Molecular and Cellular Biology Exam 1

Molecular cell biology

The study of processes in and around cells at a molecular level

Prokaryotic Cells

Cells that are small, have no nucleus, have circular DNA, and have a cell wall.

Eukaryotic Cells

Larger cells that have a nucleus and linear DNA

G1 Phase

First phase in a cell life cycle where the cell grows in size, produces proteins, and synthesizes organelles in preparation for DNA replication.

S Phase

The second phase in a cell life cycle where DNA replication occurs and genetic material doubles.

G2 Phase

The third phase in the cell life cycle where the cell continues to grow, DNA replication errors are checked, and the cell prepares for mitosis.

M Phase

The final phase of the cell life cycle where the cell undergoes mitosis.

G1 Checkpoint

At the end of G1 phase before the cell enters S phase, the cell checks it’s size, nutrient availability, growth signals, and DNA integrity.

Proteins that G1 Checkpoint checks

p53, cyclin, and cyclin-kinase

G2 Checkpoint

A checkpoint at the end of G2 phase before entering M phase. The cell checks for proper DNA replication, DNA damage, cell size, and energy levels.

M checkpoint

Checkpoint during metaphase of mitosis. Checks for proper chromosome attachment to spindle fibers and for equal tension on sister chromatids.

Cyclins

Regulatory proteins that control progression through cell cycle by activating CDKs.

CDKs

Enzymes that (when bound to specific cyclins) phosphorylate target proteins to drive cell transitions.

p53s

Proteins that halt the cell cycle if DNA damage is detected. They can also trigger apoptosis if damage is irreparable.

Carbohydrates

Subunits: Monosaccharides

Structure, C, H, and O bonds in 1:2:1 ratio

Features: Rings or linear structures with (-OH) groups

Functions: Primary energy source + structural support

Carbohydrates

Lipids

Subunits: Glycerol + fatty acids, phosphate group, or steroid rings

Structure: Mostly hydrophobic structure comprised of C,H, and O

Identifying Features: Non polar, insoluble in water; Chains can be saturated (no double bonds) or unsaturated

Functions: Long term energy storage, cell membrane structure, hormones, and signalling

Lipids

Proteins

Subunits: Amino Acids

Structure: Contain C,H,O,N and sometimes S; formed by peptide bonds between amino acids, folded into complex shapes

Identifying features: Amino group (-NH2) + Carboxyl group (-COOH)

Functions: Enzymes, structural support, transport, immune response

Protein

Nucleic Acids

Subunits: Nucleotides

Structure: C, H, O, N, and P

Identifying Features: Sugar-phosphate, nitrogenous bases

Functions: Store genetic information, protein synthesis, ATP

Nucleic Acids

Amino acids consist of:

An amino group (-NH2), carboxyl group (-COOH), R group, and H atom

Basic structure of a nucleotide has three components

A pentose sugar, a phosphate group attached to 5’ carbon on sugar, and a nitrogenous base attached to 1’ carbon on sugar

Purines

are a type of nitrogenous base that includes adenine and guanine, characterized by a two-ring structure.

Pyrimidines

are a type of nitrogenous base that includes cytosine, thymine, and uracil, characterized by a single-ring structure. Think pyrimidine —> cytosine

Nucleotide connections

A phosphodiester bond formed between 3’ -OH of one nucleotide’s sugar and the 5’ phosphate of the next nucleotide.

Catalyst

A substance that speeds up chemical reactions without being consumed in teh process.

Enzyme

Biological catalyst that are mostly proteins. They loewr the activation energy.

Activation sites

Specific regions on an enzyme where the substrate binds and the reaction occurs.

Reaction rate vs. substrate concentration

As substrate concentration increases, the reaction rate also increases. The reaction continuesuntil all enzyme active sites are occupied.

Vmax

The maximum reaction rate achieved by an enzyme when all active sites are saturated with substrate.

Kd (Dissociation Constant)

A measure of the affinity between an enzyme and its substrate, representing the concentration of substrate at which half of the enzyme's active sites are occupied.

pH

A measure of acidity. A higher pH means lower H+ concentration (basic).

DNA basic structure

The double helix formation of nucleotides, consisting of a sugar-phosphate backbone and nitrogenous bases (adenine, thymine, cytosine, guanine) that pair specifically.

DNA 5’ End

Has a phosphate group on DNA

DNA 3’ end

Has a hydroxyl group on DNA

DNA Major Groove

The larger of the two grooves in the DNA double helix, providing access for proteins to bind and interact with the DNA.

DNA Minor Groove

The smaller of the two grooves in the DNA double helix, which is less accessible for protein binding compared to the major groove.

Base content vs. melting temperatures

Higher guanine-cytosine content means a higher melting point due to increased hydrogen bonding.

Exons

Coding sequences that are translated into proteins

Introns

Non-coding sequences that are spliced out during mRNA processing

Promoter

DNA region where RNA polymerase binds to start transcription

UTRs

Regulatory regions before and after coding sequences. They affect mRNA stability, translation, and localization

Chromosomes

Structures that organize and package DNA into a compact form, visible during cell division.

Centromere

Attachment site for spindle fibers during mitosis

Telomeres

Protect chromosome ends from degradation

Origins of Replication (Ori)

Sites where DNA replication begins in chromosomes

Nucleosomes

Structural units of chromatin, consisting of DNA wrapped around histone proteins.

Octameric core

Central protein structure of a nucleosome that consists of 8 histone proteins

H1 Histone

A linker histone that binds to the nucleosome, helping to stabilize the structure and regulate gene expression.

Human genome

Approximately 3 billion base pairs in haploid cells

Euchromatin

A less condensed form of chromatin that is transcriptionally active, allowing for gene expression.

Heterochromatin

A tightly packed form of chromatin that is transcriptionally inactive, often associated with gene silencing.

Repetative DNA

DNA sequences that are repeated multiple times in the genome, often found in non-coding regions and can play roles in structural functions and regulation including centromeres, telomeres, and VNTRs.

Mitochondria

Double membrane bound organelles that generate ATP through oxidative phosphorylation.

Mitochondrial structural features

Smooth outer membrane containing porins to allow passage of small molecules. Inner membrane folded into cristae to increase surface area for ATP production. Between the inner and outer membrane is a space important for proton gradient formation. Also has a matrix containing enzymes for the krebs cycle, mitochondrial DNA, tRNAs, and ribosomes.

Mitochondrial replication

Replication done independently from the cell through binary fission.

Fission

Splitting mitochondrion into two mitochondrion. Increase number in response to high energy demand or stress.

Fusion

Two mitochondria combine to share contents. Helps repair damaged mitochondria by mixing contents.

Helicase

Unwinds DNA helix at replication fork

Single-Stranded Binding Proteins (SSBs)

Prevents reannealing of single-stranded DNA

Topoisomerase

Relieves supercoiling ahead of the replication fork

Primase

Synthesizes new DNA strands

Primase

Synthesizes short RNA primers

DNA Polymerase

Synthesizes new DNA strands

Sliding clamp

Increases processivity of DNA polymerase

Ligase

Seals gaps between okazaki fragments

DNA polymerase I

Removes RNA primer, fills in the DNA, and 3’-5’ exonuclease proofreads

Telomerase

A reverse transcriptase that extends telomeres using an RNA template

TAQ Polymerase

A heat-stable DNA polymerase used in PCR. It has low fidelity and does not proofread.

PCR

A laboratory technique used to amplify specific DNA sequences, making millions of copies from a small initial sample.

Sanger sequencing

A method for determining the nucleotide sequence of DNA using chain-terminating inhibitors.

Glocosylases

Errors: daily mistakes

Recognition: specific glycosylase

Removal: endonuclease

Repair: DNA polymerase fills in, ligase seals

Consequences: breast cancer, colorectal cancer

MMR

Errors: when proofreading is not effective, bases wrong

Recognition: muts

Removal: muts

Repair: DNA polymerase and ligase

Consequences: hereditary nonpolyposis colorectal cancer syndrome

Nucleotide Excision Repair

Errors: T-T bulges

Recognition: XPs

Removal: XP endonucleases

Repair: DNA pol and ligase

Consequences: xeroderma pigmentosum

Homologous Recombination

Errors: DS breaks

Recognition: Rec and Rad

Removal: Complicated

Repair: Strand invasion and strand extension

NHEJ SOS Repair

Errors: DS breaks

Recognition: Ku’s

Removal: Squish ends together

Repair: Trim excess