Individual nucleotides
Which of the following has the most entropy, individual nucleotides or a nucleic acid?
Of the following molecules, which has the greatest potential energy?
Second; entropy
You have entered a 5K race. As you finish the last 50 yards, you are breathing harder than at the start of the race and sweating profusely. This is an example of the _____ law of thermodynamics because _____ is increasing.
The molecules in the warm air of your house are moving faster than those outside
Imagine that you walk out of your warm house on a cold winter’s day. What is different between the air inside and outside of your house in this scenario?
Potential; covalent
Organic molecules store _____energy in their _____ bonds
Even though evolution may decrease the entropy of living organisms, it increases the entropy of the Earth (or the universe) as organisms release heat
Imagine that you are talking with one of your friends. He states that evolution has actually violated the second law of thermodynamics because complex living organisms are more ordered than the nucleic acids, amino acids, and other molecules that compose them. Why doesn’t evolution contradict the second law of thermodynamics?
Most bacteria and dogs
Which of the following organisms are considered heterotrophs?
The use of ATP by cells began eons ago and has been conserved over time
Nearly all cells use ATP as their primary energy source. This is evidence that:
As a cat pounces on a mouse, her muscles burn 10 units of potential energy (which the cat previously gained from eating). However, the pounce itself only required 4 units of kinetic energy. How many units of energy were dissipated as heat?
_______ is required for an organism to do work
T/F: As plant cells rely on energy obtained directly from the sun to carry out cellular processes, sugars are only used as backup energy sources for plants on cloudy days
Escherichia coli bacteria in your colon are categorized as:
A refrigerator removes heat from its interior and transports this energy outside, into the kitchen
Consider the refrigerator in your kitchen. Based on what you know about the first and second laws of thermodynamics, how does a refrigerator most likely work?
Phosphorylated sugar molecule is cleaved and the products rearranged
In the second phase of glycolysis:
oxidized; reduced
In cellular respiration, glucose is _____ to CO2 and oxygen is _____ to water
The oxygen atoms in both CO2 and H2O are electronegative, and glucose is considered a reducing agent
Which of the following statements is true regarding the equation C6H12O6 + 6O2 →6CO2+ 6H2O + energy?
T/F: Pyruvate oxidation is remarkably similar to glycolysis in that when one molecule of pyruvate enters into a mitochondrion, two molecules of acetyl-CoA are formed
Two pyruvate molecules
At the end of glycolysis, the carbon molecules originally found in the starting glucose molecule are in the form of:
Many of these bonds are C-C and C-H bonds
The chemical bonds of carbohydrates and lipids have high potential energy because:
Glycolysis is:
During phase 3, when glyceraldehyde 3-phosphate is phosphorylated
During what phase of glycolysis is NADH formed?
Gains electrons and is an oxidizing agent
In cellular respiration, oxygen:
None of the other answers options is correct
Which of the following statements is true regarding pyruvate and glucose?
Pyruvate oxidation forms the same number of NADH (per glucose molecule) as glycolysis
Which of the following statements is true regarding pyruvate oxidation?
T/F: Although glycolysis produces four molecules of ATP by substrate-level phosphorylation, the net gain of ATP for the cell is two molecules. This is due to the fact that glycolysis is—at first—endergonic
Oxygen consumption
Which of the following does not occur during the third phase of glycolysis?
After pyruvate oxidation, the chemical energy of how many carbons of the original glucose molecule is converted to chemical energy in the form of ATP in the remaining steps of cellular respiration?
Less energetic than the acetyl group
During pyruvate oxidation, pyruvate is broken down into CO2 and an acetyl group. The CO2 is:
Two molecules of acetyl-CoA
Which of the following is not one of the net final products of glycolysis?
T/F: The ATP produced during glycolysis is the result of substrate-level phosphorylation
Substrate-level phosphorylation
In glycolysis, ATP is synthesized by:
The first phase of glycolysis requires the input of two ATP molecules. It is therefore:
Glucose could move out of the cell, slowing cellular respiration
Imagine that a eukaryotic cell carries a mutation impairing its ability to phosphorylate glucose during glycolysis. What is a likely result of this mutation?
The inputs to glycolysis do not include:
Destabilizes the glucose molecule so that it can be broken down in phase 2
Phosphorylating glucose during phase 1 of glycolysis:
By glycolysis
How did the earliest organisms on Earth most likely produce ATP?

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