Biochemistry Quiz on Molecules and Processes

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Questions and Answers

What is the role of Taq polymerase in the process of PCR?

To anneal primers to the DNA sequence.

To extend the nucleotide chain from the primers. (correct)

To denature DNA strands by heating them.

To synthesize RNA from the DNA template.

Which strand of DNA is also referred to as the non-template strand?

Coding strand (correct)

Sense strand

Template strand

Antisense strand

What temperature is optimal for Taq polymerase to function during PCR?

100ºC

55ºC

75ºC (correct)

90ºC

What is the primary function of telomeres in chromosomes?

To protect chromosome ends from degradation. Signup and view all the answers

What is the significance of swapping the position of two groups on a chiral center?

It leads to the production of an enantiomer. Signup and view all the answers

Which type of RNA polymerase is primarily responsible for synthesizing mRNA?

RNA polymerase 2 Signup and view all the answers

Which monosaccharide is considered the sweetest?

D-Fructose Signup and view all the answers

Which term describes a sugar with six carbon atoms and an aldehyde group?

Aldohexose Signup and view all the answers

What do the vertical lines in Fisher projection formulas indicate?

Bonds behind the plane of the page. Signup and view all the answers

How many different stereoisomers can be formed from a molecule with 3 chiral centers?

16 Signup and view all the answers

What condition results from excessively high levels of glucose in the blood?

Hyperglycemia Signup and view all the answers

Which carbohydrate is stored in the body predominantly in the form of glycogen or fat?

D-Glucose Signup and view all the answers

What is the primary structural feature of cerebrosides?

Ceramide mono- or oligosaccharides Signup and view all the answers

Which lipoprotein is known as 'good cholesterol'?

HDL Signup and view all the answers

How does cholesterol impact membrane fluidity at high temperatures?

Maintains alignment of phospholipids Signup and view all the answers

What characterizes low-density lipoproteins (LDL)?

Transport cholesterol from the liver to peripheral tissues Signup and view all the answers

What occurs to LDL levels when there is a high concentration of cholesterol inside cells?

LDL synthesis is suppressed Signup and view all the answers

What is the composition of very low density lipoproteins (VLDL)?

Mostly triglycerides synthesized by the liver Signup and view all the answers

What role do HDL particles fulfill in cholesterol transport?

Deliver cholesterol for steroid hormone synthesis Signup and view all the answers

What is the impact of high levels of HDL on heart disease risk?

Decreases the risk of heart disease Signup and view all the answers

What unique feature differentiates gangliosides from cerebrosides?

Complex carbohydrate structures Signup and view all the answers

What is the primary function of lipoproteins?

Transport lipids and cholesterol Signup and view all the answers

What type of fatty acid has no double bonds in its hydrocarbon chain?

Saturated Signup and view all the answers

What is the process called that converts oils to fats by adding hydrogen?

Hydrogenation Signup and view all the answers

Which of the following fatty acids is considered mono-unsaturated?

Oleic acid (18:1) Signup and view all the answers

What distinguishes trans fatty acids from cis fatty acids?

Trans fatty acids have a higher melting point. Signup and view all the answers

Why are only even-numbered acids found in triglycerides?

The body builds acids from acetate units which are two carbons at a time. Signup and view all the answers

How does the structure of oils differ from that of fats?

Oils have less intermolecular forces due to unsaturation. Signup and view all the answers

Which statement about triglycerides is correct?

They provide a source of stored energy. Signup and view all the answers

What contributes to the lower melting point of unsaturated fatty acids?

The packing of fatty acid chains. Signup and view all the answers

What defines the primary structure of a protein?

The sequence of amino acids Signup and view all the answers

What type of fatty acid is denoted as 18:2?

Polyunsaturated fatty acid with two double bonds. Signup and view all the answers

What types of bonds are primarily responsible for the formation of secondary structures in proteins?

Hydrogen bonds Signup and view all the answers

What is the characteristic feature of tertiary structure in proteins?

It forms through interactions between R groups Signup and view all the answers

Which interaction is NOT involved in the stabilization of tertiary structures in proteins?

Peptide bonds Signup and view all the answers

How does the primary structure influence subsequent levels of protein structure?

By controlling interactions between R groups Signup and view all the answers

What stabilizes the secondary structure of proteins?

Hydrogen bonding Signup and view all the answers

What is a key feature of disulfide bridges in proteins?

They create strong bonds between cysteine residues Signup and view all the answers

Which level of protein structure is primarily responsible for forming the overall 3D shape?

Tertiary structure Signup and view all the answers

How do non-polar amino acids behave in aqueous solutions concerning tertiary structure?

They usually avoid exposure to water Signup and view all the answers

What is the significance of hydrogen bonds in the secondary structure?

They provide stability without creating a fixed shape Signup and view all the answers

Study Notes

Key Points

Understand biochemical reactions in water (10%)
Describe cell organization (8%)
Detail amino acids and peptides (6%)
Identify proteins, protein purification, and enzymes (14%)
Describe biological membranes (6%)
Understand nucleic acid structure and information conveyance (3%)
Detail nucleic acid biosynthesis and replication (8%)
Explain RNA biosynthesis (4%)
Describe genetic message translation (6%)
Understand viruses, cancer, and immunology (6%)
Describe energy and electron transfer in metabolism (10%)
Identify carbohydrate metabolism storage mechanisms (16%)
Describe glycolysis (3%)

Carbohydrates

Sugars are small carbohydrates (literally hydrates of carbons)
Monosaccharides are smaller units polymerizing to form polysaccharides

Nomenclature

Carbohydrate names are based on the number of carbons:
- 3 carbons = triose
- 4 carbons = tetrose
- 5 carbons = pentose
- 6 carbons = hexose
All carbohydrates have an aldose or ketose functional group

Fisher Projection Formulas

These are 3D representations (vertical bonds away, horizontal bonds toward viewer)
Show stereocenters and exist as enantiomers (mirror images)
Vertical lines represent bonds behind the plane
Horizontal lines represent bonds in front of the plane
D-stereoisomer has -OH on right
L-stereoisomer has -OH on left
n chiral centers = 2^n stereoisomers

Important Monosaccharides

D-Glucose: stored at 65-110 mg/dL in blood, excess stored as glycogen or fat
D-Fructose: ketohexose, sweetest monosaccharide
D-Galactose: 6C aldohexose found in lactose
Galactosemia: accumulation of galactose due to enzyme deficiency

Haworth Projections

Cyclic hemiacetals, rings
Create an anomeric carbon stereocenter (alpha or beta, based on OH position)
Alpha has -OH down, beta has -OH up

Mutarotation

Change in specific rotation due to equilibration of alpha and beta anomers in aqueous solutions
Alpha can turn into beta

Formation of Glycosides

Treatment of a monosaccharide with an alcohol produces an acetal
Water is lost to form an acetal
A cyclic acetal is a glycoside
A glycosidic bond forms from anomeric carbon to an —OR group

Reduction to Alditols

Reduces the CHO group of a monosaccharide to CH2OH
Sorbitol is a sugar substitute
Xylitol is used as a sweetening agent

Oxidation to Aldonic Acids

Aldehyde group oxidizes to an aldonic acid
Reducing sugars have an altered H to O-

Oxidation of Uronic Acids

Enzyme oxidation forms uronic acid (CH2OH to COOH)

Phosphoric Esters

Phosphoric acid reacts with alcohols
A phosphate group is added to the sugar, a first step in glycolysis

Important Disaccharides

Sucrose: glucose + fructose, a table sugar, non-reducing sugar
Lactose: glucose + galactose, present in milk
Maltose: 2 glucose units, alpha 1,4 glycosidic bond

Polysaccharides

Starch and glycogen: polymers of alpha-glucose, used for energy storage (glycogen in animals, starch in plants)
Cellulose: beta-glucose polymers, form plant cell walls, straight chains
Acidic Polysaccharides: contain carboxyl and sulfuric ester groups, important in connective tissue (e.g., hyaluronic acid, heparan)

Lipids

Classification by Function

Store energy (fats release more energy than carbs)
Part of membranes
Chemical messengers (e.g., hormones)

Classification by Structure

Simple lipids
Complex lipids
Steroids
Prostaglandins, thromboxane, leukotrienes

Fatty Acids

Fatty acids are linked to alcohols via condensation reactions to form ester linkages
Long, unbranched carbon chains with a carboxyl group
Amphipathic (insoluble in water)
Saturated vs. unsaturated (double bonds)
- Saturated have no double bonds, straight chains; unsaturated have double bonds, kinked chains
3 most common: palmitic, stearic, oleic acids

Triglyceride Structure

Glycerol backbone with 3 fatty acid chains linked by ester bonds
Important form of stored energy

Physical State (Fats vs. Oils)

Fats (saturated) : have straight chains, higher melting points
Oils (unsaturated): have kinked chains, lower melting points

Complex Lipids

Phospholipids (alcohol, 2 fatty acids, phosphate): components of membranes (e.g., glycerophospholipids, sphingolipids)
Glycolipids (alcohol, fatty acid, carbohydrate): important in nerve cells

Phospholipids

Phosphoglycerides: glycerol backbone, 2 fatty acids, phosphate group, esterified to alcohol
Sphingolipids: sphingosine backbone, 1 fatty acid, phosphate group

Phosphatidylinositols

Alcohol inositol bound by phosphate
Signaling molecules in communication

Sphingolipids

Backbone is sphingosine
Combination with fatty acid called ceramide
Can include phosphocholine or phosphoethanolamine

Glycolipids

Complex lipids containing carbohydrates and ceramides
Example: Cerebrosides(ceramide with mono or oligosaccharides)

Steroids

Compounds with a fused 3 cyclohexane and 1 cyclopentane ring
Not necessarily esters
Example: Cholesterol (modulator of membrane fluidity, most abundant steroid)

Lipoproteins

Transport cholesterol in the blood
HDL, LDL, VLDL, Chylomicrons

Transport of Cholesterol

LDL: transports cholesterol from the liver to peripheral tissues
HDL: transports cholesterol from peripheral tissues to the liver

Steroid Hormones

Adrenocorticoid hormones: regulate metabolism, immune response, and stress response.

Bile Salts

Produced in the liver from cholesterol oxidation
Important in solubilizing dietary fats

Prostaglandins, Thromboxane, Leukotrienes

Lipid molecules derived from essential fatty acids
Involved in inflammation, pain, fever, blood pressure, blood clotting, uterine smooth muscle tone, and allergic responses

Proteins

Functions

Structural material
Catalysis
Movement
Transport
Hormones
Protection
Storage
Regulation

Amino Acids

20 common amino acids
Classified as nonpolar, polar neutral, acidic, or basic
Except for glycine, all amino acids exist as two enantiomers
Acidic: COOH
Basic: Amino
Neutral: Alcohol, Cysteine

Amino Acids as Zwitterions

A zwitterion is a neutral molecule with both positive and negative charges.
Amino acids are zwitterions (both solid state and in solutions)
Amino acids are either positive or negative in an acidic or basic environment, but remain soluble either way

Protein Properties

Isoelectric Point: the pH at which a molecule carries no net electrical charge.
Amino acids can react with each other, forming peptide bonds and eventually proteins.

Primary Structure

The sequence of amino acids.
Covalent peptide bonds/links between amino acids.

Secondary Structure

Regularly repeating arrangements (alpha-helices, beta-pleated sheets)
Stabilized by hydrogen bonds between amino acids

Tertiary Structure

3D structure of a polypeptide chain
Stabilized by bonds between R groups (Hydrophobic interactions, Hydrogen bonds, Ionic bonds, Disulfide bridges)

Quaternary Structure

Multiple polypeptide chains linked together
Example: hemoglobin (four polypeptide chains)

Non-Conjugated Proteins

Proteins only consisting of peptides
Examples: Insulin and Collagen

Hemoglobin

Tetrameric protein (4 polypeptide chains)
Oxygen transport in blood, cooperatively binding oxygen

Protein Denaturation

A change in a protein's 3D structure, caused by heat or pH changes.
Causes loss of function.

Enzymes

Biological catalysts that speed up chemical reactions by lowering the activation energy.
Substrate specificity (enzyme specifically fits to the substrate), a lock and key or induced fit model.

Enzyme Activity

Measures enzyme efficiency in catalyzing the reaction.

Enzyme Substrate Concentration

Increased substrate concentration leads to increased enzyme activity up to a point of saturation.

Temperature and pH

Enzymes have optimal temperature and pH ranges
Extreme conditions denature the enzyme.

Enzyme Inhibition

Irreversible inhibitors: bind permanently to the active site; non-competitive inhibitors: bind to an allosteric site (and affect active site function; competitive inhibitors compete with substrate for the active site;
maximum rate achieved at low substrate concentration (no inhibitor); maximum rate achieved at high concentrations (inhibitor) causes substrate displacement and equilibration.

Active Sites

Site in the enzyme where the substrate binds;
Pyruvate Kinase converts phosphoenolpyruvate and ADP into pyruvate and ATP; catalytic power is caused by His, Cys, Asp, Arg, and Glu.

Allosterism

Allosteric regulation: occurs when a molecule binds to an allosteric site, altering enzyme activity (activator or inhibitor).

Protein Modification (e.g., Phosphorylation)

Modification of the protein structure; either activates or deactivates the enzyme.

Isozymes

Different forms of the same enzyme with varying protein sequences
Function in different tissues/cellular compartments and can be regulated differently.

Enzyme Medical Uses and Clinical Applications

Examples like Trypsin, Thrombin
Details of uses and application.

Nucleic Acids

Bases

Purines (Adenine, Guanine)
Pyrimidines (Cytosine, Thymine, Uracil)

Sugars

DNA: Deoxyribose; RNA: Ribose
Forming the sugar-phosphate backbone

Nucleoside

Combination of sugar and base (e.g., adenosine)

Phosphate

Phosphate bond to nucleoside forms a nucleotide (e.g, RNA and DNA structure)

Primary, Secondary, Higher Order Structure

RNA Types

mRNA: encodes protein sequence
tRNA: carries amino acids to the ribosome
rRNA: part of the ribosome

DNA Replication

Semi-conservative process
Helicase: unwinds the DNA helix
DNA Polymerase: adds nucleotides to build new strands
Ligase: joins Okazaki fragments

DNA Amplification (PCR)

Denaturation, Annealing, and Elongation steps
Critical for molecular diagnostics and other applications, uses heat-tolerant polymerase (Taq)

Telomeres

Repeating nucleotide sequences at the ends of chromosomes
Protect ends of chromosomes from degradation, important for maintaining genome stability.

Gene Expression and Protein Synthesis

Central dogma (DNA -> RNA -> Protein)
Transcription (DNA to mRNA)
Translation (mRNA to protein)

Introns and Exons

Introns are non-coding regions of DNA/RNA
Exons are coding segments of DNA/RNA

Transcription Regulation

Promoter (initial transcription); enhancer;
elongation and termination (including capping of 5' end or polyadenylation of 3' end, intron removal/splicing)

Post-transcriptional Modifications

Capping and tailing of mRNA (5' and 3' ends)
Intron splicing (removal of non-coding sequences)
Methylation

Translation

mRNA serves as a template
Initiation, elongation, translocation, and termination (using ribosomes)

Correspondence between 3 Bases (codons) and Amino Acids