Cell Biology I possible exam questions

What is the central dogma of molecular biology?

DNA replication → DNA repair → transcription → translation → protein

List the types of non-covalent protein interactions

• hydrogen bonds

• ionic interactions

• hydrophobic interactions

• van der Waals forces

Compare the differences and similarities of prokaryotic and eukaryotic cells

prok.: small and simple, unicellular, absent nucleus, circular DNA, haploid chromosomes, lack membrane-bound organelles, sexual & asexual reproduction, cell division by binary fission

euk.: large and complex, multi or unicellular, present nucleus, linear DNA, diploid chromosomes, has membrane-bound organalles, sexual reproduction, cell division by mitosis

similarities: cell membrane, cytoplasm, DNA, ribosomes

What is the endosymbiotic theory?

Mitochondira and chloroplasts used to prokaryotes and were engulfed by eukaryotes. They formed a permanent symbiotic relationship.

Name the organelles found only in plant cells

chloroplast, cell wall, vacuole

Describe the structure and the function of the chloroplast

function: site of photosynthesis; transforms light energy into glucose; produces oxygen as a by-product

structure: double membrane; inner membrane encloses the stroma; grana, stacked thylakoid membranes, sit in the grana; contains chlorophyll, the green pigment.

What are the building blocks of protein and nucleic acids? List their functions

proteins: amino acids. functions: catalysis, transport, support, movement and regulation

nucleic acids: nucleotides. functions: translation, storage and transmission of genetic information, regulation of gene expression

What is amino acid activation and why is it important?

ATP-dependent binding of amino acids to tRNA, essential for correct translation

List the types of lipids found in a cell and their functions

• phospholipids: membrane structure

• fatty acids: energy source, lipid builiding block

• cholesterol: steroid hormone precursor

• glycolipids: cell recognition

Draw and label a peptide bond

List the types of amino acids

non-polar, polar uncharged, positively charged, negatively charged

List and briefly explain the different levels of protein folding

1. primary structure: linear sequence of amino acid

2. secondary structure: local folding stabilized by hydrogen bonds, formation of α helixes and β sheets

3. tertiary structure: 3D folding of the entire polypeptide, interactions between R groups

   1. quaternary structure: the turning of the polypeptide chains into a functional protein

What is the composition of the DNA and RNA?

in table: feature, DNA, RNA

sugar: deoxyribose, ribose

bases: A T G C, A U G C

strands: double stranded, single stranded

function: stores genetic info, gene expression

Name 6 characteristics of the Watson-Crick Model

double helix structure, antiparallel strands, sugar-phosphate backbone, complementary base pairing, bases connected by hydrogen bonds, right ha

List the different levels of gene expression

transcription, post-transcription, translation, post-translation

List the 3 major types of RNAs and their functions

mRNA: messenger RNA: carries genetic info from DNA to ribosome for protein synthesis

tRNA: transfer RNA: brings amino acids to the ribosome during translation

rRNA: ribsomal RNA: structural and catalytic component of ribosomes

List all the types of RNA

3 major ones: mRNA, tRNA, rRNA

regulatory RNAs: snRNA, snoRNA, miRNA, piRNA, siRNA

Draw and label a tRNA

What are the possibilities of gene expression regulation?

regulation at every possible level: chromosomes, transcription, RNA processing, translation, post-translation

Define the terms: gene, genome, gene expression, allele, chromosome

gene: a sequence of DNA that encodes a functional product

genome: the complete set of genetic material for an organism

gene expression: the process in which the genetic info is synthesized into RNA and/or protein

allele: different versions of the same gene at a specifi

draw and label the parts of a chromosome

Characterize the proteins of chromatin

histones: positively charged proteins filled with basic amino acids, types: H1, H2A, H2B, H3, H4

non-histones: less positively charged proteins, they’re important for transcriptions and regulation

What are the 2 types of chromatin? Briefly explain their structure

euchromatin: lightly packed, active, inside of nucleus, less stained

heterochromatin: densely packed, inactive, near nuclear periphery, darkly stained

define chromatin

DNA packed with protein

Compare heterochromatin and euchromatin

euchromatin: active

heterochromatin: inactive

Define and describe the structure of a nucleosome

a fundumental unit of chromatin that packages DNA into a compact structure

DNA wounds around the histone, “beads on a string”

Define a scaffold protein

a non-histone protein that provides structural support for chromatin, organizes DNA into a loop

List the steps of chromatin condensation

1. DNA wraps around histones → forms nucleosomes

2. nucleosomes coil → form fiber

3. fiber forms loop → attach to scaffold proteins → looped domains form

   1. further folding → condensed chromatin forms

Define looped domains

sections of chromatin organized into loops anchored to scaffold proteins

Define pseudogenes

DNA sequences similar to functional genes but are actually non-functional

Name the types of ER and describe their function and structure

Rough ER: has ribosomes on cytosolic surface → protein synthesis and modification

Smooth ER: no ribosomes → lipid synthesis, detoxification, Ca2+ storage

Name the parts of the Golgi complex, describe its structure and function

parts: cis-Golgi (entry), medial-Golgi, trans-Golgi (exit)

structure: stacked flattened cisternae

function: protein/lipid modification, storing and packaging into vesicles

descrbie the structure and function of the nuclear envelope

structure: double membrane, nuclear pores

function: protects nucleus, regulates transpot of molecules with NPCs

Define the structure and function of mitochondrial membranes

outer membrane: smooth, permeable to small molecules

inner membrane: highly folded into cristae, contains e- transport chain proteins

function: ATP synthesis, compartmentalization for metabolism

Define the nucleulos

non-membrane bound dense structure inside the nucleus responsible for rRNA synthesis and ribosome assembly

compare the 2 oragnelles that have a double membrane

in a table: feature, nucleus, mitochondrion

Membrane: double membrane-pores, double membrane-cristae

function: stores genetic info, ATP synthesis, metabolism

DNA: linear chromosomal, circular mitochondiral

Replication: cell divison; binary fission

What is the endomembrane system made up of?

nuclear envelope + ER + Golgi complex + lysosome + endosome + vesicles + plasma membrane

Describe the structure of the nucleus

spherical organelle, double membrane, nuclear pores, nucleoplasm, chromatin and nucleolus

What is the nuclear matrix? Describe its structure

fibrous network inside the nucleus

structure: protein filaments supporting chromatin organizations

Describe the structure of Nuclear Pore Complexes (NPCs)

large protein complexes embedded in the nuclear envelope, central channel for transport of RNA and protein

List the functions of the nuclear lamina

mechanincal support for the nuclear envelope

organizes chromatin

anchors NPCs

Describe the structure of the mitochondrion?

outermembrane → intermembrane spaces → innermembrane

DNA, ribosome, ATP synthesis particles are flowing in the matrix

edges of the innermembrane are called cristae

Compare the structures and functions of SER and RER

SER, RER

stucture: smooth - no ribosomes, rough - ribosomes

function: lipid synthesis-detox, protein synthesis-modification

List the 3 form of SER

tubular, lamellar, vesicular

Describe the structure and function of lysosomes

structure: membrane-bound vesicle

function: digest macromolecules and cellular debris

Define endosome

membrane-bound compartment responsible for sorting, recycling or degrading of internalized material

Define tonoplasts

membrane surrounding the central vacuole in plants cells, regulates transport

Define peroxisomes

membrane-bound organelles containing oxidative enzymes

Define autophagy

cellular process for degrading damaged organelles or cytoplasmic components

List the functions of a biological membrane

• barriers the cell and organelles

• transports with selective permeabitlity

• signal transduction

  • energy storage

Define liposome

spherical fat vesicle

What can regulate the cell’s membrane fluidity?

fatty acid composition, cholesterol content, temperature

What can cause membrane assymetry?

lipid composition, enzyme activity, protein distribution

What is the role of compartmentalization?

increased concentration of molecules → more effective reactions

higher level of organization

List the types of transport across membranes

passive, active, endocytosis, exocytosis

List the organelles with double membrane systems

nucleus, mitochondrion, chloroplast

Characterize mitchondrial DNA

circular, double stranded, located inside mitochondiral matrix, inherited maternally

List the types of mutations

small scale mutations = point mutations, insertion, inversion, substitution, deletion

large scale mutations (chromosomal) = duplication, deletion, translocation, inversion

List the consequences of mutations

loss of function, conditional loss of function, gain of function, genetic diseases, cancer, death

Define point mutation

a change in a single nucleotide in DNA, can lead to coding into a different amino acid or stop/start codon

List the types of chromosomal mutations and characterize one of them

large scale mutations (chromosomal) = duplication, deletion, translocation, inversion

duplication: addition of an extra copy of a chromosome

Define monocistronic

a gene only encodes one protein from one mRNA molecule

Define aneuploiditiy mean

an abnormal amount of chromosomes, number is not an exacty copy of a haploid set

List the functions of the cytoskeleton

maintains cell shape and mechanincal strength, responsible for intracellular transport, cell movement, essential for cell division

Describe the structure of the cytoskeleton

a dynamic network of protein filaments composed of microtubules, intermediate filaments, microfilaments

List the functions of microtubules

formation of mitotic spindle, intracellular transport, structural support, formation of cilia and flagella

What are MAPs? List their functions

Microtubule Associated Proteins: proteins that interact with microtubules

functions: stabilize/destabilize microtubules, regulate microtubule assembly/disassembly

Define axonal transport

transport of material along neuronal axons, occurs along microtubules

List the 3 types of motor proteins

kinesins, dyneins, myosins

What are MTOCs? List their types and functions

Microtubule Organizing Centres: sites of microtubule nucleation

types: centrosome, basal bodies

functions: microtubule nucleation, organization of mitotic spindle

What is the role of kinesin, dynein and myosin

kinesin: plus-end directed transport on microtubules

dynein: minus-end directed transport on microtubules

myosin: movement along actin filaments

List the 2 types of myosin

unconventional = type I; conventional = type II

Describe the structure and functions of intermediate filaments

structure: rope-like fibers, made up of fibrous proteins

function: provide strength, maintain cell integrity, form nuclear lamina

List the types and functions of microfilaments

type: actin filaments

function: muscle contraction, cytokinesis, cell shape maintenance, cell cortex support

List the functions of the extracellular matrix (ECM)

holds cell together in tissues, protects, supports the plasma membrane, helps in communication, regulates cell behaviour

List the components of the ECM

fibrous proteins, proteoglycans, GAGs, adhesive glycoproteins

How do cells interact with each other and their environment?

cell signalling, integrins, chemical signalling, mechanical interaction

What are integrins? List their functions

integrins are transmembrane adhesion receptors connecting the ECM with the cytoskeleton

function: cell-ECM interaction, integration, signal transduction

List the types of cell signalling

autocrine, paracrine, endocrine, juxtacrine, neurocrine, intracrine

List the types of cell junctions

tight junctions, anchoring junctions, gap junctions

Define DNA damage

any modification of DNA that changes its coding properties or normal function in transcription or replication

Characterize DNA damage based on its origin

exogenous, endogenous

List 3 endegenous and 3 exogenous DNA damade factors

endogenous: reactive oxygen species, spontaneous depurination, replication errors

exogenous: UV radiation, ionizing radiation, chemical agents

List the types of DNA damage

base modification, AP site, SSB, DSB, cross-links, DNA-protein cross link, helix distortions

List the types of DNA repair mechanisms

direct repair, BER, NER, MMR, HEJ, NHEJ

Briefly list the steps and key enzymes of BER

1) DNA glycosylase removes damaged base 2) AP endonuclease cuts backbone 3) DNA polymerase fills gap 4) DNA ligase seals

Briefly list the steps and key enzymes of NER

1) damage recognition 2) endonuclease excision of oligonucleotide 3) DNA polymerase fills gap 4) DNA ligase seals

Briefly list the steps and key enzymes of MMR

1) mismatch recognition 2) exonuclease excision of error strand 3) DNA polymerase resynthesizes 4) DNA ligase seals

Briefly list the steps and key enzymes of HEJ

1) strand invasion using sister chromatid 2) DNA polymerase resynthesizes 3) DNA ligase seals

Briefly list the steps and key enzymes of NHEJ

1) Ku proteins bind DNA ends 2) end processing 3) direct ligation

Describe the difference between HEJ and NHEJ

HEJ requires a homologous chromosome to act as a template, NHEJ doesn’t

NHEJ has a gap in the repair, HEJ doesn’t

Compare BER and NER

table: feature, BER, NER

damage type: small base lesions, bulky lesions

repair unit: single base, oligonucleotide segment

key enzyme: glycosylase, endonuclease

How can SSBs and DSBs be fixed?

SSBs: BER, NER, MMR

DSBs: HEJ, NHEJ

List the steps of DNA replication

1) initiation 2) elongation 3) termination

Briefly explain the steps of replication

1) initiation: replication begins at the origin of replication, DNA double helix is unwound by helicase and replication machinery assembles

2) elongation: new DNA strands are synthesized by DNA polymerases, leading strands synthesized continously and lagging strands synthesized discountinously (Okazaki fragments)

3) termination: replication ends when forks meet or reach termination sites, DNA strands are seperated and finalized

What is the mechanism of DNA replication

semiconservative, bidirectional, template dependent, 5’→3’ direction

Define semiconservative in replication

each daughter DNA molecule contains one parental strand and ine newly synthesized strand

List the enzymes involved in DNA replication

helicase, primase, DNA polymerases, DNA clamps, topoisomerases, DNA ligase, telomerase

Compare eukaryotic and prokaryotic DNA replication

table: feature, prok., euk.

origin: single, multiple

chomosome shape: circular, linear

speed: fast, slow

okazaki fragments: long, short

telomeres: absent, present

polymerases: I/II/III, α/σ/ε

location: cytoplasm, nucleus

Draw and label a replication fork