Cell Biology QUIZ

Describe the structure of eukaryotic chromosomes

Linear chromosomes that are tightly coiled, genetic material that fits inside the nucleus while still allowing for regulation/ replication 

list the levels of chromosome packaging, in order, from nucleosomes to heterochromatin.

Nucleosomes: DNA wraps around small proteins called histones, like thread around a spool.

Chromatin Fibers: These nucleosomes coil together, making a thicker fiber

Looped: The fiber forms loops, making it even more compact.

Chromatin: Loosely packed DNA that can be read by the cell to make proteins.

Heterochromatin: DNA that is super tightly packaged 

Chromatin

 DNA mixed with proteins that help organize and package it. Think of it as a messy ball of yarn that can be untangled when needed.

Histone

A special type of protein that DNA wraps around. These proteins help DNA stay organized and compact.

Nucleosomes

A small bundle of DNA wrapped around histones—like beads on a string.

Role of Histone Protein in DNA folding

Since DNA is very long and negatively charged and histones are positive charge, it would get tangled without histones. Histones help by:

1. Neutralizing the DNA charge, so it can fold neatly.

2. Helping DNA coil into nucleosomes, making it easier to store.

3. Allowing the cell to control which genes are active by adjusting how tightly the DNA is packed.

Describe the process of DNA replication

is the process by which cells copy their DNA before cell division; it ensures that each daughter cell receives an identical copy of the genetic material. Each DNA molecule consists of one original stand and a new synthesis copy.

DNA replication

is the process by which cells copy their DNA before cell division; it ensures that each daughter cell receives an identical copy of the genetic material. Each DNA molecule consists of one original stand and a new synthesis copy.

Origin of Replication

Where DNA unwinds (Bubble). A+T occur more in the origin of replication because it is easier to break up, fewer C+G found in the replication 

Replication forks

Y shaped structure where DNA strands are unwound and new strands are synthesized, Moves in opposite directions 

Directionality

DNA strands run in the 5’-3’ direction, DNA polymerase runs can only add nucleotides to the 3’ end of a growing strand (replication occurs in the 5’-3’), strands travel in opposite directions from 3’-5’ 

Semi-conservative nature of replication

DNA replication molecules consist of one original strand (parent) and one new synthesized strand

DNA Polymerase

Synthesizes new DNA strands 

Primase

Synthesizes RNA primers

DNA Ligase

Connects Okazaki Fragments

DNA helicase

Unwinds DNA strands at replication fork

Topoisomerase

Relaxes supercoiling

Single-Strand Binding Proteins

Binds to separated DNA strands, prevents reannealing

Compare and contrast DNA synthesis at the leading and lagging strand. Define Okazaki fragments.

The leading strand synthesized constantly in the 5’ and 3’ direction, while the lagging strand is synthesized in the fragment

(Okazaki fragment) due to the opposite fork movement 5’-3’

Okazaki fragments

The lagging strand that is synthesized discontinuously and adds nucleotides in the 5’- 3’ direction 

Telomeres

Highly repetitive sequences at the end of linear chromosomes, it acts as a buffer preventing loss in genetic information. It plays a role in cellular lifespans, aging, and diseases  

Nucleosomes

DNA wraps around small proteins called histones, like thread around a spool

Chromatin Fibers

These nucleosomes coil together, making a thicker fiber

Looped:

The fiber forms loops, making it even more compact

Chromatin

Loosely packed DNA that can be read by the cell to make proteins

Heterochromatin

DNA that is super tightly packaged

Compare and contrast DNA synthesis at the leading and lagging strand. Define Okazaki fragments. 

The leading strand synthesized constantly in the 5’ and 3’ direction, while the lagging strand is synthesized in the fragment (Okazaki fragment) due to the opposite fork movement 

Okazaki fragments:

The lagging strand that is synthesized discontinuously and adds nucleotides in the 5’- 3’ direction 

 Define telomeres, explain why organisms with linear chromosomes need telomeres, and describe the role of  telomeres and telomerase in healthy cells, aging cells, and disease. 

Highly repetitive sequences at the end of linear chromosomes, it acts as a buffer preventing loss in genetic information. It plays a role in cellular lifespans, aging, and diseases

6.e Describe the mechanism of proofreading during DNA Replication. 

• Most DNA polymerases has 3’-5’ exonucleases (removes or breaks apart nucleotides) activity 

• Allows for the repair and removal of “incorrect” nucleotides 

6.f Define mutation. Describe the major causes and types of DNA damage, including deamination, depurination,  thymine dimers, and double-strand breaks. 

is any change in the DNA sequence, Major causes include- Errors during DNA replication, Specific Chemical reactions, Radiation 

DNA Damage

Depurination, Deamination, Thymine Dimers, Double Strand Breaks 

Describe the Central Dogma of Molecular Biology including the conversion of information encoded by the  genome (genotype) into functional gene products (the phenotype)

DNA – RNA – Proteins 

The central dogma describe the flow of genetic information from DNA and RNA proteins, determining how the (genotypes/Genetic information) is expressed as a phenotype (observable trait) 

7.b Compare and contrast the structure of DNA and RNA.

DNA is double-stranded and stores genetic information, while RNA is single-stranded and helps make proteins by copying DNA's instructions.

Recall the major stages of transcription

Binding, Initiation, Elongation, Termination 

 List the types of RNA produced by cells and describe the function of each.

mRNA- Code for protein (messenger RNA) 

rRNA- Ribosomal structure and catalyze proteins synthesis 

 miRNA- MicroRNA, regulates gene expression

tRNA- transton, adaptes between mRNA and amino acids 

Explain the physical and chemical modifications to mRNA that occur in eukaryotic cells following the formation  of the initial RNA transcript (RNA capping, polyadenylation, RNA splicing). Define introns and exons. 

RNA capping- 5’ methyLguanosine cap added to the 5’ end of the RNA transcript

Polyadenylation- Poly A tail adding (3’) added to the 3’ end of the RNA transcript 

RNA splicing- SnRPs bind DNA into loops and cuts off excess (Binds with an intron, comes close together and causing a fold, making a loop, and cuts off) 

• SnRPs form a slicing machine call Spliceosome 

• RNA molecules with catalytic activity are called Ribozymes 

Intron- Removes/ Cut out material  (Sequence that are “in between” the coding sequence)

Extron- Expressed material ( Sequence that is Expressed ) 

Compare and contrast transcription in prokaryotic and eukaryotic cells. 

Prokaryotes- Translation of MRNA can begin before the transcription ends

Eukaryotic- RNA is processed after transcription

• Additions of 5’ methylguanosine cap 

• Addition of 3’ PolyA tail 

• RNA splicing 

• Export for the Nucleus 

Describe the four main properties of the genetic code. Define codon and reading frame. 

Codon- 3 letter sequence read at a time 

Unambiguous- 1 codon = 1 amino acids

Degenerate- amino acids can be specified by 1+ codon (example: Leu and Pro) 

Non Overlapping- Codons do not overlap (one codon at a time) 

Universal- Every organism has has some genetic code  

Reading frame- which 3 Letters are read at a time  

7.i Explain the role of each of the following components in protein translation: mRNA, tRNA, Aminoacyl tRNA  Synthetases, Ribosomes. 

mRNA- contains genetic messages 

tRNA- match amino acids to a codon in mRNA (anticodons) (clover leaf) 

Aminoacyl tRNA Synthetases- “LOADS” correct AA onto tRNA

Ribosomes- Decodes mRNA messages and synthesize them into proteins 

Define polycistronic and monocistronic. 

Polycistronic- multiple genes per  RNA sequence (prokaryotic) (multiple start and stop codons)

Monocistronic- Only 1 gene start and stop in RNA sequence (eukaryotic)

7.k Describe the structure of ribosomes, including the four main sites involved in translation. Define ribozyme. 

Ribosomes: Decode the mRNA messages and synthesize proteins 

A- site (Aminoacyl)

P-site (Peptidyl) 

E-site (Exit)

mRNA Binding site 

7.l Describe the process of translation, including the role of initiation factors, elongation factors, termination  factors. 

RNA– Protein 

Initiation: Small subunits attracted to 5’ RNA ends unit it binds AUG— large subunits follows

t-RNA- is positioned in P-site, next codon is positioned on 

Translation initiation Factor- Proteins that promotes the proper mRNA + ribosomes association to the tRNA i loaded with methionine, which connects with AUG 

Elongation- Growing peptides chains 

-Everything moves down codon ( P– e, A–P, C  new AA attaches in A site) 

- New peptides bonds between AA from in P sites 

-tRNA exits in E sites 

Large subunits move down RNA first, small follows 

Termination- Polypeptide chains releases 

-Polypeptide chains starts with N-terminus (5’ prime) and ends with C’ terminus (3’) 

Define genomic equivalence and discuss how unique differentiated cell types can arise in a multicellular organism. Define stem cell.

Genomic Equivalence- Almost all cells in a multicellular organism have the same genomes (Same DNA) 

• Cells have different functions because they express different parts of the same DNA 

Stem Cells- Is a special cell that can become many different types of cells (Replicate itself) (differentiate into many cell types) 

 Explain how transcription factors regulate gene expression. Distinguish between activators, repressors, silencers, and enhancers.

Transcription factors- By binding specific DNA sequence and influencing transcription

• Reproductory sequence- Where these proteins bind to on DNA 

• Activator Proteins- Turns genes ON

• Repressor Proteins- Turns genes OFF

• Silencer- BLOCKS gene expression 

• Enhancer-  ENHANCE (boost) gene activity 

 8.c Define operon and describe the trp operon and lac operon of E. Coli.

Lac Operon- An inducible gene (Starts OFF and can turn ON)

• Group of genes that process lactose for energy 

• Glucose levels inversely proportional relate to CAMP (cystic AMP) 

TRP Operon- Group of genes that produce tryptophan (a repressible operon) ( Starts  ON and can TURN OFF)

• E coli can make trap using molecules and S enzymes 

• If TRP is low, operon is turing on ( TRP fits inside) the repressor, prevent RNA polymerase from binding

Describe examples of how cells control gene expression at multiple levels after transcription, including alternative splicing, mRNA transport, mRNA degradation, small non-coding RNAs, translation control, protein degradation, and protein activity.

Gene expression after translation

Alternative splicing- Different proteins can be made from mRNA for different functions(Allows cells to create a variety of of different mRNA from the same pre-RNA)

mRNA degradation- 

mRNA transport- can stop mRNA from leaving the nucleus and can hide it until it is needed 

Small non-coding RNAs- miRNAs and siRNA 

miRNA- Short sequence of RNA that folds upon itself can silence/ turn off DNA when binded to a protein —--> also can break down mRNA siRNA, dice enzymes that can chop up RNA 

• Can detect … mRNA so ribosome decent to make … proteins 

mRNA Degradation- miRNA and mRNA that are complementary meaning miRNA can degrade mRNA 

Transaction control

Ribosomal binding sites- Location on mRNA that binds to ribosomes small units 

• Translation repressors proteins can bind one to prevent transaction from place 

Protein Degradation- Breaking down proteins 

• Proteases- Enzymes that break down other proteins (breaks down peptide bonds) 

• Proteasome- Large complex that breaks down proteins that must be destroyed 

Describe the following mechanisms by which cells control enzymes and other proteins: allosteric regulation, post-translational covalent modifications (including phosphorylation), GTP-binding, scaffolding, quantity, and subcellular localization

• Post translational modification- Adding chemical groups 

• Acetylation - influence histons 

• Phosphorylation- Conformational change, used to turn proteins on/off 

• Allosteric Regulation- Protein inhibitor, can change shape of proteins 

• GTP/GDP binding- Some protein can bind to GTP/GDP 

• G-Protein- Active form when binding to GTP

• Scaffolding- Organizing proteins into complex 

GDP protein- inactivates proteins 

• Localization/ compartmentalization- Cells  can p… proteins in a certain sport instead of it floating around cytoplasm (protein is only active when its activated) 

Transcription occurs in

NUCLEUS 

Translation occurs in

Cytoplasm