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BSC2010 - Exam 1

Terms in this set (137)

Nucleic Acids
Polymers that store, transmit, and express hereditary (genetic) information
In sequences of monomers that make up nucleic acids.
How is genetic information encoded?
DNA and RNA
What are the two types of nucleic acids?
DNA
Stores and transmits genetic info
RNA
The information encoded in DNA is used to specify the amino acid sequences of proteins.
Nucleotide
Three components: a nitrogen containing base, a pentose sugar, and 1-3 phosphate groups
Nucleoside
Molecules consisting of a pentose sugar and base but no phosphate group
Nucleoside monophosphates
Nucleotides that contain just one phosphate group
Pyrimidine or Purine
What are the two things a base can be?
Cytosine, Thymine, Uracil
Which base groups are pyrimidines?
Adenine, Guanine
Which base groups are purines?
Pyrimidine
A six membered single ring structure
Purine
A fused double ring structure
Phosphodiester Bond
The resulting linkage that forms when the pentose sugar in the last nucleotide of an existing chain and the phosphate on the new nucleotide undergo and condensation reaction.
5' to 3 direction
Which direction are nucleic acids said to grow in?
Oligonucleotides
Include RNA molecules that function as "primers" to duplication of DNA; RNA molecules that regulate the expression of genes; and synthetic DNA molecules used for amplifying and analyzing other, longer nucleotide sequences.
Polynucleotides
Commonly referred to as nucleic acids, include DNA and most RNA. The longest polymers in the living world.
Adenine, Cytosine, Guanine, Thymine
Four bases found in DNA
Adenine, Cytosine, Guanine, Uracil
Four bases found in RNA
The lack of a hydroxyl group at the 2' position of the sugar in DNA
Why is DNA less flexible than RNA?
Two (Double)
Number of polynucleotide strands in DNA
One (Single)
Number of polynucleotide strands in RNA
Hydrogen Bonds
What are base pairs primarily held together by?
Between the partial negative charge on N or O of one base to the partial positive charge on a hydrogen atom of another base. (Remember FON)
Describe how the hydrogen bonds form between bases.
Because of hydrogen bonding between nucleotides in separate portions of the molecules.
Why can single stranded RNA fold up into three dimensional structures?
Bonding and recognition of other molecules. It occurs by complementary base pairing
RNA can fold back on itself to form a double stranded helix. What is this useful form?
The same length (they are antiparallel)
What length are the two separate polynucleotide strands in DNA?
Right handed
How does the DNA double helix usually coil?
DNA Replication
Polymerization using an existing strand as a base-pairing template. This usually involves the entire DNA molecule.
DNA sequences are copied into RNA
Transcription
The nucleotide sequences in most RNA molecules used to specify sequences of amino acids in proteins (polypeptides).
Translation
Hydrogen Bonds are broken
What occurs in both transcription and translation?
So that each new cell or organism receives a complete set of DNA from its parent.
Why must DNA be replicated completely?
The DNA code that is copied to RNA during transcription
What determines the amino acid sequence of a protein?
The transcription and translation of specific DNA sequences.
Gene expression
Sequences of DNA that encode specific proteins and are transcribed into RNA.
Genes
The complete set of DNA in a living organism
Genome
DNA base sequences
What is similar about closely related species?
3 billion
How many base pairs are in the human genome?
3
How many hydrogen bonds are created when cytosine pairs with guanine?
2
How many hydrogen bonds are created when adenine pairs with thymine?
Proteins
Polymers made up of monomers called amino acids
Nitrogen-containing amino group and the acidic carboxyl group
Which two functional groups do amino acids contain?
R group
How are amino acids identified?
Arginine, Histidine, Lysine
Amino acids with positively charged hydrophilic side chains
Aspartic acid, Glutamic acid
Amino acids with negatively charged side chains
Serine, Threonine, Asparagine, Glutamine, Tyrosine
Amino acids with polar but uncharged side chains (hydrophilic)
Alanine, Isoleucine, Leucine, Methionine, Phenylalanine, Tryptophan, Valine
Amino acids with hydrophobic side chains
Glycine
A single hydrogen atom that is small enough to fit into tight corners in the interior of a protein molecule.
Proline
Has a modified amino group that lacks a hydrogen atom. It forms a covalent bond with the hydrocarbon side chain (ring structure). Stabilizes bends or loops in proteins.
Cysteine
Has a terminal -SH group. can react with another cysteine side chain to form a covalent bond called a disulfide bridge.
Disulfide bridge
Helps determine how a protein molecule folds
Oligopeptides (Peptides)
Amino acids that form short polymers of 20 or fewer amino acids.
Polypeptides
A large molecule made up of many amino acids joined by peptide linkages.
The amino group of the new amino acid reacts with the carboxyl group of the amino acid at the end of the chain.
How are new amino groups added to existing chains?
Amino to carboxyl
Which direction does polymerization take place?
The bond formed by a condensation reaction between amino groups. Water is lost.
Peptide bond
Primary Structure
The precise sequence of amino acids in a polypeptide chain. Established by covalent bonds.
Secondary structure
Regular repeater spatial patterns in different regions of a polypeptide chain.
alpha helix
The right handed coil that turns in the same direction as a screw. The R groups extend outward from the peptide backbone of the helix. The coiling results from hydrogen bonds that form between the N-H group and C=O of amino acids.
beta pleated sheet
Formed from two or more sequences of amino acids that are extended or aligned. Stabilized by H-bonds between the N-H groups and C=O groups.
Tertiary Structure
Results in a polypeptide's definitive 3D shape. Includes a buried interior and a surface that is exposed to the environment. Determined by the interactions between the R-groups and the amino acid side chains.
Functional groups capable of interacting with other molecules.
What is on a tertiary structure of a protein on the exposed outer surfaces?
Covalent disulfide bridge
Form between specific cysteine side chains, hold a folded polypeptide together.
Hydrogen bonds
located between side chains and stabilize folds in proteins
Hydrophobic side chains
Aggregate together in the interior of a protein, away from water, folding the polypeptide in the process.
van der Waals interactions
Stabilize close associations between hydrophobic side chains.
ionic interactions
Form between positively and negatively charged side chains, forming "salt bridges" between amino acid.
Ionic
What kind of interaction occurs between a positively charged arginine and a negatively charged glutamic acid.
Ionic
What interactions occur between charged R groups?
Hydrophobically
How do two nonpolar groups interact?
Hydrogen bonds
Which bonds form between two polar groups?
digestion
What role does the protein sucrase play in humans?
the secondary and tertiary structure will begin to break down or denature because hydrogen bonds, ionic bonds, and disulfide brides will be disrupted.
If a protein is heated slowly what will happen?
subunits
Two or more polypeptide chains
Quaternary Structure
Results from the ways in which these subunits bind together and interact
Hydrophobic interactions, hydrogen bonds, ionic interactions
Which interactions help hold the four subunits of a hemglobin macromolecule?
Increase in temperature
Causes more rapid molecular movemen breaking H-bonds and hydrophobic interactions.
Altering concentration of H+ (pH)
Changes the patterns of ionization of the exposed carboxyl and amino groups. Disrupts patterns of ionic attractions and repulsions.
High concentration of polar substances
disrupts h-bonding that is crucial to protein structure
Nonpolar substances
Can denature a protein in cases where hydrophobic groups are essential for maintaining a proteins structure
When amino acids that were buried in the interior of the protein become exposed at the surface, or vice versa, causing a new structure to form, or causing different molecules to bind to the protein.
When can denaturing be irreversible?
Binding to other molecules, chemical modification, covalent bonding of a chemical group to the side chain of one or more of its amino acids.
When does a proteins tertiary structure change?
Becomes more hydrophilic and moves to the outer surface of the protein
What happens to an amino acid with a nonpolar R group when a charged phosphate group is added?
Catalyst
Speeds up a reaction without permanently altering itself.
Cause a reaction to occur
What does a catalyst NOT do?
Enzymes
Biological catalysts
Most are proteins and few are RNA molecules called ribozymes
What are most enzymes?
ribozymes
A few important RNA molecules that are enzymes
It is unchanged and available to catalyze similar reactions.
What state is an enzyme in at the end of a reaction?
Free Energy
Amount of energy in a system available to do work
Exergonic
Reaction that releases free energy
Hydrolysis of sucrose (exergonic)
What reaction takes place during digestion?
transition state
In an enzyme-catalyzed reaction, the reactive condition of the substrate after there has been sufficient input of energy (activation energy) to initiate the reaction.
Activation energy
the energy input required to reach transition state
After the transition state is reached (delta G is negative)
When can a reaction proceed spontaneously?
This is a nonspecific approach and would accelerate all reactions. (like denaturing proteins)
Why shouldn't you increase heat in a living system to speed up certain molecules?
10^3 - 10^8 (converts 100-1000 subtrate molecules per second)
How much faster to enzyme-catalyzed reactions proceed?
Lower it
What do enzymes do to the energy barrier?
Reaction will take place faster
What does a lower activation energy mean?
Substrates
What are the reactants called in an enzyme-catalyzed reaction?
active site
Substrate molecules bind to a particular site on the enzyme called? Catalysis takes place here
the exact three-dimensional shape (also called conformation) and chemical properties of its active site
What does the specificity of an enzyme result from?
E + S → ES → E + P
Enzyme substrate complex equation
Inducing Strain
Once the substrate has bound to the active site, the enzyme causes bonds in the substrate to stretch, putting it in an unstable transition state:
Substrate orientation
The enzyme lowers the activation energy needed to start the reaction, by bringing together specific atoms so that bonds can form.
acid base catalysis
the process where acidic or basic side chains of the amino acids in the active site transfer H+ ions to or from the substrate, destabilizing a covalent bond in the substrate and permitting the bond to break
hydrogen bonds, the attraction and repulsion of charged groups, hydrophobic interactions
What three things does the binding of the substrate to the active site depend on?
Molecules which the enzymes requires in order to function
What are cofactors?
Metal ions
Copper, zinc, iron bind to certain enzymes and participate in enzyme-catalyzed reactions.
coenzyme
Small carbon containing molecule. Binds to the active site of an enzyme then adds or removes a chemical group from the substrate. It then leaves the enzyme to participate in other reactions.
prosthetic groups
organic molecules that are permanently bound to their enzymes
The concentration of the subtrate
What is the rate of an uncatalyzed reaction directly proportional to?
When all the enzyme molecules are bound to substrate molecules, the enzyme is working at its maximum rate.
When are active sites considered saturated?
metabolism
All of the reactions and energy conversions within the cell which is used to harvest energy and do work
metabolic pathway
a step by step, enzyme mediated process by which a precursor molecule is converted into a final product. The product of one reactant feeds into the next reaction as a reactant.
homeostasis
a state in which internal conditions are stab;e
regulating gene expression, regulating activity of enzymes
What are two ways the body controls enzyme activity?
By increasing or decreasing it's quantity of enzymes, thus speeding up or slowing down their activity
How does the body regulate gene expression?
Cells turn enzymes on or off
How does the body regulate activity of the enzymes?
enzyme inhibitor
substances that stop an enzyme from doing its job
penicillin
Which artificial inhibitor inhibits the cell was biosynthesis and kills harmful bacteria
irreversible inhibition
when an inhibitor molecule binds to the side chain on the active site of an enzyme and blocks substrates from binding to it, permanently deactivating the enzyme
reversible inhibition
common with natural inhibitor, its effects are temporary
competitive inhibitors
attach to an enzyme's active site so the substrate cannot bind to the enzyme
non competitive inhibitors
bind to a site other than the active site so that active site cannot accept a substrate anymore
allosteric regulation
when the function of an enzyme is affected due to a non-substrate regulatory molecule binding to another site of the enzyme which is not the active site
allosteric activators
activate enzyme activity
allosteric inhibitors
inhibit (reduce) enzyme activity
protein kinases
enzymes that modify proteins by adding phosphate groups
environmental stimuli
How are protein kinases activated?
diffusion
The primary mechanism cells use to interact with their environment
surface area
What dictates a cell's ability to exchange substances with its environment?
volume
What dictates a cell's metabolic needs?
short distance movement
What is diffusion efficient for?
light microscope
Use a light that passes through a specimen and then through a glass lens to form images
electron microscope
uses an electron beam focused by magnets to illuminate a specimen and produce an image on a TV-like screen, must be stained using toxic heavy metals
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