Unit 1 MCAT BIOLOGY

Unit 1 of MCAT CAlled Molecular Biology COnatins CH 1 and CH 2

What are the three components of a nucleotide?

Phosphate group, pentose sugar, and a nitrogenous base

What is the difference between a nucleotide and a nucleoside?

A nucleotide contains 1-3 phosphate groups; a nucleoside does not.

Which sugar is found in DNA?

2'-deoxyribose

Which sugar is found in RNA?

Ribose

What are the purine bases?

Adenine and Guanine

What are the pyrimidine bases in DNA?

Cytosine and Thymine

What pyrimidine base replaces Thymine in RNA?

Uracil

What type of bond connects adjacent nucleotides in a DNA strand?

3'-5' phosphodiester bond

In what direction is DNA read by biological machinery?

3' to 5'

In what direction is DNA synthesized?

5' to 3'

Which bases pair with two hydrogen bonds?

Adenine and Thymine (A=T)

Which bases pair with three hydrogen bonds?

Guanine and Cytosine (G≡C)

What is Chargaff's Rule?

%A = %T and %G = %C (Total purines = Total pyrimidines)

Why does GC-rich DNA have a higher melting temperature (Tm)?

G-C pairs have three hydrogen bonds compared to two in A-T pairs, requiring more thermal energy to denature.

What are the four core histone proteins that form the nucleosome octamer?

H2A, H2B, H3, and H4 (two of each)

What is the role of histone H1?

Acts as a linker histone to seal DNA as it enters and leaves the nucleosome, stabilizing chromatin structure.

What is heterochromatin?

Dense, highly condensed, transcriptionally silent chromatin that appears dark under microscopy.

What is euchromatin?

Uncondensed, transcriptionally active chromatin that appears light under microscopy.

What is the function of telomeres?

Repeated sequences at chromosome ends that prevent loss of vital coding DNA during replication and prevent end-joining.

What sequence feature is high in telomeres and centromeres?

High GC content, which provides strong base pairing to hold strands/chromatids together.

What does semiconservative replication mean?

Each daughter DNA molecule consists of one original parental strand and one newly synthesized strand.

What enzyme unwinds the double helix at the replication fork?

DNA Helicase

What is the function of Single-Stranded Binding Proteins (SSBPs)?

Bind unwound DNA strands to prevent them from reannealing or being degraded by nucleases.

What enzyme relieves torsional strain and supercoiling during replication?

DNA Topoisomerase (DNA Gyrase in prokaryotes)

What enzyme synthesizes short RNA primers to initiate DNA replication?

Primase

Why is an RNA primer needed for DNA replication?

DNA polymerases cannot initiate synthesis de novo; they require a free 3'-OH group to extend.

Which enzyme is responsible for the main DNA synthesis in prokaryotes?

DNA Polymerase III

Which enzymes are primary DNA polymerases in eukaryotes?

DNA Polymerases alpha, delta, and epsilon

Which enzyme removes RNA primers in prokaryotes?

DNA Polymerase I

Which enzyme removes RNA primers in eukaryotes?

RNase H

What enzyme seals nicks in the sugar-phosphate backbone after primer replacement?

DNA Ligase

What is the leading strand in DNA replication?

The strand synthesized continuously toward the replication fork in the 5' to 3' direction.

What is the lagging strand in DNA replication?

The strand synthesized discontinuously away from the replication fork, producing Okazaki fragments.

During which phase of the cell cycle does DNA replication occur?

S phase

How does DNA polymerase proofread newly synthesized DNA?

It uses 3' to 5' exonuclease activity to remove mispaired bases by detecting unstable H-bonds.

During which cell cycle phase does Mismatch Repair (MMR) occur?

G2 phase

What type of DNA damage is repaired by Nucleotide Excision Repair (NER)?

Helix-deforming lesions such as thymine dimers caused by UV light.

What enzyme cuts the damaged strand during Nucleotide Excision Repair?

Excision Endonuclease

What type of DNA damage is repaired by Base Excision Repair (BER)?

Non-helix-distorting base modifications, such as cytosine deamination to uracil.

What site is created when a damaged base is removed by glycosylase in BER?

AP (apurinic/apyrimidinic or abasic) site

What enzyme cleaves the phosphodiester backbone at an AP site?

AP Endonuclease

What is the Central Dogma of Molecular Biology?

DNA is transcribed into RNA, which is translated into protein (DNA -> RNA -> Protein).

What is degenerate/redundant genetic code?

Multiple codons can code for the same amino acid.

What is the Wobble Position in a codon?

The 3rd nucleotide position of a codon, which allows non-standard base pairing and protects against mutations.

What is the start codon and what amino acid does it code for?

AUG; Methionine (in eukaryotes) / N-formylmethionine (in prokaryotes)

What are the three stop codons?

UAA, UGA, UAG

What is a silent mutation?

A base substitution that changes a codon but still results in the same amino acid.

What is a missense mutation?

A base substitution that changes a codon to specify a different amino acid.

What is a nonsense mutation?

A base substitution that changes a codon to a premature stop codon.

What is a frameshift mutation?

Insertion or deletion of nucleotides not in multiples of three, altering the reading frame for all downstream codons.

What enzyme synthesizes mRNA in eukaryotic cells?

RNA Polymerase II

What promoter region does RNA Polymerase II bind to in eukaryotes?

The TATA Box (located around -25)

Does RNA Polymerase require a primer or proofreading capability?

No, RNA Polymerase does not require a primer and lacks 3' to 5' proofreading activity.

What is the immediate product of eukaryotic transcription before processing?

hnRNA (heterogeneous nuclear RNA)

What post-transcriptional modification is added to the 5' end of mRNA?

7-methylguanylate triphosphate cap (5' cap)

What post-transcriptional modification is added to the 3' end of mRNA?

Poly-A tail (polyadenylation)

What are the functions of the 5' cap and 3' poly-A tail?

Protect mRNA from cytoplasmic enzymatic degradation and assist in export and ribosome binding.

What complex carries out RNA splicing?

The Spliceosome (composed of snRNA and snRNPs)

What are introns and exons?

Introns are non-coding sequences spliced out; Exons are coding sequences joined together and expressed.

What is alternative splicing?

Splicing exons of a single hnRNA transcript in different combinations to yield multiple protein isoforms from one gene.

What is the function of tRNA?

Translates mRNA codons into amino acids by bringing specific amino acids to the ribosome via its anticodon.

What enzyme attaches an amino acid to its corresponding tRNA?

Aminoacyl-tRNA Synthetase (requires ATP)

Where is rRNA synthesized in the eukaryotic cell?

In the nucleolus (by RNA Polymerase I)

What are the ribosomal subunit sizes in prokaryotes vs eukaryotes?

Prokaryotes: 30S + 50S = 70S; Eukaryotes: 40S + 60S = 80S

What happens at the A site of the ribosome?

Aminoacyl site: holds the incoming aminoacyl-tRNA complex.

What happens at the P site of the ribosome?

Peptidyl site: holds the tRNA with the growing peptide chain and forms the peptide bond.

What enzyme catalyzes peptide bond formation between amino acids in translation?

Peptidyl Transferase (a ribozyme in the large subunit)

What happens at the E site of the ribosome?

Exit site: inactivated, uncharged tRNA briefly pauses before exiting the ribosome.

What prokaryotic mRNA sequence facilitates ribosome binding during initiation?

Shine-Dalgarno sequence

What eukaryotic mRNA sequence helps the ribosome identify the start codon?

Kozak sequence

What protein factors bind to stop codons to terminate translation?

Release Factors (RFs), which cause addition of a water molecule to hydrolyze the peptide chain.

What are chaperone proteins?

Proteins that assist in the correct folding of newly synthesized polypeptides.

What is an operon in prokaryotes?

A cluster of genes under the control of a single promoter, transcribed together into a polycistronic mRNA.

What is an inducible operon system (e.g., Lac operon)?

Off by default; turned on when an inducer binds and removes the repressor protein from the operator.

What is a repressible operon system (e.g., Trp operon)?

On by default; turned off when a corepressor binds the repressor protein, allowing it to bind the operator.

In the Lac operon, what condition leads to maximal transcription?

Low glucose (high cAMP -> CAP binds) AND high lactose (allolactose binds repressor).

What are enhancers?

DNA regulatory elements located far from the promoter that bind transcription factors to increase transcription rates.

How do enhancers interact with promoters located thousands of base pairs away?

DNA loops around so the enhancer-bound proteins directly contact the promoter complex.

What effect does histone acetylation have on gene transcription?

Decreases positive charge on lysine residues, loosening chromatin (euchromatin) and INCREASING transcription.

What enzyme removes acetyl groups from histones?

Histone Deacetylase (HDAC), leading to chromatin condensation and gene silencing.

What effect does DNA methylation generally have on gene expression?

Silences gene expression by adding methyl groups to cytosine bases, inhibiting transcription factor binding.

What enzyme converts RNA into cDNA (complementary DNA)?

Reverse Transcriptase

Why is cDNA used for cloning human genes into bacteria?

cDNA is synthesized from mature mRNA, so it lacks non-coding introns that bacteria cannot splice.

What laboratory technique is used to amplify specific DNA sequences?

Polymerase Chain Reaction (PCR)

What are the key reagents required for PCR?

DNA template, primers (high GC content), dNTPs, and heat-stable Taq DNA polymerase.

What technique separates DNA fragments based on size using an electric field?

Agarose Gel Electrophoresis

In gel electrophoresis, in which direction does DNA migrate?

Toward the positive anode because DNA has a negatively charged phosphate backbone.

What is Southern Blotting used to detect?

Specific DNA sequences

What is Northern Blotting used to detect?

Specific RNA sequences

What is Western Blotting used to detect?

Specific proteins

What mnemonic helps remember Southern, Northern, and Western blotted targets?

SNOW DROP (Southern-DNA, Northern-RNA, O-O, Western-Protein)

What feature of dideoxynucleotides (ddNTPs) causes chain termination in Sanger sequencing?

They lack a 3'-OH group, preventing phosphodiester bond formation with the next incoming nucleotide.

What are restriction endonucleases (restriction enzymes)?

Enzymes isolated from bacteria that cleave double-stranded DNA at specific palindromic sequences.

What is a palindromic sequence in DNA?

A 5' to 3' sequence on one strand that is identical to the 5' to 3' sequence on the complementary strand.

What is B-DNA vs Z-DNA?

B-DNA is a right-handed helix (normal, stable); Z-DNA is a left-handed zigzag helix (rare, high GC/salt).

Why is RNA chemically less stable than DNA in basic conditions?

RNA has a 2'-OH group that can perform intra-molecular nucleophilic attack on its own phosphodiester backbone.

What post-translational modification involves adding carbohydrate chains to proteins?

Glycosylation (helps direct protein destination and membrane localization)

What post-translational modification involves adding lipid groups to anchor proteins in membranes?

Prenylation

What are the three steps of PCR cycle in order?

Denaturation (heat), Annealing (cool to allow primers to bind), Extension (heat to Taq optimal temp).

What is epigenetics?

Heritable changes in gene expression/phenotype caused by mechanisms other than changes in the underlying DNA sequence.