chapter 3: cellular structures and functions

Question 1

what is the cell theory?

Answer 1

it states that:
- cells are the smallest, basic unit of life

• it is the basic unit of structure and function in all living organisms and is three-dimensional in nature
• all living organisms are made of cells
• living organisms can be unicellular, consisting of a single cell, or complex, multicellular organisms, consisting of billions of cells
• all cells come from pre-existing cells via cell division and involces the passing of heredity information encoded in DNA from one generation to the next

Question 2

what are the differences in the structure of prokaryotic and eukaryotic cells?

Answer 2

presence of membrane-bound organelles:
eukaryotic cell: has true membran-bound organelles
prokaryotic cells: lacks true membrane-bound organelles

DNA structure and location:
eukaryotic cell: DNA is linear and enclosed within a membrane-bound structure known as the nucleus
prokaryotic cells: DNA is circular, not enclosed within a membrane but lies freely in the cytoplasm in a region called the nucleoid

size of ribosome:
eukaryotic cell: has 80S ribosomes (except mitochondria and chloroplasts, which have 70S ribosomes)
prokaryotic cells: has 70S ribosomes

Question 3

what are prokaryotic and eukaryotic cells?

Answer 3

• organisms of the domains bacteria and archaea consists of prokaryotic cells
  > organisms are known as prokaryotes
  > prokaryotes are unicellular
• organisms of fungi, animals, plants and protists all consists of eukaryotic cells
  > organisms are known as eukaryotes

Question 5

name the cells and their components from largest to smallest.

Answer 5

Plant cell
Animal cell
Nucleus
Bacterium
Mitochondion
Chloroplast
Lysosome
Cilium and flagellum
Microtubule
Ribosome
Microfilament
DNA molecule

Peter ate nine burgers, made carla laugh, cry and fart. Meanwhile, Roger managed DNA

Question 6

describe cell fractionation

Answer 6

step 1: homogenisation of cells
- cells can be broken up in various ways; can be subjected to osmotic shock, ultrasonic vibration or ground up in a blender

• samples of cell suspension must be kept cold so that metabolism is slowed, and autophagy ( self-digestion, sounds like autofatty-eating itself) of organells is prevented
  > they must also be buffered so that pH does not change drastically, and enzymes are not denatured
• these procedures break the cell surface membrane and internal membranes of the cell into fragments that immediately reseal to form small, close vesicles
  > if carefully applied, the procedures leave membrane bound organells largely intact
  > like nuclei, mitochondria, chloroplasts, golgi apparatus, ribosomes and lysosomes
• the suspension of cells is thereby reduced to a thick homogenate that contains a variety of membrane-bound organells, each with a distinctive charge and density

step 2: differential centrifugation
- different components of the homogenate are separated by a process known as differential centrifugation

the homogenate is filters, and then placed in a centrifuge tube to be rotated at high speeds in a machine known as a centrifuge. this treatment separates cellular structures/ components by size and density. generally the larges cellular structures experience the largest centrifugal force and move the most rapidly
- at relatively low speed, large components such as nuclei sediment to form a pellet at the bottom of the centrifuge tube
- at a slightly higher speed, a pellet/ sediment of mitochondria/ chloroplasts is deposited
- at even higher speeds and with longer periods of centrifugation, first the small vesicles and then the ribosomes can be collected in the pellet/ sediment

• all these fractions are impure, but many of the contaminants can be removed by resuspending the pellet/ sediment and repeating the centrifugation procedure several times

Question 7

what are some non- membrane bound organelles?

Answer 7

• nucleolus
• ribosomes
• centrioles

Question 8

what is the endomembrane system?

Answer 8

• it is a group of membranes inside a eukaryotic cell
• these membranes divide the cell into functional and structural compartments, and work together to modify, package and transport lipids and proteins

organelles that are in the endomembrane system:
- rough endoplasmic reticulum
- smooth endoplasmic reticulum
- golgi apparatus
- lysosome
- vesiciles
- nuclear envelope
- cell surface membrane
- plasma membrane

Question 9

structure and function of organelles in a typical eukaryotic cell

what are the structure and functions of the nucleus?
(NUCLEAR ENVELOPE)

Answer 9

• most prominent organelle and visible under the light microscope
• consists of the nuclear envelope, nuclear pore, nucleoplasm and nucleolus
• absent in mature sieve tube cells in plants and red blood cells
• spherical in shae

**S: **
- surrounded by a nuclear envelope which is a double membrane
- the outer membrane of the nuclear envelope is continuous with the rough endoplasmic reticulum with ribosomes attached to the surface
- the inner membrane is in contact with the nucleoplasm
- each membrane is a phospholipid bilayer with proteins attached
- the nuclear envelope has numerous tiny openings called nuclear pores

**F: **
- the nuclear envelope regulates the movement of substances into and out of the nucleus via the nucleus pores
> eg. entry of histone proteins, DNA and RNA polymerase, ribosomel proteins
> eg. exit of mRNA, tRNA, ribosomal subunits

• the nuclear envelope disintegrates during prophase of mitosis, and prophase I and II of meiosis
• this is to allow the attachmet of kinetochore microtubules to centromere of chromosomes so that sister chromatids can be pulled to opposite poles of the cell at anaphase

Question 10

structure and function of organelles in a typical eukaryotic cell

what are the structure and functions of the nucleus?
(NUCLEOPLASM)

Answer 10

S:
- the nucleoplasm is a gel-like matrix that fills the space in the nucleus, between chromatin fibres and nucleoli
- contains nearly all the cell’s heredity material, DNA that is usually in the form of chromatin fibres> theres two types
- heterochromatin: tightly coiled and condensed thus does not allow transcription
- euchromatin: loosely coiled and condensed thus allow transcription to take place
- chromatin fibres further coil, condense into chromosomes during cell division
- it also contains proteins, ions and nucleotides
- which are materials required for synthesis of DNA and RNA

F:
- DNA in the nucleoplasm control cellular activities by regulating protein synthesis, such as synthesis of enzymes

Question 11

structure and function of organelles in a typical eukaryotic cell

what are the structure and functions of the nucleus?
(NUCLEOLUS)

Answer 11

S:
- one or more nucleolus are found in the nucleoplasm
> it is a region made up of chromatin fibres that carry the ribosomal RNA (rRNA) genes
> it also contains ribosomal proteins that are imported from the cytoplasm
> it is not bound by any membrane
> the nucleolus disappears during prophase of mitosis, prophase I and II of meiosis and
> reforms during telophase of mitosis, telophase I and II of meiosis

**F: **
- it is the site of transcription of rRNA genes to rRNA
- the rRNA then assembles with ribosomal proteins that are imported from the cytoplasm to form the large and small ribosomal subunits, which then come together to form a ribosome

• chromatin fibres coil and condense to form chromosomes during prophase
• since the nucleolus is a region of chromatin fibres which has genes (DNA) coding for rRNA, the nucleolus disappears when all chromatin fibres coil and condense to become chromosomes

Question 12

what is the structure and functions of centrioles?

Answer 12

structure:
- a pair of hollow cylindrical structures lying at right angles to each other
- each cylindrical structure is made of nine triplets of microtubules arranged in a ring
- each centrioles is located in a distinctly stained region of the cytoplasm known as the centrosome
> the region is also knwon as microtubule organising centre (MTOC)

functions:
- centrioles migrate to opposite poles of the cell during prophase of mitosis/ prophase I and II of meiosis
> location of the centrioles determines the polarity of the cell
- from each pair of centrioles, short microtubules develop and radiate to form an aster
> the DO NOT make asters, they organise microtubules that form the ester

• centrioles aid in spindle fibre formation during cell and nuclear division
• the spindle fibres that form then aid the alignment of the sister chromatids / chromosomes and separate sister chromatids/ chromosomes when they shorten

Question 13

what are the differences between prokaryotic and eukaryotic ribosomes?

Answer 13

• ribosomes are present in both prokaryotic and eukaryotic cells
  > but they are different in structure
• in eukaryotes, each ribosome consists of a large (60S) and a small subunit (40S), making up an 80S ribosome
• ## in prokaryotes, each ribosome consists of a large (50S and a (30S) small subunit, making up an 70S ribosome

Question 14

compare free ribosomes and bound ribosomes
feature of comparison: the attachment to other organelles

Answer 14

free ribosomes: not attached to the endoplasmic reticulum
bound ribosomes: arracted to the endoplasmic reticulum and the nuclear envelope

Question 15

compare the function of free ribosomes and bound ribosomes

Answer 15

free ribosomes: synthesise protein for that remain or are in use in cytoplasm

bound ribosomes: synthesise proteins that are transported through the endomembrane system
- these proteins may be proteins found on vacuoles, lysosomes, or proteins to be embedded in the cell membrane or secreted out of the cell

Question 16

in what type of cells are nucleus absent?

Answer 16

• the nucleus is absent in mature sieve tube cells in plants and red blood cells in mammals

Question 17

what are the functions to these structural features: (RIBOSOMES)

structural feature:
each ribosome has
- 1 messenger RNA (mRNA) bidning site at its small ribosomal subunit
- 3 transfer RNA (tRNA) bidning sites at its large ribosomal subunit
which are:
- Exit (E) site
- Peptidyl-tRNA (P) site
- Aminoacyl-tRNA (A) site

Answer 17

• Holds tRNA and mRNA in close proximity
  for translation to take place.
• Exit (E) site allows the discharged
  tRNA (not carrying amino acid) to
  leave the ribosome.
• Peptidyl-tRNA (P) site holds the
  tRNA carrying the growing
  polypeptide chain.
• Aminoacyl-tRNA (A) site holds
  the tRNA carrying the next amino
  acid to be added to the chain.

Question 18

what are the functions to these structural features: (RIBOSOMES)

*structural feature: *
- contains ribozyme: an rRNA molecule with enzymatic/ catalytic function that is complexed to the large ribosomal subunit

Answer 18

• the ribozyme is a peptidyl transferase which catalyses the formation of peptide bond between adjacent amino acids

Question 19

what are the functions to these structural features: (RIBOSOMES)

structural feature:
- can exist as polysomes/ polyribosomes
- which refers to a cluster of ribosomes present on a strand of mRNA

Answer 19

• Carry out translation of one mRNA to
  synthesise proteins at a faster rate
• since many ribosomes are translating one mRNA to form many of the same polypeptide chain at the same time.

Question 19

what is the function of the rough endoplasmic reticulum to this structure?

• Network of interconnected, single membrane bound tubules and sacs called cisternae (singular: cisterna)
• Continuous with outer membrane of
  nuclear envelope.

Answer 19

• To isolate, package and transport proteins into
  transport vesicles, which pinch /bud off the RER
  and are transported to the Golgi apparatus

These proteins include:
- secretory proteins (proteins that are for secretion out of the cell) or
- proteins that stay in organelles in the
endomembrane system (nuclear envelope, RER,
Golgi apparatus, vacuoles, lysosomes, and plasma
membrane)

Question 20

what is the function of the rough endoplasmic reticulum to this structure?

• Extensive folding of the RER membrane leads to a large surface area, which allows many
  translocation complexes to be embedded in the membrane of the RER

Answer 20

• The SRP protein receptor in the translocation
  complex is the site of attachment of a polypeptide chain that is newly synthesised by an 80S ribosome
  This allows:
• The originally free ribosome in the cytoplasm to become a bound ribosome on the surface of the RER.
• The newly synthesised polypeptide chain to pass through the RER membrane into the RER lumen/ cisternal space via a protein pore / channel in the translocation complex.

Question 20

what is the function of the rough endoplasmic reticulum to this structure?

*structural feature: *
- Presence of internal compartment called the lumen or cisternal space

Answer 20

• Allows polypeptide chains to fold into the
  secondary, tertiary and sometimes quaternary
  structures
• because chaperone proteins that help polypeptide chains fold are found in the RER lumen.
• Site of initial glycosylation (addition of
  carbohydrate chain) of synthesised proteins to form glycoproteins
• because enzymes that catalyse glycosylation reactions are found in the RER lumen.

Question 21

what is the function of the smooth endoplasmic reticulum to this structure?

structural feature:
- network of interconnected single membrane bound tubules and sacs called cisternae
- extensive folding of the SER membrane leads to a large surface area

Answer 21

• detoxification of lipid soluble drugs, metabolites and poisons especially in liver cells
• these lipid soluble compounds are converted to water-soluble compounds by enzymes
• which can be excreted in the urine
• the enyzymes that catalyse these metabolic reactions are embedded in the SER membrane
• allows many Ca2+ pumps to be embedded in the membrane of the sarcoplasmic reticulum in muscle cells

Question 22

what is the function of the smooth endoplasmic reticulum to this structure?

structural feature:
- Presence of internal compartment called the lumen or cisternal space

Answer 22

Metabolism (more of anabolism) of lipids:
- Synthesis and transport of lipids such as,
- membrane phospholipids
- cholesterol: because the SER lumen has
enzymes that catalyse reactions in the metabolic pathway to synthesise cholesterol
- steroid hormones: because the SER lumen has enzymes that catalyse reactions which modify cholesterol to form steroid hormones.
- triglycerides in intestinal epithelial cells

Metabolism of carbohydrates in liver cells:
- Glycogenolysis, which is the breakdown of glycogen to a-glucose monomers
- because the SER lumen has enzymes that catalyse the reaction.

Storage and regulation of Ca²+ concentration in muscle cells:

Question 23

what is the function of the **golgi apparatus** to this structure? structural feature: - A stack of flattened, elongated, single membrane-bound sacs called cisternae (singular:cisterna). - Presence of internal compartment called the lumen * NOTE: the sacs are not interconnected like the ER. They exist as separate sacs.

Answer 23

- Chemical modification of proteins from RER and lipids from SER. For example, - Glycosylation; addition of carbohydrate chain to proteins and lipids to form glycoproteins and glycolipids, respectively - because enzymes that catalyse glycosylation reactions are found in the lumen of the Golgi apparatus. - Phosphorylation: Addition of phosphate group to proteins - because enzymes that catalyse phosphorylation reactions of proteins are found in the lumen of the Golgi apparatus.

Question 24

what is the function of the **golgi apparatus** to this structure? structural feature: Has 2 faces - the forming cis face and the maturing trans face. - At the cis face, - transport vesicles from RER and SER continuously fuse and release proteins and lipids into the lumen of the Golgi body. - At the trans face, - secretory vesicles, Golgi vesicles and lysosomes continuously bud/ pinch off.

Answer 24

**Sorting and packaging of proteins into: ** - **secretory vesicles **for secretion out of the cell by exocytosis / to be embedded in the cell surface membrane. - Formation of secretory vesicles is particularly prominent in secretory cells - **Golgi vesicles** for delivery to other parts of the cell. - **Site of formation of lysosomes**, which stay in the cytoplasm in animal cells. Lysosomes contain active hydrolytic enzymes that hydrolyse compounds transported into the cell. - **Maintenance of cell surface membrane.** - When secretory vesicles fuse with the cell surface membrane, its phospholipids become part of the cell surface membrane. - This offset the loss of phospholipids due to the formation of endocytic vesicles from the process of endocytosis.

Question 25

how are lysosomes formed?

Answer 25

Formed from vesicles containing hydrolytic enzymes budding off from the Golgi apparatus.

Question 26

what is the function of the **lysosomes** to this structure? *structural feature: * - Small, spherical vesicles surrounded by a single membrane.

Answer 26

function: - Isolate hydrolytic enzymes in lysosomes to maintain low pH for the hydrolytic enzymes to function and catalyse reactions.

Question 26

what is the function of the **lysosomes** to this structure? *structural feature: * - Presence of proton pumps embedded in the lysosomal membrane. - The proton pump in the lysosomal membrane actively transports H+ from the cytosol into the lysosome. - This process requires energy from АТР hydrolysis.

Answer 26

function: - The hydrolytic enzymes within the lysosome are only active at an acidic pH. (The cytosol has a neutral pН). - The requirement of these hydrolytic enzymes for acidic pH provides double protection against uncontrolled digestion of the contents of the cytosol. - Even if the lysosomal membrane were to break down, the hydrolytic enzymes released would be inactive at the neutral pH of the cytosol.

Question 27

what is the function of the **lysosomes** to this structure? *structural feature: * Contain (about 50 different) hydrolytic enzymes

Answer 27

**Lysosomes are involved in:** **- Phagocytosis / Endocytosis** - **Autophagy**: Process where worn-out organelles within a cell are engulfed and digested within lysosomes. - Through this process, old cytoplasmic organelles are being replaced by new ones. **Autolysis**: - Self-digestion of a cell by release of lysosome contents within the cell, resulting in cell death. **Release of enzymes outside the cell via exocytosis.**

Question 28

what is the function of the **mithochondrion** to this structure? *structural feature: * - Bound by a double membrane which consists of an: - outer mitochondrial membrane - inner mitochondrial membrane - A small intermembrane space separates the outer and inner membrane.

Answer 28

function: Both the outer and inner mitochondrial membranes are selectively permeable, allowing the - entry of molecules required for aerobic respiration (such as O2, ADP, inorganic phosphate and NADH) and - exit of molecules produced during aerobic respiration (such as CO2, ATP). - Both the outer and inner mitochondrial membranes are hydrophobic, hence they are impermeable to protons / H+, which are positively charged - Therefore, the small intermembrane space allows rapid build-up of H+ to generate a proton gradient across the inner mitochondrial membrane during oxidative phosphorylation.

Question 29

what is the function of the **mithochondrion** to this structure? **(INNER MITOCHONDRIAL MEMBRANE)** *structural feature: * - extensively / highly folded. - Each folding is known as a crista (plural: cristae)

Answer 29

- in aerobic respiration, the inner mitochondrial membrane is the site of oxidative phosphorylation - Extensive folding of the inner membrane increases surface area for electron carriers (coupled to proton pumps) and ATP synthases to be embedded.

Question 30

what is the function of the **mithochondrion** to this structure? **(INNER MITOCHONDRIAL MEMBRANE)** ​ *structural feature: * - has electron carriers embedded in linear sequence from highest energy level to lowest energy level, forming an electron transport chain (ETC)

Answer 30

function: - Electrons are passed down the series of electron carriers in the ETC, from electron carriers at higher energy levels to those at lower energy levels - Drop in energy levels results in energy released (reject: produced), which is harnessed by proton pumps that are coupled to the electron carriers

Question 31

what is the function of the **mithochondrion** to this structure? **(INNER MITOCHONDRIAL MEMBRANE)** *structural feature:* - has proton pumps, which are coupled to to the electron carriers in the ETC

Answer 31

function: -The proton pumps use the energy released to actively transport H+ against its concentration gradient - from the mitochondrial matrix to the intermembrane space, to generate a proton gradient across the inner mitochondrial membrane.

Question 32

what is the function of the **mithochondrion** to this structure? **(INNER MITOCHONDRIAL MEMBRANE)** ​ *structural feature:* - has ATP synthase embedded (sometimes referred to as stalk particles)

Answer 32

- ATP synthase synthesise ATP (adenosine triphosphosphate) from ADP and inorganic phosphate: - ATP synthase links the phosphorylation of ADP to electron transport chain (ETC) during chemiosmosis. - Diffusion of protons / H+ down its concentration gradient from the intermembrane space to mitochondrial matrix through hydrophilic pore of ATP synthase - generates a proton motive force for ATP synthase to catalyse the synthesis of ATP from ADP and inorganic phosphate.

Question 33

what is the function of the **mithochondrion** to this structure? **(INNER MITOCHONDRIAL MEMBRANE)** *structural features:* - Mitochondrial matrix is the compartment enclosed by the inner mitochondrial membrane. - Contains enzymes that catalyse the reactions occurring during the link reaction and Krebs cycle of aerobic respiration - Contains hereditary material (circular mitochondrial DNA and RNA) and 70S ribosomes

Answer 33

- In aerobic respiration, the matrix is the site of link reaction and Krebs cycle. - Allow synthesis (via transcription of genes on mitochondrial DNA and translation of the RNA into proteins) of the some of the mitochondrion's own proteins and enzymes.

Question 34

what is the shape of a mitochondria?

Answer 34

spherical, rod or cylindrical in shape

Question 35

what is the structure of a chloroplast?

Answer 35

usually oval and biconvex shaped

Question 36

what is the function of the **mithochondrion** to this structure? *structural feature:* - Each chloroplast is enclosed by a double membrane, called the chloroplast envelope. The envelope consists of: - outer membrane - inner membrane Both membranes are separated by a thin intermembrane space.

Answer 36

function: - Compartmentalises / separates organelle from cytoplasm for photosynthesis. - Both the outer and inner membranes are selectively permeable, allowing the - **entry of molecules** required for photosynthesis (such as CO2, water, inorganic phosphate, minerals) and - **exit of molecules** produced during photosynthesis (such as O2, glyceraldehyde 3-phosphate).

Question 37

what is the function of the **chloroplasts** to this structure? *structural feature:* - form a system of thylakoids inside the chloroplast - Thylakoids are **flattened, single-membrane bound, fluid-filled sacs** - thylakoids are stacked to form **grana** (singular: granum), which are joined to other grana by ** intergranal lamellae** - The thylakoid membrane is a phospholipid bilayer.

Answer 37

- Thylakoid membrane is the site for light dependent reactions in photosynthesis - Thylakoid membrane provides a large surface area for the embedment of: * Photosystems I and II * Electron carriers coupled to proton pumps *ATP synthase - The thylakoid membrane is hydrophobic, hence it is impermeable to protons / H+, which are positively charged. - Therefore, this allows the rapid build-up of H+ in the thylakoid space to generate a proton gradient across the thylakoid membrane during light-dependent reactions.

Question 38

what is the function of the **chloroplasts** to this structure? **(THYLAKOID MEMBRANES)** *structural feature:* thylakoid membranes (including those at the intergranal lamellae have the following embedded) photosystems I and II that contain: - **light harvesting complexes** which have accessory pigments (chlrophyll a, chlorophyll b and carotenoids - **reaction centre** with primary electron acceptor and a primary pigment: either called a special chlorophylla called P680 in photosystem II or P700 in photosystem I

Answer 38

function: - For maximum light absorption, since different accessory pigments absorb different wavelengths of light, hence broadening the action spectrum of photosynthesis. - The accessory pigments absorb photons (packets of light energy) and transfer the energy from one pigment molecule to another in the light-harvesting complex, and eventually to the special chlorophyll a at the reaction centre. - When sufficient energy is channelled to special chlorophyll a, photoactivation occurs - an electron of special hlorophyll a is excited and ejected. The electron is accepted by the primary electron acceptor and passed to the ETC.

Question 39

what is the function of the **chloroplasts** to this structure? **(THYLAKOID MEMBRANES)** *structural feature:* embedded in the membrane are: - **electron carriers** in linear sequence from highest energy level to lowest enery level, forming an electron transport chain (ETC)

Answer 39

- electrons are passed down the series of electron carriers in the ETC, from electron carriers at higher energy levels to those at lower energy levels - Drop in energy levels results in energy released (reject: produced), which is harnessed by proton pumps that are coupled to the electron carriers.

Question 40

what is the function of the **chloroplasts** to this structure? **(THYLAKOID MEMBRANES)** *structural feature:* embedded in the membrane are: - **proton pumps** which are coupled to the electron carriers in the ETC

Answer 40

function: - the proton pumps use the energy released to actively transport H+ against its concentration gradient - from the stroma to the thylakoid space, to generate a proton gradient across the thylakoid membrane

Question 41

what is the function of the **chloroplasts** to this structure? **(THYLAKOID MEMBRANES)** ​ *structural feature:* embedded in the membrane are: - **ATP synthase**

Answer 41

- ATP synthase synthesise AТР (adenosine triphosphosphate) from ADP and inorganic phosphate: - ATP synthase links the phosphorylation of ADP to electron transport chain (ETC) during chemiosmosis. - Diffusion of protons / H+down its concentration gradient rom the thylakoid space to the stroma through hydrophilic pore of ATP synthase. - generates a proton motive force for ATP synthase to catalyse the synthesis of ATP from ADP and inorganic phosphate .